bluuebunny/crossref_metadata_2025 huggingface dataset:
ANALISIS POLICY CONTENT PENATAAN TRANSPORTASI ANGKUTAN UMUM DI KOTA BANDUNG
Authors: Edie Arif Moelia
Published: January 2022

This study aims to analyze the policy content of Local Regulation 16/2012. Data are collected through interviews, observation and documentary study. In term of content of policy, the policy has affected the interests of community, transportation operator and the government as regulator. The policy does not offer economic benefits that can be directly accessed, thus community and the operators do not support the implementation. The change envisioned by the policy has large scope, which are not only about the system and infrastructure, but also driving behaviors and mindset about social prestige. Although the Office of transportation is the main site of decision making, there are many programs made politically beyond the formal mechanism. Program implementers consists of Office of Transportation, Office of Roads and Waters, Office of Land Use and Public Works and Office of Local Revenues, thus many overlaps and miss-coordination. The financial resources is insufficiently allocated for the policy.

Keywords: Policy Implementation, Public Transportation Arrangement
DISKURSUS TEORETIS PENERAPAN GOOD GOVERNANCE DALAM FORMULASI KEBIJAKAN DAERAH
Authors: Mote Simon
Published: January 2022

This study aims to describe and explore the connectivity of the concept of good governance in various sets of existing government theories, and contextualized in the process of policy formulation in the regions. The method used is literature study. This study found a very strong logical relationship between various theories of government and the theory of good governance. The concept of Good Governance is a derivative or part of the theory of governance, which emphasizes efforts to build governance based on community participation, rule of law, transparency, caring for stakeholders, oriented to consensus, equality, effectiveness and efficiency, accountability, and strategic vision. The prerequisites for the successful implementation of good governance include: participatory policy formulation, optimal regional institutional capacity, and transformative leadership in applying the principles of good governance.

 

Keywords: Good Governance; Regional autonomy; Regional Policy
EFEKTIVITAS PEMBERLAKUAN PEMBATASAN KEGIATAN MASYARAKAT DI KECAMATAN BANJARWANGI KABUPATEN GARUT
Authors: Febriani Indah Aqilah , Fahlawi Muhammad Khainur , Parluhutan Menara Yosua
Published: January 2022

Pembatasan pemberlakuan kegiatan masyarakat is one of the government's programs in tackling and breaking the chain of covid-19 spread that continues to grow in Indonesia. Covid-19 is rapidly developing and becoming a global issue that impacts all lives in different countries. This makes the government both central and village level must think about various strategies in an effort to prevent its spread. In addition to strategic from the government, participation from the community is also indispensable in efforts to prevent its spread. In addition, we also found participation from the people of Kecamatan Banjarwangi, Kabupaten Garut who participated in the prevention of Covid-19 by implementing policies that have been set by the government. The purpose of this research is to know in detail the form of community participation in the handling of Covid-19 in Kecamatan Banjarwangi, Kabupaten Garut. The research method is descriptive and uses qualitative methods. Meanwhile, for data collection is used library studies derived from data sources derived from scientific journals, book literature, and official websites that are then described through analysis that describes the application of government policies, namely with Pembatasan pemberlakuan kegiatan masyarakat (PPKM) in the response to the Covid-19 pandemic outbreak in Kecamatan Banjarwangi, Kabupaten Garut. The results of this study explain that the application of government policies through PPKM in the district of Banjarwangi, Garut includes participation in planning, participation in the implementation, with the use of masks when traveling, restrictions on community activities without clear purpose, and restrictions on the operating hours of vehicle activities and business activities (shops). The implementation of PPKM activities in countering the Covid-19 pandemic in Kecamatan Banjarwangi, Kabupaten Garut seems to have been running effectively. With the involvement of the village community is very petrified this government program in tackling Covid-19, because the villagers are very understanding of the situation and conditions of the community in the environment. After the involvement of other agencies such as the TNI / POLRI is also very helpful smoothly this program with the creation of security and order during the activities. The purpose of restrictions on the implementation of community activities is to suppress and stop the positive number of Covid-19 in Kecamatan Banjarwangi, Kabupaten Garut.

Keywords: Effectiveness: Restrictions on Community Activities; Kabupaten Garut
KEPEMIMPINAN LURAH DALAM PENGELOLAAN BANK SAMPAH DI KELURAHAN RAYA KECAMATAN SINGKEP BARAT KABUPATEN LINGGA PROVINSI KEPULAUAN RIAU
Authors: Nurrahman Agung , Gatiningsih Gatiningsih , Syaputra Muhammad Tri
Published: January 2022

This research focuses on how leadership has a major role in addressing environmental issues, especially through the garbage bank program as a form of case study. Furthermore, the problems that occur in the midst of society are often rely solely on political will or political desire to solve them. The research is to know and learn Lurah's (head of village) leadership in the management of waste banks specifically. This research is qualitative descriptive research. Data collection techniques through structured interviews, documentation and observations. Researchers conducted an analysis using leadership theory from Yukl, where the theory discusses leadership comprehensively. Researchers only focus on five parts of the concept that are considered relevant, namely: visionary, guidance, affiliative, democratic and communicative concepts. The results of this study based on these dimensions are good enough Lurah (head of village) leadership. But there are several things that are considered able to optimize the running of the program through the role of Lurah (Head of village) leadership, namely: first, involving active knots and community leaders such as MUI, academics to support scientific aspects, and professionals in the field of practical management.

