bluuebunny/crossref_metadata_2025 huggingface dataset:
Analisis Pembagian Nisbah Dalam Akad Mudharabah Antara Shahibulmal Dengan Mudharib Ditinjau dari Aspek Hukum dan Aspek Ekonomi Syariah di Bank BNI Kantor Cabang Pembantu Boyolali
Authors: Faizal Dewantara
Published: August 2024

Analysis of the distribution of the ratio in the Mudharabah agreement between Shahibul Mal and Mudharib in terms of legal and economic aspects of sharia at Bank Bni, Boyolali Sub-Branch Office, is in accordance with the regulations according to Islam. PT. Bank Negara Indonesia (BNI) Syariah is a company engaged in banking whose activities are to provide services to the community, both services and other banking products. BNI Syariah was formed independently through the Internal Project Team. The pattern used by PT. Bank Negara Indonesia (Persero) tbk. Sharia to enter into the Islamic banking market is a dual banking system. Mudharabah agreement is an agreement for financing or investing funds from the owner of funds (shahibul maal) to fund management (mudharib) to carry out certain business activities that are in accordance with sharia, with the sharing of business results between the two parties based on a ratio that has been previously agreed. It was concluded that the distribution of the ratio carried out by shahibul maal with mudharib in the mudharabah agreement at the BNI syariah bank Boyolali sub-branch office in funding (deposits) was in accordance with Islamic law and the distribution of the Nisbah in the mudharabah contract at Bank BNI Syariah Boyolali Sub-Branch Office was not found elements that containing Maisir, Gharar and usury in the implementation of the contract between Islamic banking and customers. The contract in the implementation of the agreement has been known and agreed upon at the beginning of both parties. The agreement is in accordance with the regulations by the DSN-MUI and Islamic law.
Berinvestasi pada Reksadana Syariah ; Suatu Tinjauan Kritis
Authors: Muhamad Johari
Published: August 2024

Investment or asset placement either property or thing as a mean to result income or will increase value in the future known as investing. Return in an investment is influenced by the risks that accompany it. The greater return on offer, it mean is the greater  risk, and vice versa. Investments in mutual funds are suitable for novice investors, because it does not require huge funds, also the rate of return is better than saving. Along the improving investment climate and economy  in Indonesia, the tendency of society to invest tobe higher, especially in mutual funds. Mutual fund developments can be seen at NAV (net asset value), is one of the benchmarks for monitoring the outcome of a mutual fund. If the total NAV increase, that mean NAV per unit also increased, then the investor will earn huge profits. And if the total NAV decline, that mean the investor will suffer losses.
Pemberdayaan Ekonomi Masyarakat Berbasis Pariwisata Perspektif Ekonomi Islam(Studi Pada Pengrajin Gerabah di Desa Banyumulek Kabupaten Lombok Barat NTB)
Authors: Muh Zidni syukran
Published: August 2024

This study aimed (1) to describe the existing economic empowerment for a tourism-based community from the perspective of Islamic economy and the communityâ€™s efforts to develop entrepreneurship in Banyumulek Village, a tourist destination for pottery handicrafts, from the perspective of Islamic economy, by establishing a CBT (community-based tourism) in Banyumulek Village, Kediri District, Lombok Barat Regency, NTB, (2) to identify the tourism potential to be developed into a CBT in Banyumulek Village, (3) to describe the forms of economic empowerment suitable for tourism-based community in Banyumulek Village, and (4) to formulate a model of CBT development as a strategy for communityâ€™s economic empowerment in Banyumulek Village. This research used the descriptive-qualitative design. The researcher became the active instrument in the efforts to collect data from the field. Data was obtained from the Office of Cooperatives and Trade, the local administrators of Banyumulek Village, Womenâ€™s Cooperative of Pottery Craftsmen (KOPWAN), and the craftsmen in Banyumulek Village. The techniques for data gathering included interview, observation, and documentation. Data analysis was conducted using the analytical-interactive model. The results showed that (1) the effort of the local administrators of Banyumulek Village was done through the Womenâ€™s Cooperative of Pottery Craftsmen (KOPWAN) with their various working programs, and the forms and strategies of economic empowerment for the tourism-based community in Banyumulek Village included (a) socialization and counseling, (b) training/workshop, (c) cooperation with tourism entrepreneurs, (d) accommodating pottery craftsmen and vendors, and (e) empowerment for pottery craftswomen, (2) some of the achievements or impacts of tourism-based community empowerment conducted by KOPWAN were (a) employment opportunities, (b) improvement in communityâ€™s skills, (c) progress in communityâ€™s attitude and courtesy, and (d) use of local customs as a tourism attraction.
Peningkatan Peran Orang Tua dalam Pengawasan Penggunaan Gadget pada Anak Usia Dini
Authors: Winarsih Biyanti Dwi , Widyaningsih Heriyanti , Fatmawati Yayuk , Hartini Sri , Faidah Noor , Yusianto Wahyu , Nurdiana Nova Fitri
Published: August 2024

