bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples
Authors:   on behalf of the REHAB consortium, Gweon H. Soon , Shaw Liam P. , Swann Jeremy , De Maio Nicola , AbuOun Manal , Niehus Rene , Hubbard Alasdair T. M. , Bowes Mike J. , Bailey Mark J. , Peto Tim E. A. , Hoosdally Sarah J. , Walker A. Sarah , Sebra Robert P. , Crook Derrick W. , Anjum Muna F. , Read Daniel S. , Stoesser Nicole 
Published: October 2019

Abstract

Background
Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, ‘ResPipe’.

Results
Taxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve < 1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike of Thermus thermophilus DNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment.

Conclusions
Sequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available (https://gitlab.com/hsgweon/ResPipe).
Disorders of Arousal in adults: new diagnostic tools for clinical practice
Authors: Loddo Giuseppe , Lopez Régis , Cilea Rosalia , Dauvilliers Yves , Provini Federica 
Published: October 2019

AbstractDisorders of Arousal (DOA) are mental and motor behaviors arising from NREM sleep. They comprise a spectrum of manifestations of increasing intensity from confusional arousals to sleep terrors to sleepwalking.Although DOA in childhood are usually harmless, in adulthood they are often associated with injurious or violent behaviors to the patient or others. Driving motor vehicles, suspected suicide, and even homicide or attempted homicide have been described during sleepwalking in adults. Furthermore, adult DOA need to be differentiated from other sleep disorders such as Sleep-related Hypermotor Epilepsy or REM Sleep Behavior Disorder.Although many aspects of DOA have been clarified in the last two decades there is still a lack of objective and quantitative diagnostic criteria for DOA.Recent advances in EEG analysis and in the semiological characterization of DOA motor patterns have provided a better definition of DOA diagnosis.Our article focuses on the DOA diagnostic process describing accurately the newest DOA clinical, EEG and video-polysomnographic tools in order to aid clinicians in DOA assessment.
Implementation challenges of the mandatory health insurance scheme
Authors: Rashidul Hossain Shaik Sayed Md , Salman Shoaib Mohammad 
Published: October 2019

Abstract

Background
Implementation of a mandatory insurance scheme depends on several issues, and among them are regulation, management, and program design which are very crucial. Sometimes a well-designed insurance scheme cannot attract an adequate number of people toward the scheme. Therefore, this study is aimed to explore the implementation challenges of Sajida Foundation’s health insurance scheme.

Methods
An exploratory qualitative research design has been applied to explore the challenges that normally exist in regular implementation process. The study population was both field and official level employees who are directly involved in the implementation process of Nirapotta scheme in Karanigoni branch.

Results
Successful implementation of the health insurance scheme of Sajida Foundation is getting constraints by several factors, and among them are lack of dedicated staff for this program, less involvement with community people, inadequate program knowledge dissemination to the people, and not providing incentive for work of Nirapotta are considered as the major challenges of implementation of Nirapotta Scheme. Challenges faced by policy-makers include incoordination with Microfinance Regulatory Authority and not having the latest software for perfect monitoring and evaluation of the Nirapotta program. Apart from this, there are some challenges in implementation which are normally faced in program; some of the most noteworthy findings are incoordination between employees especially in branch level, transient position of Sajida bondhu in the Nirapotta program, and low payment scale compared to other organizations.

Conclusions
Implementation of Nirapotta scheme is getting constraints by multiple factors which can easily be overcome by involving all necessary stakeholders and taking their valuable concern for further development of the scheme to ensure long-term sustainability of the program.
Thrombophilia in hepatocellular carcinoma
Authors: Selim Fayrouz O. , Abdalla Taghrid M. , Hosny Thoraya A. M. 
Published: October 2019

Abstract

Background
Chronic liver disease and hepatocellular carcinoma (HCC) can cause a disturbance in the coagulation system. In this study, we aimed to assess the risk factors for venous thromboembolism either acquired or hereditary in patients with HCC.

Results
Serum levels of proteins C and S, AT activity, and lipoprotein (a) were significantly lower in both HCC and cirrhotic patients while homocysteine levels were significantly higher in HCC patients. The prevalence of activated protein C resistance (APCR) and factor V Leiden (FVL) mutation was higher in HCC patients but with no significant differences between the studied groups. With multivariate analysis, prothrombin time, Fbg, protein C and S deficiency, increased lipoprotein (a), hyperhomocysteinemia, APCR, and FVL mutation were independent risk factors for thromboembolic complications in HCC patients.