Keywords: Leadership, Head of Village, Environmental Issues, Waste Management, Waste Bank
PERAN BADAN NASIONAL PENANGGULANGAN BENCANA DALAM PENANGANAN PANDEMI COVID-19 DI KABUPATEN GARUT
Authors: Wiratami Desvita Dianti , Nasrul Muhammad , Fajriyah A. Inayah Ainun
Published: January 2022

The COVID-19 pandemic that has emerge and attacked Indonesia since the beginning of 2020 has intensified the demands for the role of the government to formulate a specific kind of policies that can address and accommodate social, economic, and political problems that arise as a consequence of this non-natural disaster. In an effort to cope with this disaster, the government has given a mandate to BNPB to take the strategic steps needed so that this pandemic is quickly finished, not least in Garut Regency, West Java. By implementing a qualitative descriptive research method, this study aims to methodologically and comprehensively analyze the role of BNPB in handling the COVID-19 pandemic in Garut Regency. The role of BNPB is very crucial considering the magnitude of the mandate carried out in an effort to mitigate the risk of the COVID-19 Pandemic disaster in Garut Regency, West Java.

 Keywords: COVID-19 Pandemic; BNPB’s Role; Disaster Management; Comprehensive Studies.
PERAN SATUAN POLISI PAMONG PRAJA KOTA PALEMBANG DALAM PENGAWASAN, PENGENDALIAN DAN PENCEGAHAN PENYEBARAN VIRUS COVID-19 SELAMA PEMBATASAN SOSIAL BERSKALA BESAR (PSBB)
Authors: Wijaya Raden
Published: January 2022

The city government of Palembang in this case the mayor of Palembang has issued the Palembang Mayor's Instruction No. 1 of 2020 on April 21, 2020 which instructs the improvement of control, prevention, and handling of transmission of corona virus diseases 2019 (COVID-19) in the city of Palembang.  This research aims to maintain public peace in facing the spread of COVID-19 in Indonesia conducted by the Civil Service Police Unit.  The research method uses an empirical legal approach.  Data collection techniques sourced from primary data and secondary data.  The results showed that the Palembang City Civil Service Police Unit had tried to overcome the existing problems, it was found obstacles in the field such as the people who did not wear masks and still clustered on the grounds of family members.  However, this can be handled by the PP policemen by arranging patrol schedules so that they routinely check the activities of the people with the firmness of the Sat Pol PP leaders in the city of Palembang. The commitment is supported by infrastructure to always stop appealing to the public both through print and online media.  This is influenced by factors that influence the success of COVID-19 supervision, control and prevention during PSBB, including internal factors including the Palembang Municipal Civil Service Police Unit in monitoring, controlling, preventing the spread of COVID-19 always prioritizing coordination and synchronization with cross-sectoral .  While external factors include the interests of the community itself.
IMPLEMENTASI KEBIJAKAN PENERTIBAN PASAR BARABAI DI KABUPATEN HULU SUNGAI TENGAH PROVINSI KALIMANTAN SELATAN
Authors: Azhari Ahlul Hadi
Published: January 2022

Trade is an activity with the hope of being able to trigger the movement of the community's economy and have an impact on people's welfare. But the Barabai Modern Traditional Market has not been able to provide convenience for buyers to transact and the arrangement of traders is still chaotic because there is no orderly place to trade. Control of Barabai Modern Traditional Market aims to provide convenience in buying and selling transactions at Barabai Modern Traditional Market. The factors causing this disorder are 1) lack of public awareness 2) unclear arrangements and 3) inadequate facilities.

This study uses a qualitative descriptive method with an inductive approach, for data collection methods in the form of observation, interviews and documentation. Furthermore, this study uses implementation theory from Merilee S. Grindle. The results of this study indicate that the enforcement of Barabai Modern Traditional Market has not been good with the inhibiting factor is the lack of public awareness to maintain order, the absence of decisive action and the facilities of the Barabai Modern Traditional Market. As for the socialization efforts and appeals to the community. Suggestions for the implementation of modern barabai traditional market control are in the form of making SOPs for controlling the modern barabai traditional market.
IMPLEMENTASI KEBIJAKAN PERDA NOMOR 14 TAHUN 2009 DALAM MENINGKATKAN KINERJA PEMERINTAH DESA PADALARANG KECAMATAN PADALARANG KABUPATEN BANDUNG BARAT
Authors: Supriatna Dadang
Published: January 2022

Village apparatuses as elements of village government administrators who are tasked with assisting the village head, capacity village officials is still low so that they lack understanding of government policies in carrying out their duties and functions as community servants. From this, the village apparatus needs attention so that the performance of the village equipment increases.

The research objective was to analyze the increase in performance village relationship between the implementation Perda increased performance. The research method uses a mix method. Data collection techniques are observation, documentation, documentation and questionnaires.

The results showed less than optimal, which was caused by: 1) Not yet optimal performance of village officials in accommodating and channeling community aspirations. 2) Lack of socialization regarding new policies by the Regional Government to the Village Government 3) Limited facilities and infrastructure owned by the Village Government in providing services to the community 4) Ununderstanding of Village officials regarding Regional Government policies. 5) Lack of motivation to work village officials in Padalarang Village. From this, positive implementation PERDA No. 14 of 2009 and the performance of village officials. In this case the regional government of West Bandung district can provide guidance and evaluate the performance of village heads and village officials regularly so as to improve the performance of village officials.
PENATAAN PEDAGANG KAKI LIMA (PKL) OLEH SATPOL PP DALAM UPAYA MENJAGA KETENTRAMAN DAN KETERTIBAN LALU LINTAS DAN PEJALAN KAKI PADA PASAR TANJUNGSARI KECAMATAN TANJUNGSARI
Authors: Supriatna Dadang
Published: January 2022