Gadget merupakan sebuah sebuah alat elektronik kecil dengan berbagai macam fungsi. Gadget sendiri dapat berupa komputer atau laptop, tablet PC, dan juga telepon seluler atau smartphone yang dirancang lebih canggih jika dibandingkan dengan perangkat teknologi yang telah diciptakan sebelumnya. Anak-anak sering menggunakan gadget dengan tujuan selain belajar, seperti menonton youtube, mencari informasi, menggunakan media sosial, bermain game online, menonton film online dengan durasi waktu yang lama. Penggunaan gadget bagi anak-anak perlu pengawasan dari orang tua. Orang tua harus sepenuhnya mengawasi dan membimbing anak-anak mereka saat menggunakan gadget apalikasi yang digunakan maupun pengawasan dalam waktu penggunaan.Tujuan kegiatan ini untuk meningkatkan peran orang tua dalam pengawasan penggunaan gadget pada anak-anak. Peningkatan peran orang tua dilakukan dengan pemberian edukasi kepada 31 ibu anak usia dini. Peran orang tua pada anak usia dini ini menunjukkan sebagian besar dari ibu masuk dalam kategori kurang membimbing anaknya menggunakan gadget. Setelah dilakukan edukasi terjadi peningkatan peran ibu membimbing penggunaan gadget pada anak
Penerapan Senam Ergonomik terhadap Penurunan Tekanan Darah (Hipertensi)
Authors: Purwandari Nila Putri , Putri Devi Setya , Ridholloh Budi Nur , Irsyad Muhammad Yusuf , Maulidika Nailil Hidayati , Sari Putri Arum , Ismayati Wahyu
Published: August 2024

Penyakit darah tinggi yang lebih dikenal sebagai hipertensi merupakan penyakit yang mendapat perhatian dari semua kalangan masyarakat, mengingat dampak yang ditimbulkannya baik jangka pendek maupun jangka panjang sehingga membutuhkan penanggulangan jangka panjang yang menyeluruh dan terpadu. Di Ruang Lily RSUD Sunan Kalijaga Demak banyak pasien yang mengalami hipertensi. Hal ini antara lain dihubungkan dengan adanya gaya hidup masyarakat yang berhubungan dengan resiko penyakit hipertensi seperti stress, obesitas (kegemukan), kurangnya olahraga, merokok, alkohol, dan makan makanan yang tinggi kadar lemaknya. Tujuan program pengabdian ini setelah dilakukan penyuluhan selama 30 menit, pasien dengan hipertensi di Ruang Lily dapat menjelaskan kembali tentang penyakit hipertensi dan senam ergonomik penurun tekanan darah dengan benar. Metode yang digunakan dalam penelitian ini adalah ceramah, diskusi interaktif dan demontrasi. Hasil didapatkan pasien dan keluarga pasien mampu menjelaskan terkait materi tentang hipertensi dan senam ergonomis dan juga dapat mempraktikkan langkah-langkah  senam ergonomik penurun tekanan darah. Simpulan kegiatan penyuluhan kepada pasien hipertensi dan keluarganya di Ruang Lily RSUD Sunan Kalijaga bertujuan untuk memberikan edukasi hipertensi dan senam ergonomis kepada pasien dan keluarganya. Hasil penyuluhan mendapatkan bahwa pasien dan keluarga mampu menjelaskan materi tentang hipertensi dan senam ergonomik dan juga mampu mempraktikkan senam ergonomik penurun tekanan darah.
Казахстан Школа стоматологии НАО «Казахский национальный медицинский университет имени С.Д. Асфендиярова»
Authors: Алтынбеков К.Д. , Тезекбаева Г.А.
Published: August 2024

История создания и развития стоматологического факультета берет начало со дня подписания министром здравоохранения Казахской ССР, профессором Карынбаевым С.Р. приказа № 245 от 28 июля 1959 года (об открытии стоматологического факультета). С этой даты, со дня открытия первого стоматологического факультета в Казахстане, начинается точка отсчета высшего стоматологического образования страны.
Asymmetric distribution of color-opponent response types across mouse visual cortex supports superior color vision in the sky
Authors: Franke Katrin , Cai Chenchen , Ponder Kayla , Fu Jiakun , Sokoloski Sacha , Berens Philipp , Tolias Andreas S
Published: August 2024

Color is an important visual feature that informs behavior, and the retinal basis for color vision has been studied across various vertebrate species. While many studies have investigated how color information is processed in visual brain areas of primate species, we have limited understanding of how it is organized beyond the retina in other species, including most dichromatic mammals. In this study, we systematically characterized how color is represented in the primary visual cortex (V1) of mice. Using large-scale neuronal recordings and a luminance and color noise stimulus, we found that more than a third of neurons in mouse V1 are color-opponent in their receptive field center, while the receptive field surround predominantly captures luminance contrast. Furthermore, we found that color-opponency is especially pronounced in posterior V1 that encodes the sky, matching the statistics of natural scenes experienced by mice. Using unsupervised clustering, we demonstrate that the asymmetry in color representations across cortex can be explained by an uneven distribution of green-On/UV-Off color-opponent response types that are represented in the upper visual field. Finally, a simple model with natural scene-inspired parametric stimuli shows that green-On/UV-Off color-opponent response types may enhance the detection of “predatory”-like dark UV-objects in noisy daylight scenes. The results from this study highlight the relevance of color processing in the mouse visual system and contribute to our understanding of how color information is organized in the visual hierarchy across species.
Inhibition of mitochondrial protein import and proteostasis by a pro-apoptotic lipid
Authors: Fita-Torró Josep , Garrido-Huarte José Luis , Michel Agnès H , Kornmann Benoît , Pascual-Ahuir Amparo , Proft Markus
Published: August 2024