Conclusions
Thrombophilic abnormalities are prevalent in HCC patients, and they have a substantial increased risk of venous thromboembolism.
IPC—Individual Parental Coaching —A Journey to “Value-land”
Authors: Barkan Iris 
Published: October 2019

AbstractThis article presents an individual parental coaching model (IPC) designed and examined for a PhD dissertation. Here we shall examine one aspect from the PhD, which explores the connection and influence that this IPC model has on the ‘teenager-parent’ relationship.Essentially, the research had two main goals, firstly to examine the possible influence of a unique parental coaching process, with respect to the parents’ ability to form better connections and communication with their adolescent children. Furthermore, it sought to validate a certain perception of parenting - the notion that a parent must first establish a firm sense of “self” before taking part in parenting, thus self-definition, purpose and meaning, are the individual’s significant guidelines when establishing relations with others, especially the demanding relations with teenagers.This was a qualitative narrative piece of research, since the parents’ life stories, as perceived and related by them, were at the core of this research. Seven Israeli families participated; heterosexual married couples who had raised at least one teenager between the ages of 13 to 18. The parents took an active part in a comprehensive coaching process consisting of ten weekly sessions. While the teenagers took part in an indirect manner, by filling out questionnaires. The data collected during the coaching sessions and open interviews were analyzed using the “Theme Analysis” method. This revealed some prominent individual and parental issues that contemporary Israeli parents had to deal with.The results indicated the following central findings, apart from the parent’s appreciation of the opportunity to enter a deep process of ‘self-encounter’, resulting in great benefits despite the challenges along the way. The finding’s below address both the research question itself and the explicit change process in the communication and connection between the parents and their teenagers from both perspectives. Improvements included spending more time together, less anger and friction, more patience and tolerance, better awareness to discourse style and word choices plus an overall improvement in the atmosphere at home. All the participating parents without exception stated that it was a worthy journey, which they would recommend to all parents to experience.
Sistemas piezoeléctricos en el tren urbano de Guadalajara, México: entropía y negentropía
Authors: Barragán Arturo Arizaga , González Pérez Mario Guadalupe , Lara Yefer Asprilla 
Published: October 2019

Contexto: La homeostasis del tren urbano de Guadalajara, México, experimenta entropía relativa a la conglomeración de usuarios en las denominadas horas pico. Esto conlleva un mayor consumo de energía eléctrica en los desplazamientos cotidianos; no obstante, el peso proveniente de los usuarios puede ser utilizado como negentropía termodinámica para reducir sus niveles de entropía. En este sentido, el objetivo de esta investigación determina la viabilidad de utilizar la piezoelectricidad en la obtención y consumo de energía eléctrica para la operatividad del sistema.
Método: La investigación se fundamenta en datos proprocionados por el Sistema de Tren Eléctrico Urbano (Siteur) y la Comisión Federal de Electricidad (CFE). Complementariamente, esta información se triangula con datos realizados en ejercicios de campo y en función de la oferta y demanda energética; se calculan el peso aproximado de los usuarios y la energía que puede producir el sistema de generación piezoeléctrica por persona. Finalmente, es utilizado el modelo entropía-homeostasis-negentropía (EHN), para determinar el escenario de la piezoelectricidad en el consumo energético del tren eléctrico urbano de la metrópoli de Guadalajara.
Resultados: La utilización de piezoeléctricidad puede lograr eficiencias significativas para la optimización energética de sistemas de movilidad urbana; inclusive de hasta un 89,7 % como en el ejemplo de la línea 2 del Siteur en Guadalajara. Esto por las condiciones homeostáticas propias de este sistema, relativas a la afluencia promedio diaria en horas pico; cuando se llega a los 83.059 usuarios. Por tanto, es posible generar negentropía termodinámica, a través de la energía eléctrica proveniente de los sistemas piezoeléctricos y el peso de los usuarios.
Conclusiones: La energía autoproducida por piezoelectricidad en el sistema, mediante el aprovechamiento del peso de los usuarios puede ser almacenada para alimentar la líneas de la red del tren eléctrico urbano. De esta manera, se optimiza el consumo energético en los desplazamientos cotidianos, con ahorros económicos para la empresa y como negentropía en la reducción de la energía no utilizada para producir trabajo (entropía).
Industria 4.0 y Manufactura Digital: Un Método de Diseño Aplicando Ingeniería Inversa
Authors: Carro Suárez Jorge , Flores Salazar Fabiola , Flores Nava Irma , Hernández Hernández Ramón 
Published: October 2019