Tujuan dari penulisan ini adalah untuk mendeskripsikan penataan PKL oleh SATPOL PP di Pasar Tanjungsari dalam Menjaga Keamanan dan Ketertiban Lalu Lintas Dan Pejalan Kaki  Pada Pasar Tanjungsari Kecamatan Tanjungsari dan mendeskripsikan upaya SATPOL PP dalam menata PKL di Pasar Tanjungsari. Metode yang digunakan dalam penelitian ini adalah deskriptif  kualitatif, dengan Teknik Pengumpulan Data dilakukan melalui observasi, wawancara, dan dokumentasi dengan mereduksi data, penyajian data, triangulasi sebagai, verivikasi data dari hasil wawancara dan data kunci sebagai informasi. Hasil penelitian ini menunjukan bahwa penataan pedagang kaki lima di wilayah pasar tanjungsari belum dapat dilakukan secara optimal oleh pihak satpol PP tanjungsari walaupun secara garis besar petugas lapangan telah melaksanakan tugas sesuai denagn SOP. Hai ini dapat terjadi dikarenakan mutu SDM dan sarana prasarana baik secara kuantitas maupun kualitas di jajaran satpol PP Tanjungsari belum memadai, sehingga masih terdapat kekurang optimalan dalam penertiban PKL di seputan pasar Tanjungsari. Upaya penertiban yang dilakukan oleh satpol PP wilayah kerja Tanjungsari meliputi beberapa tahapan yaitu pertama,  upaya tindakan pencegahan secaar persuasif  dengan melakukan penyusunan aturan dan penyusunan agenda kerja yang lebih rapi dan terstrutur, menyusun panduan kerja sebagai penguat SOP yang telah ditetapkan, melakukan evalusi kerja dengan melakukan reposisi  pelaksaaan penugasan di lapangan oleh pimpinan sebagai bagian kewenangan dan penugasan, melaksanakan tugas dengan mengedapankan pendekatan secara humanis. Tahap kedua adalah upaya penindakan secara reprensif dengan memberikan solusi relokasi PKL ketempat yang telah disediakan yaitu lapangan pacuan kuda Tanjungsari yang terletak kurang lebih 100 meter fari pasar Tanjungsari.  Tahapan yag ketiga adalah upaya pengawasan dengan pemberian punishent kepada pelanggar peraturan penertiban. Peneguran dilakukan oleh pihak Satpol PP sebanyak tiga kali teguran. Mulai dari teguran pertama yang bersifat membujuk untuk dapat mematuhi aturan, sampai dengan peneguran yang ketiga berupa eksekusi bagi pelanggar dengan konsekuensi seluruh pelatan pelanggar dianggku dan ditampung di kantor satpol PP Kabupaten Sumedang dan dapat dimbil oleh pemiliknya denga membawa dan menunjukan kepada petugas kartu identitas diri.

Kata Kunci: Pedagang Kaki Lima, Satpol PP, Trantibmas
SATUAN POLISI PAMONG PRAJA SEBAGAI ORGANISASI PERANGKAT DAERAH YANG MENJAGA WIBAWA PEMERINTAH DENGAN MENEGAKAN PERATURAN DAERAH
Authors: Suhendi Dedy
Published: January 2022

Di beberapa wilayah masih terdapat anggapan bahwa Satuan Polisi Pamong Praja (Satpol PP) sering dianggap sebagai musuh pedagang kaki lima (PKL). Anggapan itu mengemuka dikarenakan kegiatan operasi lapangan anggota Satpol PP terhadap para PKL yang dianggap liar menempati yang bukan peruntukannya; termasuk masih adanya anggapan bahwa anggota Satpolpp bersikap arogan dan sering betindak di luar kewenangan. Dalam konteks penegakan Peraturan Daerah dan/atau Peraturan Kepala Daerah, Satpol PP memiliki kedudukan yang cukup strategis. Berdasarkan ketentuan Pasal 255 ayat (1) Undang-Undang Nomor 23 Tahun 2014 tentang Pemerintahan Daerah, bahwa “Satuan Polisi Pamong Praja dibentuk untuk menegakkan perda dan perkada, menyelenggarakan ketertiban umum dan ketenteraman, serta menyelenggarakan pelindungan masyarakat. Metode yang digunakan adalah Metode deskriptif dengan menekankan untuk mendeskripsikan suatu kejadian berdasarkan pengalaman partisipan pada saat bertugas di daerah. Hasil akhir diharapkan dapat memberikan pemahaman bahwa SatpolPP sebagai satuan kerja perangkat daerah atau organisasi perangkat daerah yang menjaga wibawa pemerintah melalui penegakan Peraturan Daerah dan Peraturan atau Keputusan kepala Daerah. Kesimpulan dari tulisan ini adalah untuk memberikan pemahaman bahwa kedudukan dan tugas Satpolpp memegang peran yang sangat strategis sebagai organisasi perangkat daerah yang membantu tugas-tugas Kepala Daerah di bidang Penegakkan Peraturan Daerah dan Peraturan Kepala Daerah termasuk Keputusan Kepala Daerah; menyelenggarakan ketertiban umum dan ketenteraman; dan menyelenggarakan pelindungan masyarakat.