Mitochondria mediated cell death is critically regulated by bioactive lipids derived from sphingolipid metabolism. The lipid aldehyde trans-2-hexadecenal (t-2-hex) induces mitochondrial dysfunction in a conserved manner from yeast to humans. Here we apply unbiased transcriptomic, functional genomics and chemoproteomic approaches in the yeast model to uncover the principal mechanisms and biological targets underlying this lipid-induced mitochondrial inhibition. We find that loss of Hfd1 fatty aldehyde dehydrogenase function efficiently sensitizes cells for t-2-hex inhibition and apoptotic cell death. Excess of t-2-hex causes a profound transcriptomic response with characteristic hallmarks of impaired mitochondrial protein import like activation of mitochondrial and cytosolic chaperones or proteasomal function and severe repression of translation. We confirm that t-2-hex stress induces rapid accumulation of mitochondrial pre-proteins and protein aggregates and subsequent activation of Hsf1- and Rpn4-dependent gene expression. By saturated transposon mutagenesis we find that t-2-hex tolerance requires an efficient heat shock response and specific mitochondrial and ER functions and that mutations in ribosome, protein and amino acid biogenesis are beneficial upon t-2-hex stress. We further show that genetic and pharmacological inhibition of protein translation causes t-2-hex resistance indicating that loss of proteostasis is the predominant consequence of the pro-apoptotic lipid. Several TOM subunits, including the central Tom40 channel, are lipidated by t-2-hex in vitro and mutation of accessory subunits Tom20 or Tom70 confers t-2-hex tolerance. Moreover, the Hfd1 gene dose determines the strength of t-2-hex mediated inhibition of mitochondrial protein import and Hfd1 co-purifies with Tom70. Our results indicate that transport of mitochondrial precursor proteins through the outer mitochondrial membrane is sensitively inhibited by the pro-apoptotic lipid and thus represents a hotspot for pro- and anti-apoptotic signaling.
Kunnskapsoppsummering og klassifisering av tiltaket: De Utrolige Årenes (DUÅs) skole- og barnehageprogram (1. utg.)
Authors: Sørlie Mari-Anne , Breivik Kyrre
Published: August 2024

Bakgrunn: Artikkelen er en kunnskapsoppsummering om effektene av det norske DUÅs skole- og barnehageprogram som bygger på Webster-Strattons indikerte program IY-TCM (Incredible Years Teacher Classroom Management Training). Den universelle versjonen tilbys personell (maks 25 personer pr. gruppe) som jobber med barn i 3-8 års alder i skoler, fritidsordning og barnehager, hovedsakelig i kommuner som har implementert DUÅs foreldretreningsprogram.
Skole- og barnehageprogrammets mål er en felles faglig plattform for målrettet arbeid med barns psykisk helse og forebygging av atferdsproblemer. Programopplæringen ledes av to gruppeledere over ca. ett skole-/barnehageår, og innbefatter seks opplæringsdager med påfølgende veiledning. Den strukturerte opplæringen fokuserer på emner som: 1) positiv relasjonsbygging, 2) ros, oppmuntring, oppmerksomhet, veiledning 3) belønningssystemer, 4) reduksjon av negativ atferd, 5) naturlige/arrangerte konsekvenser, og 6) emosjonell regulering og problemløsning. Oppfølgingsveiledning gis. Programeier er Regionalt kunnskapssenter for barn og unge Nord (RKBU Nord), UiT Norges arktiske universitet (Tromsø).
Metode: Kunnskapsoppsummeringen bygger på et systematisk litteratursøk i de nasjonale og internasjonale databasene Embase, Medline, Psykinfo, NORART, Cochrane, Cristin, NORA, SCOPUS, SweMed, Bibsys og Google Scholar. Det ble også innhentet informasjon om tiltaket fra tiltakseier.
Resultater: Resultatene inkluderer en vurdering av tiltakets beskrivelse, foreliggende effektstudier, forskningsmetodisk kvalitet og implementeringskvalitet. Programmet har et solid teoretisk fundament og det gis en god beskrivelse av programmets innholdskomponenter og opplæringsstrategier. To norske kvasi-eksperimentelle studier basert på lærervurderinger, publisert i fire artikler, ble inkludert i kunnskapsoppsummeringen. Resultatene indikerer at programmet kan redusere problematferd og øke sosial kompetanse hos barn i 3-8 års alderen, samt bidra til positive endringer i elev-lærer relasjoner og foreldres involvering i barnas skolegang. Med utgangspunkt i totalutvalget synes kortidseffektene imidlertid å være små til marginale. Resultatene tyder på at programmet har en større effekt på redusering av eksternaliseringsproblemer og elev-lærer konflikter for høyrisikobarn. Innenfor denne gruppen ble det i tillegg funnet en moderat effekt på skolefaglige prestasjoner. Det knytter seg noe usikkerhet til evalueringsresultatenes pålitelighet (særlig indre validitet). Per dags dato bør ikke programmet omtales som skoleomfattende, da det kun implementeres på 1. – 3. klassetrinn. Det er behov for en implementeringsmanual for skoler og barnehager og bedre kvalitetskontroll.
Konklusjon: DUÅs skole- og barnehageprogram klassifiseres på evidensnivå 4 – Tiltak med tilfredsstillende dokumentasjon på effekt.
Demystifying Polyhouse Microclimates: A Review of Modelling Tools and Strategies
Authors: Supraja K.V.L. , K.Krupavathi  , Babu R.Ganesh , Rao Ch. Someswara
Published: August 2024

