nils-herrmann/clean_scirepeval huggingface dataset:
Commentary: Innovation in the Biochemistry/Molecular Biology laboratory
Venue: Biochemistry and molecular biology education a bimonthly publication of the International Union of Biochemistry and Molecular Biology

The special section on Innovation in the Biochemistry/Molecular Biology (BMB) laboratory was initiated in 2009. The first 3 years we chose general laboratory exercises that introduced students to basic skills and techniques important in the modern laboratory. Previous manuscripts selected for this series have been published in the January/February issues of BAMBED (2009 2011) Since then, we have selected a specific topic for each year: BMB laboratory in Australia  genomic annotation  laboratory notebooks  and ethics  Our primary goal for each series has been to provide examples of experiments based on modern BMB themes that are presented in a creative manner, preferably using student centered, active learning styles such as PBL, research based learning, process oriented inquiry learning, and other high impact educational practices [5 7] Although traditional "wet lab" BMB approaches are still the foundation of most published BMB discoveries, increasingly computational models are providing increased insight into BMB findings and the formulation of new hypotheses that can be tested in vitro. Computational models of kinetics data from stopped flow or rapid quench experiments, for example, have been around for decades. It is possible now to augment structure function studies by the use of molecular dynamics (MD) simulations that consider molecular motions over time, enzyme plasticity (in the presence and absence of ligands) energy landscapes for enzyme catalysis, and so forth. As noted in many of the contributions in this issue, MD is increasingly common in the biochemical literature, and we have anecdotally observed increased interest in MD and other computational methods among undergraduate biochemistry students. Thus, for the 2016 series, our focus is on the use of MD simulations and related computational approaches to introduce students to computational BMB. Professor Donald Elmore of Wellesley College provides an opening editorial discussing the use of MD in undergraduate BMB laboratories followed by four articles with specific activities that can be adapted and adopted by our readers. We hope you enjoy this series and use these articles as an opportunity to gain interdisciplinary collaborations with colleagues across STEM disciplines as MD activities intersect various disciplines, including biochemistry, molecular biology, computer science, physics, and chemistry.
An Auction Bidding Protocol for Distributed Bit Allocation in RSSI based Localization Networks

Several factors (e.g. target energy, sensor density) affect estimation error at a point of interest in sensor networks. One of these factors is the number of allocated bits to sensors that cover the point of interest when quantization is employed. In this paper, we investigate bit allocation in such networks such that estimation error requirements at multiple points of interest are satisfied as best as possible. To solve this nonlinear integer programming problem, we propose an iterative distributed auctionbidding protocol. Starting with some initial bit distribution, a network is divided into a a number of clusters each with its own auction. Each cluster head (CH) acts as an auctioneer and divides sensors into buyers or sellers of bits (i.e. commodity) With limited messaging, CHs redistribute bits among sensors, each bit at a time such that the difference between achieved and required estimation errors within each cluster is reduced in each round. We propose two bit pricing schemes used by sensors to decide on exchanging bits. Finally, simulation results show that our proposed 'distributed' protocol's error performance can be within 5% 10% of that of a 'centralized' genetic algorithm (GA) solution
Soft Computing techniques for Rainfall Runoff modeling: A Review

Rainfall Runoff models are dependent on the physiographic, climatic and biotic characteristics of the basin. These factors induce either a linear, non linear or highly complex behaviour among the rainfall and runoff parameters. Rainfall Runoff relations are unstructured nature which diverted the attention of researchers towards Soft Computing tools for reasoning, consciousness, intuition and wisdom possessed by human beings. These are multi disciplinary field uses a diversely of statistical, optimization and probabilistic tools which complement each other to produce its three main branches viz. Fuzzy Logic, Artificial Neural Networks and Genetic Algorithms. Soft computing techniques either complementing each other or working on their own. They are able to model complex or unknown relationships which are either nonlinear or noisy. These review paper explains an introduction to these techniques and discusses their applications in modeling Rainfall Runoff relations replaces time consuming conventional mathematical techniques with intelligent and time saving computing tools.  Artificial neural networks, fuzzy logic, genetic algorithms, hybrid soft computing, Rainfall runoff modeling, soft computing.
Children with Developmental Verbal Dyspraxia: Changes in articulation and perceived resilience with intensive multimodal intervention

Research into intervention strategies for developmental verbal dyspraxia (DVD) clearly demonstrates the need to identify effective interventions. The goals of this study were to examine changes in articulation skills following the use of phonetic, multimodal intervention and to consider the relationship between these improved articulation skills and perceptions of resilience behaviors. These changes were related to components of the World Health Organization (WHO) International Classification of Functioning, Disability, and Health, Children and Youth version (ICF CY) The intervention was implemented daily for 12 children diagnosed with DVD, ages 3 to 10 years, enrolled in a school for children with speech, language, and hearing impairments on a university campus in the southeast of the USA. Eleven children presented with significant comorbid conditions. Changes in articulation, along with changes in parents' and speech language therapists' (SLTs' perceptions of resilience behaviors were measured. At the end of a 2 year period, statistically significant gains in articulation and parents' and SLTs' perceptions of resilience behaviors were noted. The relationship between improved articulation skills and increased resilience behaviors is discussed.
Qualitative and Quantitative Study on Listening Anxiety of Jordanian Students Majoring in English Language at Jerash University