Kata Kunci : Satuan Polisi Pamong Praja, Kedudukan, Tugas
GAMBARAN PELAKSANAAN PROGRAM PAS KENCAN DALAM PENYELENGGARAAN KETENTERAMAN DAN KETERTIBAN UMUM OLEH SATUAN POLISI PAMONG PRAJA DI KABUPATEN GARUT
Authors: Eviany Eva , Wasistiyana Alvita Kumara , Fitria Rahman Andi Dina Noor , Yogaswara Adrian Rianda
Published: January 2022

Jawa Barat dengan luas wilayah 3.074,07 km². Menyikapi hal tersebut, Satpol PP Kabupaten Garut mengembangkan inovasi program Patroli Siaga Keamanan Kecamatan Kabupaten Garut atau yang dikenali dengan Pas Kencan guna meminimalisir segala gangguan tibumtranmas. Tujuan penelitian ini untuk memahami gambaran pelaksanaan program Pas Kencan beserta faktor penghambatnya. Penelitian ini menggunakan metode deskriptif analisis sedangkan data dikumpulkan melalui kajian pustaka dan wawancara dengan Kepala Bidang Ketenteraman dan Ketertiban Umum Satpol PP Kabupaten Garut. Penelitian ini juga menggunakan model evaluasi CSE-UCLA. Hasil penelitian menunjukkan bahwa Program Pas Kencan dapat dikatakan sudah berjalan dengan baik, tetapi dalam pelaksanaannya masih terdapat hal-hal yang perlu dievaluasi. Hambatan-hambatan yang dihadapi yakni terkait minimnya anggaran dan kurangnya jumlah personel. Upaya yang dapat dilakukan dalam menghadapi hambatan-hambatan tersebut ialah dengan mengembangkan dan menyempurnakan program Pas Kencan ini dengan sistem berbasis internet atau call center.

Kata kunci: Satpol PP, Kabupaten Garut, Inovasi, Ketenteraman dan Ketertiban Umum
IMPLEMENTASI PEMBERLAKUAN PEMBATASAN KEGIATAN MASYARAKAT OLEH SATPOL PP DALAM PENANGANAN COVID-19 DI KABUPATEN PURWAKARTA
Authors: Eka Putra M.Nuril Anwari , Aswar A.Muh Alim , Putri Riska Rahim
Published: January 2022

Kondisi krisis akibat Corona Virus dalam struktur negara kesatuan adalah kewajiban pemerintah pusat, selain itu juga merupakan tugas dari pemerintah daerah. Pemerintah Daerah diharapkan mampu untuk menciptakan inovasi agar mata rantai Covid-19 dapat terputus. Berdasarkan Inpres No 6 Tahun 2020 dan Inmendagri No 4 Tahun 2020, maka diarahkannya salah satu cabang dalam pemerintahan yaitu Satpol PP yang dalam Penelitian ini bertujuan untuk mengetahui apa saja kendala yang terjadi dalam Pemberlakuan Pembatasan Kegiatan Masyarakat (PPKM) di Kabupaten Purwakarta dalam rangka percepatan penanggulangan Covid-19. Metode penelitian dilakukan menggunakan metode deskriptif kualitatif. Informan penelitian ini yaitu Kepala Satuan Polisi Pamong Praja Kabupaten Purwakarta. Teknik pengumpulan data yang digunakan adalah wawancara via daring dan studi dokumentasi melalui media massa. Hasil penelitian menunjukan bahwa Pemberlakuan Pembatasan Kegiatan Masyarakat (PPKM) pada pelaksanaanya masih belum efektif. Terdapat beberapa kendala dalam pelaksanaannya yaitu masyarakat tidak mengikuti kebijakan PPKM tergantung kepada alasan tidak mengetahui adanya kebijakan PPKM serta tidak mau menyetujui kebijakan PPKM dan ketidakmampuan untuk mengikuti kebijakan PPKM tergantung dari beberapa faktor mulai dari dirinya sendiri dan/atau faktor yang berasal dari lingkungan.

Kata kunci: Satpol PP, Protokol Kesehatan, Peraturan Bupati
Anticuerpos monoclonales: aplicaciones en hematología no oncológica y trasplante
Authors: Carrasco-Yalán Antonio
Published: January 2022

En el presente tema se revisará el uso clínico de anticuerpos monoclonales en hematología no oncológica, así como su uso en trasplante de órganos y tejidos. En hematología se utilizan ampliamente los anticuerpos monoclonales tanto en patologías oncológicas como no oncológicas. Varias enfermedades hematológicas no  oncológicas venían siendo consideradas enfermedades “huérfanas” o con pocas opciones terapéuticas hasta el advenimiento de los anticuerpos monoclonales. El área de trasplante de órganos sólidos y tejidos, ha crecido en forma importante en cantidad y complejidad de los procedimientos, que incluyen el trasplante de órganos y tejidos no completamente compatibles, hipersensibilidad de transfusiones y manejo de rechazo del trasplante. Esta área de igual forma ha tenido importantes logros terapéutico con el uso de anticuerpos monoclonales y policlonales.
Reflexiones sobre la neurología en el siglo XXI: a propósito de la enfermedad de Parkinson
Authors: Cosentino Carlos
Published: January 2022

La neurología ha sufrido una beneficiosa transformación en los últimos veinte años gracias a los nuevos descubrimientos fruto de la investigación básica y clínica así como también al acelerado desarrollo de una serie de disciplinas relacionadas que conforman las denominadas neurociencias. Los avances más importantes se han dado en la precisión de la etiología de muchas enfermedades como las genéticas o las autoinmunes así como en la comprensión de los mecanismos biomoleculares subyacentes a muchas de ellas. Se comenta el caso de la enfermedad de Parkinson como modelo de enfermedad neurodegenerativa y en donde ha habido muchos avances aunque aún insuficientes, y se hace un comentario final sobre el futuro de la neurología.
Vacunas contra el COVID-19
Authors: Calderón-Velasco Rolando
Published: January 2022

El acceso equitativo a vacunas seguras y efectivas contra el COVID-19 es crítico para parar la pandemia, por lo tanto es auspicioso ver numerosas pruebas y vacunas en desarrollo.
Structural time series: computational efficiency in estimating economic parameters in industry
Authors: Fiorucci Jose Augusto , Andrade Marinho Gomes , Nascimento Diego , Ferreira Letícia , Leite Alessandro , Cavalcante Léo , Frota Diego , Egbon Osafu , Bressiani Michael , Louzada Francisco
Published: January 2022