It is impossible to feed the entire population of the world with conventional agriculture in this period of sudden climate change and degradation of natural resources. It makes it essential to adapt the protected cultivation, which makes it possible to provide favorable conditions for plant growth all-round the year. Thus, efficient management of protected cultivation techniques helps to obtain sustainable agriculture. For this, modelling of microclimate inside the greenhouse helps to better understand the dynamic variability of the microclimatic characteristics and their impact on crop growth. For this study, nearly 480 papers were reviewed on different aspects of microclimate modeling and machine learning algorithms out of which, 150 articles published in journals of high impact factors were selected and up to 80 references were cited in this article. This paper explored the available modelling techniques which include Physical-based models (offer high accuracy but require extensive computation time) and Data-driven models (faster but necessitate large datasets for analysis.). This review helps the researchers to get a detailed knowledge regarding the microclimate inside a polyhouse and various models available for greenhouse microclimate modelling and their ability to simulate the microclimate efficiently and accurately. Microclimate modeling helps understand the dynamic variations within a greenhouse and their impact on crops. The limitations of current models (computational time vs. data requirements) emphasize the need for hybrid model development. The rise of greenhouse automation and precision agriculture underscores the importance of accurate microclimate modeling. This paper, thus highlights the critical role of microclimate modeling in sustainable greenhouse agriculture, providing a comprehensive analysis of existing modeling techniques and their limitations. Thus, supporting the development of automated and data-driven greenhouse management practices.
The Role of Real Earnings Management (REM) in The Relationship between Financial Distress and Tax Planning
Authors: Souisa Angeline Grece , Tjondro Elisa , Kusumawardhani Adhityawati , Sadjiarto Arja , Eoh Tonny Stephanus
Published: August 2024

The aim of this study is to test the impact of real earnings management (REM) on the relationship between financial distress and tax planning. To survive and maximise financial potential in the face of financial distress, management tends to use accounting tactics to increase revenue in order to reach the company's target. The study sample comprises manufacturing sector firms listed in the IDX between 2018 and 2022. The total company sample consisted of 124 companies with 542 observations. The study employed robust random effect panel regression techniques. This research reveals that there is a negative link between financial distress and tax planning. This study fails to prove that REM strengthens the relationship between financial distress and tax planning. Furthermore, the study discovered that two groups of firms with high and low REM abnormal cash flows exhibited distinct financial distress behaviours towards tax planning. The practical implications are that increased regulatory attention and decreased financial resources create a lower motivation to evade taxes, as exhibited by the negative correlation between financial distress and tax planning.
The Analysis of Corporate Governance on Integrity Financial Statements in Banking Companies Listed on The Indonesia Stock Exchange
Authors: Devie Devie , Anggono Nathania Marchella Angelina , Pradana Vincent Christian Satya , Kwistianus Hendri
Published: August 2024

The integrity of financial statements is often questioned due to manipulation of accounting data, involving directors, commissioners, audit committees, and company owners. This study empirically demonstrates the impact of corporate governance - through board size, independent commissioners, audit committees, and institutional ownership - on financial statement integrity. Using quan­titative methods, the study involved 37 banking companies listed on the Indonesia Stock Exchange from 2017 to 2022. The results show that board size, independent commissioner, audit committee, institutional ownership, and leverage do not affect the integrity of financial state­ments, but firm size does.
PPG Peptide Nucleic Acids that Promote DNA Guanine Quadruplexes
Authors: Englund Ethan A. , Gupta Pankaj , Micklitsch Christopher M. , Onyshchenko Mykola I. , Remeeva Evgenia , Neumann Ronald D. , Panyutin Igor G. , Appella Daniel H.
Published: July 2014

Recent studies have shown that guanine‐rich (G‐rich) sequences with the potential to form quadruplexes might play a role in normal transcription as well as overexpression of oncogenes. Chemical tools that allow examination of the specific roles of G‐quadruplex formation in vivo, and their association with gene regulation will be essential to understanding the functions of these quadruplexes and might lead to beneficial therapies. Properly designed peptide nucleic acids (PNAs) can invade G‐rich DNA duplexes and induce the formation of a G‐quadruplex in the free DNA strand. Replacing guanines in the PNA sequence with pyrazolo[3,4‐d]pyrimidine guanine (PPG) nucleobases eliminates G‐quadruplex formation with PNA and promotes invasion of the target DNA.
Epithelial to mesenchymal transition correlates with tumor budding and predicts prognosis in esophageal squamous cell carcinoma
Authors: Niwa Yukiko , Yamada Suguru , Koike Masahiko , Kanda Mitsuro , Fujii Tsutomu , Nakayama Goro , Sugimoto Hiroyuki , Nomoto Shuji , Fujiwara Michitaka , Kodera Yasuhiro
Published: June 2014

Background and Objectives

Epithelial to mesenchymal transition (EMT) is considered to play an important role in cancer invasion. Tumor budding is a prognostic factor in esophageal squamous cell carcinoma (ESCC). The aim of this study was to explore the correlation between EMT and tumor budding.

Methods

Surgical specimens from 78 cases of ESCC resected without preoperative treatment between 2001 and 2013 were enrolled in the study. The mRNA expressions of E‐cadherin and vimentin were measured in cancerous tissues using real‐time PCR, and each tumor was classified into either epithelial or mesenchymal group. Tumor budding was evaluated in H&E‐stained slides and divided into two groups; low‐grade budding (<3) and high‐grade budding (≥3).