Contexto: Para la presente investigación se revisó la literatura y actualidad sobre Ingeniería 4.0 e Ingeniería Inversa con el objetivo de proponer un método de diseño para la digitalización y fabricación de piezas en 3D a través del uso de Manufactura Digital.
Método: Se realiza una revisión teórica y sistemática sobre Industria 4.0 e Ingeniería Inversa para determinar la relación entre ambos conceptos. Posteriormente, se analizan diversos métodos de diseño publicados para seleccionar uno como referencia. Finalmente, de los resultados obtenidos del análisis teórico, se presenta una propuesta de método de diseño para realizar la digitalización y manufactura de una pieza 3D. Como comprobación, el método se aplica en la captura, modelado e impresión 3D de una pieza.
Resultados: Se encuentra que el punto de relación entre Industria 4.0 e Ingeniería Inversa es la Manufactura Aditiva y que el método de diseño ideal para el desarrollo de la investigación es el de Archer a través de las perspectivas de Liu y Boyle, ya que el modelo propuesto se enfocará en el criterio del diseñador a través de un proceso de digitalización. Finalmente, su aplicación demuestra la relevancia de considerar a la Manufactura Digital como un componente determinante para la Industria 4.0 en la actualidad.
Conclusiones: Las condiciones, particularidades y costos de los nuevos procesos aplicados por la Industria 4.0 hacen necesario que se planteen nuevos modelos que generen beneficios a las empresas para ser más competitivas, rentables y sustentables. En este contexto, la Manufactura Digital se presenta como una alterativa de diseño, que a pesar de que lleva años siendo aplicada, no ha sido reconocida como una nueva tendencia tecnológica, por lo que su inclusión en la Industria 4.0 es pertinente y necesaria.
Swimming training by affecting the pancreatic Sirtuin1 (SIRT1) and oxidative stress, improves insulin sensitivity in diabetic male rats
Authors: Ghiasi Rafighe , Naderi Roya , Sheervalilou Roghayeh , Alipour Mohammad Reza 
Published: October 2019

Abstract

Background
Sirtuin1 is a regulator of oxidative stress involved in the management of diabetes complications. Due to the beneficial effects of swimming training in diabetes, this study aimed to investigate the effects of swimming training on pancreatic Sirtuin1, oxidative stress and metabolic parameters in type 2 diabetic male rats.

Materials and methods
Twenty-eight male Wistar rats (200–250 g) were randomly divided into four groups: control, diabetic, swim trained and swim trained diabetic rats (n = 7). Diabetes was induced by a high-fat diet and streptozotocin injection [35/kg intraperitoneally]. After 72 hours, animals with blood glucose levels ≥300 mg/dL were considered diabetic. Seven days after the induction of diabetes, animals in the exercise groups were subjected to swimming training (60 min/daily, 5 days/week) for 12 weeks. At the end of the intervention, the animals were anesthetized, and tissue/blood samples were prepared for measurements of metabolic parameters, albumin, the Sitruin1 gene and its protein expression levels, oxidative stress and histological study.

Results
This study indicated that the diabetic rats had a significant decrease (p < 0.01, p < 0.05) in pancreatic Sitruin1 gene and its protein expression levels, antioxidant enzymes, serum albumin, and the quantitative insulin sensitivity check index, but a significant increase (p < 0.01) in malondialdehyde level. Swimming training resulted in a considerable improvement (p < 0.01, p < 0.05) in pancreatic Sitruin1 gene and its protein expression levels, antioxidant enzymes, serum levels of albumin and metabolic parameters. In addition, histological findings indicated the beta-cells conservation.

Conclusions
This study suggested that pancreatic Sitruin1 may be a promising therapeutic target for diabetic complications.
Coulomb forces in THz electromechanical meta-atoms
Authors: Calabrese Allegra , Gacemi Djamal , Jeannin Mathieu , Suffit Stéphan , Vasanelli Angela , Sirtori Carlo , Todorov Yanko 
Published: October 2019

Abstract
Thanks to their large sensitivity to electromagnetic fields, microelectromechanical systems are becoming attractive for applications in the THz band (0.1–10 THz). However, up to date all THz electromechanical systems couple electromagnetic fields to mechanical motion only through photothermal dissipative forces: such mechanism allows for sensitive detection but prevents applications that require coherent transfer of information. In this work, we present a THz electromechanical meta-atom where the coupling between an electromagnetic mode and the displacement of a metallic micro-beam is substantially controlled by a conservative Coulomb force due to charge oscillations in the nanometric-size capacitive part of the meta-atom. We present experiments, performed at room temperature, which allow distinguishing and precisely quantifying the contributions of conservative and dissipative forces in the operation of our electromechanical resonator. Our analysis shows that the Coulomb force becomes the dominant contribution of the total driving force for high-order mechanical modes. Such system paves the way for the realization of coherent THz to optical transducers and allows the realization of fundamental optomechanical systems in the THz frequency range.
Comprehensive insights into intracellular fate of WS2 nanosheets for enhanced photothermal therapeutic outcomes via exocytosis inhibition
Authors: Kong Na , Ding Li , Zeng Xiaobin , Wang Junqing , Li Wenliang , Shi Sanjun , Gan Silvia Tian , Zhu Xianbing , Tao Wei , Ji Xiaoyuan 
Published: October 2019