A growing field is related to automatized Time Series analysis, through complicated due to the dependence of observed and hidden dimensions often presented in these data types. In this report the problem is motivated by a Brazilian financial company interested in unraveling relation structure explanation of the Japanese' CPI ex-fresh Food \& Energy across 157 economical exogenous variables, with very limiting data. The problem becomes more complex when considering that each variable can enter the model with lags of 0 to 8 periods, as well as an additional restriction of admitting only a positive relationship. This report discusses three possible treatments involving models for structured time series, the most relevant approach found in this study is a Dynamic Regression Model combined with a Stepwise algorithm, which allows the most relevant variables, as well as their respective lags, to be found and inserted in the model with low computational cost.
Enhanced l-Malic Acid Production by Aspergillus oryzae DSM 1863 Using Repeated-Batch Cultivation
Authors: Schmitt Vanessa , Derenbach Laura , Ochsenreither Katrin
Published: January 2022

l-Malic acid is a C4-dicarboxylic acid and a potential key building block for a bio-based economy. At present, malic acid is synthesized petrochemically and its major market is the food and beverages industry. In future, malic acid might also serve as a building block for biopolymers or even replace the commodity chemical maleic anhydride. For a sustainable production of l-malic acid from renewable resources, the microbial synthesis by the mold Aspergillus oryzae is one possible route. As CO2 fixation is involved in the biosynthesis, high yields are possible, and at the same time greenhouse gases can be reduced. In order to enhance the production potential of the wild-type strain Aspergillus oryzae DSM 1863, process characteristics were studied in shake flasks, comparing batch, fed-batch, and repeated-batch cultivations. In the batch process, a prolonged cultivation time led to malic acid consumption. Keeping carbon source concentration on a high level by pulsed feeding could prolong cell viability and cultivation time, however, did not result in significant higher product levels. In contrast, continuous malic acid production could be achieved over six exchange cycles and a total fermentation time of 19 days in repeated-batch cultivations. Up to 178 g/L l-malic acid was produced. The maximum productivity (0.90 ± 0.05 g/L/h) achieved in the repeated-batch cultivation had more than doubled than that achieved in the batch process and also the average productivity (0.42 ± 0.03 g/L/h for five exchange cycles and 16 days) was increased considerably. Further repeated-batch experiments confirmed a positive effect of regular calcium carbonate additions on pH stability and malic acid synthesis. Besides calcium carbonate, nitrogen supplementation proved to be essential for the prolonged malic acid production in repeated-batch. As prolonged malic acid production was only observed in cultivations with product removal, product inhibition seems to be the major limiting factor for malic acid production by the wild-type strain. This study provides a systematic comparison of different process strategies under consideration of major influencing factors and thereby delivers important insights into natural l-malic acid production.
Removing the Bottleneck: Introducing cMatch - A Lightweight Tool for Construct-Matching in Synthetic Biology
Authors: Casas Alexis , Bultelle Matthieu , Motraghi Charles , Kitney Richard
Published: January 2022

We present a software tool, called cMatch, to reconstruct and identify synthetic genetic constructs from their sequences, or a set of sub-sequences—based on two practical pieces of information: their modular structure, and libraries of components. Although developed for combinatorial pathway engineering problems and addressing their quality control (QC) bottleneck, cMatch is not restricted to these applications. QC takes place post assembly, transformation and growth. It has a simple goal, to verify that the genetic material contained in a cell matches what was intended to be built - and when it is not the case, to locate the discrepancies and estimate their severity. In terms of reproducibility/reliability, the QC step is crucial. Failure at this step requires repetition of the construction and/or sequencing steps. When performed manually or semi-manually QC is an extremely time-consuming, error prone process, which scales very poorly with the number of constructs and their complexity. To make QC frictionless and more reliable, cMatch performs an operation we have called “construct-matching” and automates it. Construct-matching is more thorough than simple sequence-matching, as it matches at the functional level-and quantifies the matching at the individual component level and across the whole construct. Two algorithms (called CM_1 and CM_2) are presented. They differ according to the nature of their inputs. CM_1 is the core algorithm for construct-matching and is to be used when input sequences are long enough to cover constructs in their entirety (e.g., obtained with methods such as next generation sequencing). CM_2 is an extension designed to deal with shorter data (e.g., obtained with Sanger sequencing), and that need recombining. Both algorithms are shown to yield accurate construct-matching in a few minutes (even on hardware with limited processing power), together with a set of metrics that can be used to improve the robustness of the decision-making process. To ensure reliability and reproducibility, cMatch builds on the highly validated pairwise-matching Smith-Waterman algorithm. All the tests presented have been conducted on synthetic data for challenging, yet realistic constructs - and on real data gathered during studies on a metabolic engineering example (lycopene production).
Yeast Surface Display System: Strategies for Improvement and Biotechnological Applications
Authors: Teymennet-Ramírez Karla V. , Martínez-Morales Fernando , Trejo-Hernández María R.
Published: January 2022