Results

The 5‐year survival rate in the epithelial group was significantly higher than that in the mesenchymal group (62.0% vs. 31.5%, P = 0.021). Survival rate of patients in the low‐grade budding group was significantly higher than that of patients in the high‐grade budding group (75.1% vs. 25.9%, P < 0.001). High‐grade tumor budding was significantly associated with the mesenchymal group (P = 0.009).

Conclusion

EMT was found to occur in ESCC and was significantly associated with tumor budding. Tumor budding was identified as a significant independent prognostic factor among the current population of ESCC. J. Surg. Oncol. 2014 110:764–769. © 2014 Wiley Periodicals, Inc.
Epithelial to mesenchymal transition might be induced via CD44 isoform switching in colorectal cancer
Authors: Mashita Naoki , Yamada Suguru , Nakayama Goro , Tanaka Chie , Iwata Naoki , Kanda Mitsuro , Kobayashi Daisuke , Fujii Tsutomu , Sugimoto Hiroyuki , Koike Masahiko , Nomoto Shuji , Fujiwara Michitaka , Kodera Yasuhiro
Published: June 2014

Background

Isoform switching of CD44 is associated with epithelial to mesenchymal transition (EMT) in several cancers; however, the clinical implications of this remain unclear for colorectal cancer (CRC).

Methods

We measured expression levels of E‐cadherin, vimentin, CD44 standard (CD44s) and CD44 variant 9 (CD44v9) transcripts in 14 CRC cell lines and 150 CRC patients. We determined EMT and CD44 status by calculating vimentin/E‐cadherin and CD44s/CD44v9 expression ratios, respectively. Associations between EMT status and CD44 isoform switching, and between clinicopathological factors and prognosis were analyzed.

Results

CD44s was highly expressed in mesenchymal‐type cell lines, while CD44v9 was highly expressed in epithelial‐type cell lines. CD44 knockdown resulted in decreased levels of vimentin expression, and significantly reduced proliferation, migration and invasion of cells. In CRC patients, the mesenchymal group and the high CD44 status group exhibited significantly poorer survival than that for the epithelial group (5‐year survival; 62.1% vs. 85.5%, P = 0.0085) and the low CD44 status group (5‐year survival; 66.1% vs. 85.0%, P = 0.0251). On multivariate analysis, CD44 status was an independent prognostic factor.

Conclusions

The status of EMT and CD44 is a critical prognostic factor, with CD44 isoform switching a possible trigger for EMT in CRC. J. Surg. Oncol. 2014 110:745–751. © 2014 Wiley Periodicals, Inc.
Hereditary colorectal cancer syndromes and genetic testing
Authors: Macaron Carole , Leach Brandie H. , Burke Carol A.
Published: June 2014

Colorectal cancer (CRC) is a leading cause of cancer and cancer deaths in the Western world. Approximately 5–10% of CRC are hereditary, due to a defined genetic cause. Individuals and families affected with a hereditary CRC syndrome exhibit benign and malignant extra‐intestinal tumors, require aggressive cancer screening and benefit from management by a multi‐disciplinary team of professionals. The clinical manifestations, genetic causes and current management of patients with hereditary colon cancer syndrome is provided. J. Surg. Oncol. 2015 111:103–111. © 2014 Wiley Periodicals, Inc.
Impact of infiltrative growth on the outcome of patients with undifferentiated pleomorphic sarcoma and myxofibrosarcoma
Authors: Iwata Shintaro , Yonemoto Tsukasa , Araki Akinobu , Ikebe Dai , Kamoda Hiroto , Hagiwara Yoko , Ishii Takeshi
Published: June 2014

Background and Objectives

Infiltrative growth, frequently observed in undifferentiated pleomorphic sarcoma (UPS) and myxofibrosarcoma (MFS), is often associated with a positive surgical margin as well as a local failure. The purpose of our study was to determine whether the radiographic growth patterns were associated with the outcomes of patients with UPS and MFS.

Methods

We reviewed 89 patients diagnosed with UPS or MFS and underwent initial surgery at our institute between 1994 and 2011. Growth patterns were assessed radiographically on preoperative MRI. Clinicopathological factors were collected and uni‐ and multivariate analyses were performed for survival.

Results

Infiltrative growth was observed in 21 patients (24%), which correlated with superficial tumors and positive surgical margin. Infiltrative growth correlated with poor disease‐specific and distant failure‐free survivals relative to non‐infiltrative growth. Multivariate analysis confirmed that these factors remained as significant factors. Patients with non‐infiltrative tumors resected inadequately exhibited slightly more favorable local control with postoperative radiotherapy, although no clinical benefit was seen for those with infiltrative tumors.

Conclusions

Infiltrative growth was an adverse prognostic factor for not only local control, but also disease‐specific and metastasis‐free survival in patients with UPS and MFS. Radiotherapy could not salvage inadequately resected infiltrative tumors. J. Surg. Oncol. 2014 110:707–711. © 2014 Wiley Periodicals, Inc.
A comparison of microvascular responses to visible and near‐infrared lasers
Authors: Li D. , Farshidi D. , Wang G.X. , He Y.L. , Kelly K.M. , Wu W.J. , Chen B. , Ying Z.X.
Published: June 2014

Background and Objective

Pulsed dye laser (PDL) is a commonly used treatment for Port Wine Stain birthmarks (PWS). However, deeper components of PWS are often resistant to PDL. Deeper penetrating lasers, including the long pulsed Neodymium:Yttrium Aluminum Garnet (Nd:YAG) laser have been used, but carry greater risk. This study evaluates the distinct blood vessel thermal responses to visible (595 nm) and near infrared (1,064 nm) lasers using animal and numerical models.