Abstract
Two-dimensional (2D) nanosheet (NS)-based photothermal agents (PTAs), such as transition-metal dichalcogenides, have shown immense potential for their use in cancer photothermal therapy (PTT). However, the nano-bio interaction study regarding these NS-based PTAs is still in its infancy. In this study, we used WS2-PEG NS-based PTA as an example to provide comprehensive insights into the experimental understanding of their fate in cancer cells. The data revealed that three different endocytosis pathways (macropinocytosis, clathrin-dependent, and caveolae-dependent endocytosis), autophagy-mediated lysosome accumulation, and exocytosis-induced excretion contribute to the integrated pathways of WS2-PEG NSs within cells. These pathways are consistent with our previous reports on MoS2-PEG NS-based drug delivery platform, indicating that the composition difference of 2D NSs with PEGylation may have little influence on their intercellular fate. Moreover, by blocking the revealed exocytosis pathway-mediated secretion of WS2 NSs in tumor cells, an effective approach is proposed to attain enhanced photothermal therapeutic outcomes with low doses of WS2 NSs and under a low power of a near-infrared (NIR) laser. We expect that the exocytosis inhibition strategy may be a universal one for 2D NSs to achieve combination cancer therapy. This study may also provide more experimental basis for the future development of 2D NS’s application in biomedicine (e.g. PTT).
A Functional Analysis of theDrosophilaGenehindsight: Evidence for Positive Regulation of EGFR Signaling
Authors: Kim Minhee , Du Olivia Y , Whitney Rachael J , Wilk Ronit , Hu Jack , Krause Henry M , Kavaler Joshua , Reed Bruce H 
Published: October 2019

AbstractWe have investigated the relationship between the function of the gene hindsight (hnt), which is the Drosophila homolog of Ras Responsive Element Binding protein-1 (RREB-1), and the EGFR signaling pathway. We report that hnt mutant embryos are defective in EGFR signaling dependent processes, namely chordotonal organ recruitment and oenocyte specification. We also show the temperature sensitive hypomorphic allele hntpebbled is enhanced by the hypomorphic MAPK allele rolled (rl1). We find that hnt overexpression results in ectopic DPax2 expression within the embryonic peripheral nervous system, and we show that this effect is EGFR-dependent. Finally, we show that the canonical U-shaped embryonic lethal phenotype of hnt, which is associated with premature degeneration of the extraembyonic amnioserosa and a failure in germ band retraction, is rescued by expression of several components of the EGFR signaling pathway (sSpi, Ras85DV12, pntP1) as well as the caspase inhibitor p35. Based on this collection of corroborating evidence, we suggest that an overarching function of hnt involves the positive regulation of EGFR signaling.
RANCANG BANGUN PEMBANGKIT LISTRIK TENAGA SURYA SEBAGAI SUMBER LISTRIK UNTUK KAPAL PERIKANAN SKALA KECIL DI KABUPATEN PANGKEP, SULAWESI SELATAN
Authors: Daging I Ketut , Alirejo M. Subroto , Antara I Putu Wirta , Dwiyatmo Emil F. , Wahyu Tri 
Published: October 2019

Kebutuhan akan listrik untuk kalangan industri, perkantoran, perumahan, termasuk untuk kapal-kapal perikanan meningkat dengan pesat. Peningkatan kebutuhan listrik ini tidak diiringi dengan penambahan pasokan listrik. Energi surya dapat dijadikan alternatif penghasil energi listrik. Sel surya dapat mengkonversi langsung radiasi sinar matahari menjadi energi listrik (proses photovoltaic). Energi listrik yang dihasilkan dari sel surya dapat dimanfaatkan pada malam hari, dengan cara menyimpan energi listriknya ke baterai yang dikontrol oleh regulator pada siang hari. Pemanfaatan energi listrik dalam di atas kapal dilakukan dengan menghubungkan inverter dari arus DC ke AC pada keluaran regulator. Hasil pengujian modul surya (photovoltaic) diperoleh daya terbesar yang dihasilkan dari jam 08:00-16:00 adalah pada jam 12:00 dengan daya yang dihasilkan sampai 45,76 watt. Pengukuran tegangan dan arus setiap jam dari rentang jam 08:00 – 16:00, diperoleh daya rata-ratanya sebesar 32,389 Watt. Keluaran daya rata-rata selama 5 hari mencapai 32,386 Watt.