Yeast surface display (YSD) is a “whole-cell” platform used for the heterologous expression of proteins immobilized on the yeast’s cell surface. YSD combines the advantages eukaryotic systems offer such as post-translational modifications, correct folding and glycosylation of proteins, with ease of cell culturing and genetic manipulation, and allows of protein immobilization and recovery. Additionally, proteins displayed on the surface of yeast cells may show enhanced stability against changes in temperature, pH, organic solvents, and proteases. This platform has been used to study protein-protein interactions, antibody design and protein engineering. Other applications for YSD include library screening, whole-proteome studies, bioremediation, vaccine and antibiotics development, production of biosensors, ethanol production and biocatalysis. YSD is a promising technology that is not yet optimized for biotechnological applications. This mini review is focused on recent strategies to improve the efficiency and selection of displayed proteins. YSD is presented as a cutting-edge technology for the vectorial expression of proteins and peptides. Finally, recent biotechnological applications are summarized. The different approaches described herein could allow for a better strategy cascade for increasing protein/peptide interaction and production.
Prognostic Autophagy-Related Model Revealed by Integrating Single-Cell RNA Sequencing Data and Bulk Gene Profiles in Gastric Cancer
Authors: Tong Tianying , Zhang Jie , Zhu Xiaoqiang , Hui Pingping , Wang Zhimin , Wu Qiong , Tang Jiayin , Chen Haoyan , Tian Xianglong
Published: January 2022

Autophagy has been associated with tumor progression, prognosis, and treatment response. However, an autophagy-related model and their clinical significance have not yet been fully elucidated. In the present study, through the integrative analysis of bulk RNA sequencing and single-cell RNA sequencing, an autophagy-related risk model was identified. The model was capable of distinguishing the worse prognosis of patients with gastric cancer (GC), which was validated in TCGA and two independent Gene Expression Omnibus cohorts utilizing the survival analysis, and was also independent of other clinical covariates evaluated by multivariable Cox regression. The clinical value of this model was further assessed using a receiver operating characteristic (ROC) and nomogram analysis. Investigation of single-cell RNA sequencing uncovered that this model might act as an indicator of the dysfunctional characteristics of T cells in the high-risk group. Moreover, the high-risk group exhibited the lower expression of immune checkpoint markers (PDCD1 and CTLA4) than the low-risk group, which indicated the potential predictive power to the current immunotherapy response in patients with GC. In conclusion, this autophagy-associated risk model may be a useful tool for prognostic evaluation and will facilitate the potential application of this model as an indicator of the predictive immune checkpoint biomarkers.
Role of EGF Receptor Regulatory Networks in the Host Response to Viral Infections
Authors: Carlin Cathleen R.
Published: January 2022

In this review article, we will first provide a brief overview of EGF receptor (EGFR) structure and function, and its importance as a therapeutic target in epithelial carcinomas. We will then compare what is currently known about canonical EGFR trafficking pathways that are triggered by ligand binding, versus ligand-independent pathways activated by a variety of intrinsic and environmentally induced cellular stresses. Next, we will review the literature regarding the role of EGFR as a host factor with critical roles facilitating viral cell entry and replication. Here we will focus on pathogens exploiting virus-encoded and endogenous EGFR ligands, as well as EGFR-mediated trafficking and signaling pathways that have been co-opted by wild-type viruses and recombinant gene therapy vectors. We will also provide an overview of a recently discovered pathway regulating non-canonical EGFR trafficking and signaling that may be a common feature of viruses like human adenoviruses which signal through p38-mitogen activated protein kinase. We will conclude by discussing the emerging role of EGFR signaling in innate immunity to viral infections, and how viral evasion mechanisms are contributing to our understanding of fundamental EGFR biology.
Public Perceptions on the Procedural Values and Proposed Outcomes of the Finnish Climate Change Act Amendment
Authors: Albrecht Eerika , Pietilä Iikka , Saarela Sanna-Riikka
Published: January 2022

This article examines the public perceptions on the drafting process of Finnish Climate Act amendment, which is a legislation on the climate policy that aims to mitigate climate change and secure adaptive capacity. In this paper we present results of a thematic analysis, which reveals citizens' perceptions of the procedural values, with respect to transparency, participation, and acceptance, and the objectives of the amendment, such as the climate neutrality target for 2035. The research data consisted of 2,458 answers to a citizen survey on the Finnish Climate Change Act amendment. Our results reveal that the opinions of citizens ranged from highlighting the urgency of political action to climate denials, with varying perceptions on process and proposed outcomes. While over half of citizens felt positively about the 2035 climate neutrality target created in the Climate Change Amendment Act, only a third believed that there was appropriate opportunity for public participation in the amendment process. Based on these findings, we suggest that participatory and transparent processes in legislative drafting are prerequisites for the sustainability transition and the implementation of international climate mitigation targets.
Syncope as the Initial Manifestation of Advanced Nasopharyngeal Carcinoma: A Case Report
Authors: Zhang Si-Cheng , Lin Mao-Qing , Zhang Li-Wei , Lin Xue-Qin , Luo Man-Qing , Lin Kai-Yang , Guo Yan-Song
Published: January 2022

Carotid sinus syndrome is a principal cause of syncope in the elderly. Syncope, associated with carotid sinus syndrome which is secondary to metastasis of advanced nasopharyngeal carcinoma, rarely occurs. The current study reported a 66-year-old woman, who presented with a history of frequent and recurrent syncope as the initial symptom, and was eventually diagnosed with advanced nasopharyngeal carcinoma. The positron emission tomography scan demonstrated a diagnosis of advanced nasopharyngeal carcinoma with involvement in carotid sheath space, and nasopharyngeal biopsy revealed non-keratinized nasopharyngeal carcinoma. After diagnosis and treatment, the patient had no recurrence of syncope. In summary, our case study suggests that great importance should be attached to potential intrinsic causes of syncope especially in the case of nasopharyngeal carcinoma, as it is an insidious malignancy which needs to be precisely identified.
Petrogenesis of Dacites in a Triassic Volcanic Arc in the South China Sea: Constraints From Whole Rock and Mineral Geochemistry
Authors: Wei Wu , Liu Chuan-Zhou , Mitchell Ross N. , Yan Wen
Published: January 2022