Study Design/Materials and Methods

Blood vessels in the rodent dorsal skin chamber (DSC) were irradiated by a 595 nm PDL and a long‐pulsed 1,064 nm Nd:YAG laser. Laser‐induced immediate and 1‐hour post‐structural and functional changes in the vessels were documented. Numerical simulations were conducted using a 1,000 µm depth SD mouse skin fold to simulate experimental conditions.

Results

PDL irradiation produced immediate blood vessel hemorrhage. Modeling indicated this occurs due to preferential heating of the superior parts of large blood vessels. Nd:YAG irradiation resulted in blood vessel constriction; modeling indicated more uniform heating of vessel walls.

Conclusion

PDL and Nd:YAG lasers result in distinct tissue responses. This supports different observable clinical treatment end points when using these devices. Vessel constriction associated with the Nd:YAG may be more difficult to observe and is one reason this device may carry greater risk. Lasers Surg. Med. 46:479–487, 2014. © 2014 Wiley Periodicals, Inc.
NNK reduction pathway gene polymorphisms and risk of lung cancer
Authors: Modesto Jennifer L. , Hull Anna , Angstadt Andrea Y. , Berg Arthur , Gallagher Carla J. , Lazarus Philip , Muscat Joshua E.
Published: June 2014

The tobacco‐specific nitrosamine NNK is a potent carcinogen found in tobacco smoke and implicated in the development of lung cancer. The major route of NNK metabolism is carbonyl reduction by AKR1C1, AKR1C2, CBR1, and 11β‐HSD1 to form NNAL. This study investigated the potential role of variants in this pathway on lung cancer risk by examining 53 tag‐SNPs representing the common variations inAKR1C1,AKR1C2,CBR1, andHSD11B1in 456 lung cancer cases and 807 controls. One SNP inCBR1(rs2835267) was significantly associated with overall risk of lung cancer, but did not pass multiple testing adjustment (OR: 0.76 95% CI: 0.58–0.99,P = 0.048, FDRP = 0.20). After stratification and multiple testing correction, three SNPs showed significance. One SNP (rs2835267) inCBR1showed a significant decreased risk for smokers with a high pack‐years (OR: 0.3595% CI: 0.17–0.69,P = 0.018) and in SCC (OR: 0.4895% CI: 0.29–0.76,P = 0.018). Another SNP located inCBR1(rs3787728) also showed a significant decreased risk in SCC (OR: 0.4695% CI: 0.26–0.80,P = 0.024) and small cell carcinoma (only in current smokers) (OR: 0.06895% CI: 0.01–0.42,P = 0.028). TheHSD11B1SNP (rs4844880) showed a significant increased risk for adenocarcinoma within former smokers (OR: 3.9495% CI: 1.68–9.22,P = 0.011). Haplotype analysis found significance with six haplotypes and lung cancer risk. These findings indicate that select variants in genes in the carbonyl reduction pathway of NNK may alter the risk of lung cancer. © 2014 Wiley Periodicals, Inc.
Butein, a novel dual inhibitor of MET and EGFR, overcomes gefitinib‐resistant lung cancer growth
Authors: Jung Sung Keun , Lee Mee‐Hyun , Lim Do Young , Lee Sung Young , Jeong Chul‐Ho , Kim Jong Eun , Lim Tae Gyu , Chen Hanyong , Bode Ann M. , Lee Hyong Joo , Lee Ki Won , Dong Zigang
Published: June 2014

Lung cancer is a leading cause of death worldwide and MET amplification is a major therapeutic limitation in acquired‐resistance lung cancer. We hypothesized that butein, a phytochemical, can overcome gefitinib‐induced resistance by targeting both EGFR and MET in non‐small cell lung cancer (NSCLC). To investigate the ability of butein to target EGFR and MET, we used in silico docking, a library of natural compounds and kinase assays. The effects of butein on growth, induction of apoptosis and expression of EGFR/MET signaling targets were examined in HCC827 (gefitinib‐sensitive) and HCC827GR (gefitinib‐resistant) NSCLC cells. Results were confirmed in vivo by a HCC827 or HCC827GR cell xenograft mouse model, each treated with vehicle, butein or gefitinib. Butein inhibited phosphorylation and kinase activity of EGFR and MET as well as soft agar colony formation and decreased viability of HCC827 and HCC827GR cells. Butein increased apoptosis‐related protein expression in these cells. Results were confirmed by co‐treatment with inhibitors of EGFR/MET or double knock‐down. Finally, xenograft study results showed that butein strongly suppressed HCC827 and HCC827GR tumor growth. Immunohistochemical data suggest that butein inhibited Ki‐67 expression. These results indicate that butein has potent anticancer activity and targets both EGFR and MET in acquired‐resistance NSCLC. © 2014 Wiley Periodicals, Inc.
Urinary retention rates after intravesical onabotulinumtoxinA injection for idiopathic overactive bladder in clinical practice and predictors of this outcome
Authors: Osborn David James , Kaufman Melissa R. , Mock Stephen , Guan Michael J. , Dmochowski Roger R. , Reynolds W. Stuart
Published: June 2014

Aims

The purpose of this study was to find the rate of urinary retention in clinical practice after treatment with onabotulinumtoxinA (BTN/A) for refractory overactive bladder (OAB) symptoms and determine factors that predict this outcome.

Methods

This is a retrospective study of BTN/A for treatment of non‐neurogenic, refractory OAB symptoms. Patients were analyzed with respect to their first and second BTN/A injections. The primary outcome measure was postoperative urinary retention. Statistical significance was assessed with multivariate logistic regression.

Results

Based on inclusion and exclusion criteria, the study population was 160. Mean age was 64 ± 13.2 years and 24% of the patients were men. The rate of urinary retention was 35% (n = 56). For the first BTN/A treatment, multivariate analysis revealed that preoperative PVR (post‐void residual volume) (OR 1.27, 95% CI 1.13–1.43, P < 0.001) and preoperative bladder capacity (OR 1.05, 95% CI 1.01–1.08, P = 0.005) were associated with postoperative urinary retention. In patients with a preoperative PVR of ≥100 ml, 94% (n = 17) went into urinary retention. For those who underwent a second BTN/A treatment, preoperative PVR, BTN/A units injected and retention after the first BTN/A were associated with an increased rate of postoperative retention.

Conclusions

Increased preoperative PVR was associated with urinary retention. The retention rate is higher than that reported in recent clinical trials. The inclusion of patients with a preoperative PVR ≥100 ml and a lower threshold to initiate clean intermittent catheterization contributed to this high rate of retention. Neurourol. Urodynam. 34:???–???, 2015. © 2014 Wiley Periodicals, Inc.
Comparative analysis of the pressure profilometry of vesicocutaneous continent catheterizable conduits between patients with and without rectus abdominis neosphincter (Yachia principle)
Authors: Rondon Atila , Leslie Bruno , Arcuri Leonardo Javier , Ortiz Valdemar , Macedo Antonio
Published: June 2014

Aims

To assess whether crossing rectus abdominis muscle strips, as proposed by Yachia, would change urinary catheterizable conduit's pressure profilometry, in static and dynamic conditions.

Methods

Non‐randomized selection of 20 continent patients that underwent Macedo's ileum‐based reservoir, 10 including Yachia's technique (Study Group) and 10 without this mechanism of continence (Control Group). Demographics and cystometric data were assessed. Conduit's pressure profilometry was obtained by infusing saline through a multichannel catheter, at rest and during Valsalva maneuver. We assessed the pressure: (a) in the bladder; (b) in conduit's proximal segment; and (c) in conduit's distal segment, which is presumably the abdominal wall and crossed muscle strips site.

Results

Mean age at surgery was 6.1 years in the Control Group and 7.7 years in the Study Group. There was no statistically significant difference between groups regarding maximum cystometric bladder capacity and leakage point pressure. At rest, the pressure profilometry showed similar results between groups in all segments analyzed. During Valsalva maneuver, pressure profilometry showed similar results between groups in bladder and conduit's proximal segment pressure. In this condition, conduit's distal segment pressure in the Study Group (Mean = 72.9 and Peak = 128.7 cmH2O) was significantly greater (P < 0.05) than conduit's distal segment pressure in the Control Group (Mean = 48.3 and Peak = 65.1 cmH2O).

Conclusions

Crossing muscle strips over the conduit significantly increases the pressure in its distal segment during contraction of the rectus abdominis muscle, which can be important in moments of sudden increase in abdominal pressure in order to keep continence. Neurourol. Urodynam. 34:???–???, 2015. © 2014 Wiley Periodicals, Inc.
Prevalence of dementia in urban and regional Aboriginal Australians
Authors: Radford Kylie , Mack Holly A. , Draper Brian , Chalkley Simon , Daylight Gail , Cumming Robert , Bennett Hayley , Delbaere Kim , Broe Gerald A.
Published: June 2014

Background

This study aimed to determine the prevalence of dementia in collaboration with urban/regional Aboriginal communities.

Methods

A census of Aboriginal and Torres Strait Islander men and women aged 60 years and above in the target communities identified 546 potential participants, with 336 (61.5%) participating in this cross‐sectional study. Participants completed a structured interview and cognitive screening tests. One hundred fifty‐three participants also completed a detailed medical assessment. Assessment data were reviewed by a panel of clinicians who determined a diagnosis of dementia or mild cognitive impairment (MCI) according to standard criteria.

Results

Crude prevalence of dementia was 13.4%, and age‐standardized prevalence was 21.0%. The most common types of dementia were Alzheimer's dementia (44%) and mixed dementia diagnoses (29%). Estimated prevalence of MCI was 17.7%.

Conclusion

Consistent with previous findings in a remote population, urban and regional Aboriginal Australians face high rates of dementia at younger ages, most commonly Alzheimer's dementia.
Cyanobiphenyl versus Alkoxybiphenyl: Which Mesogenic Unit Governs the Mesomorphic Properties of Guanidinium Ionic Liquid Crystals?
Authors: Haenle Johannes Christian , Neidhardt Manuel M. , Beardsworth Stuart , Kirres Jochen , Baro Angelika , Laschat Sabine
Published: June 2014