Triassic volcanic rocks, including basalts and dacites, were drilled from Meiji Atoll in the South China Sea (SCS), which represents a rifted slice from the active continental margin along the Cathaysia Block. In this study, we present apatite and whole rock geochemistry of Meiji dacites to decipher their petrogenesis. Apatite geochronology yielded U-Pb ages of 204–221 Ma, which are identical to zircon U-Pb ages within uncertainty and thus corroborate the formation of the Meiji volcanic rocks during the Late Triassic. Whole rock major elements suggest that Meiji dacites mainly belong to the high-K calc-alkaline series. They display enriched patterns in light rare earth elements (LREE) and flat patterns in heavy rare earth elements (HREE). They show enrichment in large-ion lithophile elements (LILE) and negative anomalies in Eu, Sr, P, Nb, Ta, and Ti. The dacites have initial 87Sr/86Sr ratios of 0.7094–0.7113, εNd(t) values of -5.9–-5.4 and εHf(t) values of -2.9–-1.7, whereas the apatite has relatively higher initial 87Sr/86Sr ratios (0.71289–0.71968) and similar εNd(t) (-8.13–-4.56) values. The dacites have homogeneous Pb isotopes, with initial 206Pb/204Pb of 18.73–18.87, 207Pb/204Pb of 15.75–15.80, and 208Pb/204Pb of 38.97–39.17. Modeling results suggest that Meiji dacites can be generated by <40% partial melting of amphibolites containing ∼10% garnet. Therefore, we propose that the Meiji dacites were produced by partial melting of the lower continental crust beneath the South China block, triggered by the underplating of mafic magmas as a response to Paleo-Pacific (Panthalassa) subduction during the Triassic. Meiji Atoll, together with other microblocks in the SCS, were rifted from the South China block and drifted southward due to continental extension and the opening of the SCS.
Simultaneous Inversion of Layered Velocity and Density Profiles Using Direct Waveform Inversion (DWI): 1D Case
Authors: Liu Zhonghan , Zheng Yingcai , Zhou Hua-Wei
Published: January 2022

To better interpret the subsurface structures and characterize the reservoir, a depth model quantifying P-wave velocity together with additional rock’s physical parameters such as density, the S-wave velocity, and anisotropy is always preferred by geologists and engineers. Tradeoffs among different parameters can bring extra challenges to the seismic inversion process. In this study, we propose and test the Direct Waveform Inversion (DWI) scheme to simultaneously invert for 1D layered velocity and density profiles, using reflection seismic waveforms recorded on the surface. The recorded data includes primary reflections and interbed multiples. DWI is implemented in the time-space domain then followed by a wavefield extrapolation to downward continue the source and receiver. By explicitly enforcing the wavefield time-space causality, DWI can recursively determine the subsurface seismic structure in a local layer-by-layer fashion for both sharp interfaces and the properties of the layers, from shallow to deep depths. DWI is different from the layer stripping methods in the frequency domain. By not requiring a global initial model, DWI also avoids many nonlinear optimization problems, such as the local minima or the need for an accurate initial model in most waveform inversion schemes. Two numerical tests show the validity of this DWI scheme serving as a new strategy for multi-parameter seismic inversion.
Statistical Seasonal Forecasting of Tropical Cyclone Landfall on South China Utilizing Preseason Predictors
Authors: Zhang Oscar Y. W. , Chan Kelvin T. F. , Xu Lifeng , Wu Zhenzhen
Published: January 2022

Predicting tropical cyclone (TC) activities has been a topic of great interest and research. Many existing seasonal forecasting models of TC predict the numbers of TC geneses and landfalls based on the environmental factors in the peak TC season. Here, we utilize the mainstream reanalysis datasets in 1979–2005 and propose a statistical seasonal forecasting model, namely the SYSU model, for predicting the number of TC landfalls on South China based on the preseason environmental factors. The multiple linear regression analysis shows that the April sea level pressure over the tropical central Pacific, the March-April mean sea surface temperature southwest to Australia, the March 850-hPa zonal wind east to Japan, and the April 500-hPa zonal wind over Bay of Bengal are the significant predictors. The model is validated by the leave-one-out cross validation and recent 15-year observations (2006–2020). The correlation coefficient between the modeled results and observations reaches 0.87 (p < 0.01). The SYSU model exhibits 90% hit rate (38 out of 42) in 1979–2020. The Antarctic Oscillation, and the variations of the western North Pacific subtropical high and Intertropical Convergence Zone could be the possible physical linkages or mechanisms. The model demonstrates an operational potential in the seasonal forecasting of TC landfall on South China.
Profile Screening of Differentially Expressed lncRNAs of Circulating Leukocytes in Type 2 Diabetes Patients and Differences From Type 1 Diabetes
Authors: Lv Jianyi , Liu Yihan , Cui Jia , Fang Hongjuan , Wu Ying , Zhu Xiao , Guo Meng , Li Changlong , Dou Jingtao , Chen Zhenwen , Du Xiaoyan
Published: January 2022