A series of phenylguanidinium salts 3·X, which are linked via an alkoxy spacer either to a 4-decyloxy- or 4-cyano-substituted biphenyl mesogen, was prepared and the mesomorphism studied. A decyloxybiphenyl core and a spacer of at least C6 chain length were required for mesophase formation. Replacement of the chloride counterion by other anions like bromide or tetrafluoroborate improved the thermal stability of the mesophase. A comparison of substitution pattern (meta v. para) on the phenyl ring revealed decreased melting and clearing points for the bent cationic head group. All guanidinium ionic liquid crystals 3 displayed only smectic A (SmA) phases. A packing model is assumed where the molecules in a bilayer stack over each other in opposite direction with interdigitated terminal decyloxy groups and spacers.
An enigmatic new tapeworm, Litobothrium aenigmaticum, sp. nov. (Platyhelminthes : Cestoda : Litobothriidea), from the pelagic thresher shark with comments on development of known Litobothrium species
Authors: Caira J. N. , Jensen K. , Waeschenbach A. , Littlewood D. T. J.
Published: June 2014

An enigmatic new tapeworm is described from pelagic thresher sharks in México and Taiwan. While lsrRNA (D1-D3) data robustly place it in the Litobothriidea, it bears essentially no morphological resemblance to other members of the order. Instead it superficially resembles the freshwater fish-inhabiting Caryophyllidea. Its scolex consists of a simple dome-shaped scolex proper and an extensive cephalic peduncle housing four distinct tissue types. It is hyperapolytic, thus reproductive anatomy is unknown. Developmental data show typical litobothriideans bear basic elements of their adult scolex upon entering the definitive host, undermining the notion that the new cestode represents a distinct litobothriidean life cycle stage. Scanning electron microscopy revealed the new species shares bands of distinctive microtriches with its congeners. In combination these data justify establishment of Litobothrium aenigmaticum, sp. nov.; the generic, familial and ordinal diagnoses are emended accordingly. Unlike typical litobothriideans, each worm is associated with a mucosal expansion at its attachment site, like those seen in some caryophyllideans. This pathological change may represent a worm-induced host response serving to reinforce attachment of the simple scolex to the mucosa. If so, the convergence of this litobothriidean on a morphology like that seen in the distantly related Caryophyllidea is a result of similarity in mode of attachment.
Toward better understanding of artifacts in variant calling from high-coverage samples
Authors: Li Heng
Published: June 2014

Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls and the leading causal artifacts still remain unclear even given the great efforts in the evaluation of variant calling methods.

Results: We made 10 single nucleotide polymorphism and INDEL call sets with two read mappers and five variant callers, both on a haploid human genome and a diploid genome at a similar coverage. By investigating false heterozygous calls in the haploid genome, we identified the erroneous realignment in low-complexity regions and the incomplete reference genome with respect to the sample as the two major sources of errors, which press for continued improvements in these two areas. We estimated that the error rate of raw genotype calls is as high as 1 in 10–15 kb, but the error rate of post-filtered calls is reduced to 1 in 100–200 kb without significant compromise on the sensitivity.

Availability and implementation: BWA-MEM alignment and raw variant calls are available at http://bit.ly/1g8XqRt scripts and miscellaneous data at https://github.com/lh3/varcmp .

Contact:  hengli@broadinstitute.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Efficient initial volume determination from electron microscopy images of single particles
Authors: Vargas Javier , Álvarez-Cabrera Ana-Lucia , Marabini Roberto , Carazo Jose M. , Sorzano C. O. S.
Published: June 2014

Motivation: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis.

Results: We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy.

Availability: The algorithm is freely available as part of the Xmipp 3.1 package [ http://xmipp.cnb.csic.es ].

Contact:  jvargas@cnb.csic.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Amordad database engine for metagenomics
Authors: Behnam Ehsan , Smith Andrew D.
Published: June 2014

Motivation: Several technical challenges in metagenomic data analysis, including assembling metagenomic sequence data or identifying operational taxonomic units, are both significant and well known. These forms of analysis are increasingly cited as conceptually flawed, given the extreme variation within traditionally defined species and rampant horizontal gene transfer. Furthermore, computational requirements of such analysis have hindered content-based organization of metagenomic data at large scale.

Results: In this article, we introduce the Amordad database engine for alignment-free, content-based indexing of metagenomic datasets. Amordad places the metagenome comparison problem in a geometric context, and uses an indexing strategy that combines random hashing with a regular nearest neighbor graph. This framework allows refinement of the database over time by continual application of random hash functions, with the effect of each hash function encoded in the nearest neighbor graph. This eliminates the need to explicitly maintain the hash functions in order for query efficiency to benefit from the accumulated randomness. Results on real and simulated data show that Amordad can support logarithmic query time for identifying similar metagenomes even as the database size reaches into the millions.

Availability and implementation: Source code, licensed under the GNU general public license (version 3) is freely available for download from http://smithlabresearch.org/amordad

Contact:  andrewds@usc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The effective founder effect in a spatially expanding population
Authors: Peter Benjamin
Published: June 2014

1

The gradual loss of diversity associated with range expansions is a well known pattern observed in many species, and can be explained with a serial founder model. We show that under a branching process approximation, this loss in diversity is due to the difference in offspring variance between individuals at and away from the expansion front, which allows us to measure the strength of the founder effect, dependant on an effective founder size. We demonstrate that the predictions from the branching process model fit very well with Wright-Fisher forward simulations and backwards simulations under a modified Kingman coalescent, and further show that estimates of the effective founder size are robust to possibly confounding factors such as migration between subpopulations. We apply our method to a data set ofArabidopsis thaliana, where we find that the founder effect is about three times stronger in the Americas than in Europe, which may be attributed to the more recent, faster expansion.