Long noncoding RNAs (lncRNAs) have been reported to have multiple functions and can be used as markers of various diseases, including diabetes. This study was conducted to determine the lncRNA profile in leukocytes from patients with type 2 diabetes (T2D). Differential expression of lncRNAs in T2D and type 1 diabetes (T1D) was also examined. RNA sequencing was performed in a critically grouped sample of leukocytes from T2D patients and healthy persons. A total of 845 significantly differentially expressed lncRNAs were identified, with 260 downregulated and 585 upregulated lncRNAs in T2D. The analysis of functions of DE-lncRNA and constructed co-expression networks (CNC) showed that 21 lncRNAs and 117 mRNAs harbored more than 10 related genes in CNC. Fourteen of 21 lncRNAs were confirmed to be significantly differentially expressed was detected by qPCR between the T2D and control validation cohorts. We also identified a panel of 4 lncRNAs showing significant differences in expression between T1D and T2D. Collectively, hundreds of novel DE-lncRNAs we identified in leukocytes from T2D patients will aid in epigenetic mechanism studies. Fourteen confirmed DE-lncRNAs can be regarded as diagnostic markers or regulators of T2D, including 4 lncRNAs that chould distinguish T1D and T2D in clinical practice to avoid misdiagnosis.
Climate-Related Development Finance, Energy Structure Transformation and Carbon Emissions Reduction: An Analysis From the Perspective of Developing Countries
Authors: Li Nan , Shi Beibei , Wu Lei , Kang Rong , Gao Qiang
Published: January 2022

With the frequent occurrence of extreme weather in cities, economic, ecological and social activities have been greatly impacted. The adverse effects of global extreme climate and effective governance have attracted more and more attention of scholars. Considering the differences between developed and developing countries in climate response capacity, a key issue is how to encourage developed countries to provide adequate assistance to developing countries and enhance their enthusiasm to participate in addressing climate change challenges. Given this background, we evaluated the carbon emission reduction effects of developing countries before and after a “quasi-natural experiment” which involved obtaining the assistance of climate-related funding from developed countries. Specifically, we analyzed the assistance behavior for recipient countries and found that climate assistance can effectively reduce the carbon emissions level of recipient countries, and this result has a better impact on non-island types and countries with higher levels of economic development. Furthermore, the achievement of this carbon emissions reduction target stems from the fact that climate assistance has promoted the optimization of the energy structure of recipient countries and promoted the substitution of renewable energy for coal consumption. In addition, climate-related development finance plays a significant role in promoting the scientific and technological level of recipient countries, especially the development impact of the adaptive climate-related development finance. Therefore, this paper suggests that the direction of climate assistance should focus more on island countries and countries with low economic development level, and pay more attention to the “coal withdrawal” of recipient countries and climate adaptation field.
Organochlorine Compounds in Beached Plastics and Marine Organisms
Authors: Nunes Luís M.
Published: January 2022

Here we compare bioaccumulation factors in marine organisms to partition ratios in marine debris for dichlorodiphenyltrichloroethane and polychlorinated biphenyls. Both organochlorines are synthetic persistent organic pollutants emitted into the environment since the beginning of the last century in approximately equal amounts. Their vast use and dispersion have resulted in approximately similar median concentrations of the two organochlorines in some pelagic organisms, namely in the liver and muscle tissue of fish. Molluscs, on the other hand, show higher median uptake of PCBs (median = 2.34 ng/g) than of DDTs (median = 1.70 ng/g), probably reflecting more localized conditions. We found that the bioaccumulation factors can be several orders of magnitude higher than the partition ratios. For instance, the median concentrations of organochlorines in the different matrices of fish, birds, and mammals are between one to four orders of magnitude higher than those found in marine debris, when lipid-normalized; or up to two orders of magnitude when measured as wet-weight. But, in molluscs, bioaccumulation/partition equals unity, which agrees with previous studies using passive samplers. Future research should focus on reducing sources of uncertainty by 1) homogenization of chemical procedures; 2) better assessment of chemical partition equilibrium between water and polymers in environmental conditions; 3) use of (multi)polymer passive samplers better aimed at mimicking uptake of specific living tissues.
Systematic Evaluation of a Novel 6-dye Direct and Multiplex PCR-CE-Based InDel Typing System for Forensic Purposes
Authors: Fan Haoliang , He Yitong , Li Shuanglin , Xie Qiqian , Wang Fenfen , Du Zhengming , Fang Yating , Qiu Pingming , Zhu Bofeng
Published: January 2022

Insertion/deletion (InDel) polymorphisms, combined desirable characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), are considerable potential in the fields of forensic practices and population genetics. However, most commercial InDel kits designed based on non-Asians limited extensive forensic applications in East Asian (EAS) populations. Recently, a novel 6-dye direct and multiplex PCR-CE-based typing system was designed on the basis of genome-wide EAS population data, which could amplify 60 molecular genetic markers, consisting of 57 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels), and Amelogenin in a single PCR reaction and detect by capillary electrophoresis, simultaneously. In the present study, the DNA profiles of 279 unrelated individuals from the Hainan Li group were generated by the novel typing system. In addition, we collected two A-InDel sets to evaluate the forensic performances of the novel system in the 1,000 Genomes Project (1KG) populations and Hainan Li group. For the Universal A-InDel set (UAIS, containing 44 A-InDels) the cumulative power of discrimination (CPD) ranged from 1–1.03 × 10–14 to 1–1.27 × 10–18, and the cumulative power of exclusion (CPE) varied from 0.993634 to 0.999908 in the 1KG populations. For the East Asia-based A-InDel set (EAIS, containing 57 A-InDels) the CPD spanned from 1–1.32 × 10–23 to 1–9.42 × 10–24, and the CPE ranged from 0.999965 to 0.999997. In the Hainan Li group, the average heterozygote (He) was 0.4666 (0.2366–0.5448), and the polymorphism information content (PIC) spanned from 0.2116 to 0.3750 (mean PIC: 0.3563 ± 0.0291). In total, the CPD and CPE of 57 A-InDels were 1–1.32 × 10–23 and 0.999965, respectively. Consequently, the novel 6-dye direct and multiplex PCR-CE-based typing system could be considered as the reliable and robust tool for human identification and intercontinental population differentiation, and supplied additional information for kinship analysis in the 1KG populations and Hainan Li group.