Research on second and foreign language acquisition reveals that both cognitive and affective factors have a significant effect on the listening process and strategies employed by students as well as the outcome of their listening. Among the affective and cognitive factors that have played a crucial role in terms of listening is the listening anxiety. Therefore, this study aims to investigate how listening anxiety affects the listening process of EFL students at Jerash University in Jordan. 60 Jordanian undergraduates majoring in English language from Jerash University took part in this research. The research methodology was based on a qualitative as well as quantitative approach. The findings of the study revealed that 43 of them experienced a high level of listening anxiety. The Qualitative findings from the interviews with students corroborate the findings generated from the quantitative part of the study. The findings of this study not only support current opinion regarding the state of EFL teaching in Jordan, but more pertinently, it highlights the fact that remedial action needs to be taken to address the inherent failure of the educationists to produce proficient listeners of English among Jordanian graduates. One way of doing so would be to use the findings of this study to look into the possibility of teaching EFL in a holistic and integrative manner. Finally, this study suggests further research to be conducted based on its findings.
BATMAN TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine
Venue: Scientific reports

Traditional Chinese Medicine (TCM) with a history of thousands of years of clinical practice, is gaining more and more attention and application worldwide. And TCM based new drug development, especially for the treatment of complex diseases is promising. However, owing to the TCM's diverse ingredients and their complex interaction with human body, it is still quite difficult to uncover its molecular mechanism, which greatly hinders the TCM modernization and internationalization. Here we developed the first online Bioinformatics Analysis Tool for Molecular mechANism of TCM (BATMAN TCM) Its main functions include 1) TCM ingredients' target prediction; 2) functional analyses of targets including biological pathway, Gene Ontology functional term and disease enrichment analyses; 3) the visualization of ingredient target pathway/disease association network and KEGG biological pathway with highlighted targets; 4) comparison analysis of multiple TCMs. Finally, we applied BATMAN TCM to Qishen Yiqi dripping Pill (QSYQ) and combined with subsequent experimental validation to reveal the functions of renin angiotensin system responsible for QSYQ's cardioprotective effects for the first time. BATMAN TCM will contribute to the understanding of the "multi component, multi target and multi pathway" combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCM's molecular mechanism. BATMAN TCM is available at http:/bionet.ncpsb.org/batman tcm.
Traditional Chinese Medicine (TCM) and Herbal Hepatotoxicity: RUCAM and the Role of Novel Diagnostic Biomarkers Such as MicroRNAs
Venue: Medicines

Traditional Chinese Medicine (TCM) with its focus on herbal use is popular and appreciated worldwide with increased tendency, although its therapeutic efficacy is poorly established for most herbal TCM products. Treatment was perceived as fairly safe but discussions emerged more recently as to whether herb induced liver injury (HILI) from herbal TCM is a major issue;  To analyze clinical and case characteristics of HILI caused by herbal TCM, we undertook a selective literature search in the PubMed database with the search items Traditional Chinese Medicine, TCM, alone and combined with the terms herbal hepatotoxicity or herb induced liver injury;  HILI caused by herbal TCM is rare and similarly to drugs can be caused by an unpredictable idiosyncratic or a predictable intrinsic reaction. Clinical features of liver injury from herbal TCM products are variable, and specific diagnostic biomarkers such as microsomal epoxide hydrolase, pyrrole protein adducts, metabolomics, and microRNAs are available for only a few TCM herbs. The diagnosis is ascertained if alternative causes are validly excluded and causality levels of probable or highly probable are achieved applying the liver specific RUCAM (Roussel Uclaf Causality Assessment Method) as the most commonly used diagnostic tool worldwide. Case evaluation may be confounded by inappropriate or lacking causality assessment, poor herbal product quality, insufficiently documented cases, and failing to exclude alternative causes such as infections by hepatotropic viruses including hepatitis E virus infections;  Suspected cases of liver injury from herbal TCM represent major challenges that deserve special clinical and regulatory attention to improve the quality of case evaluations and ascertain patients' safety and benefit.
Toxin antitoxin systems in bacterial growth arrest and persistence.
Venue: Nature chemical biology

Bacterial persister cells constitute a subpopulation of genetically identical, metabolically slow growing cells that are highly tolerant of antibiotics and other environmental stresses. Recent studies have demonstrated that gene loci known as toxin antitoxin (TA) modules play a central role in the persister state. Under normal growth conditions, antitoxins potently inhibit the activities of the toxins. In contrast, under conditions of stress, the antitoxins are selectively degraded, freeing the toxins to inhibit essential cellular processes, such as DNA replication and protein translation. This inhibition results in rapid growth arrest. In this Review, we highlight recent discoveries of these multifaceted TA systems with a focus on the newly uncovered mechanisms, especially conditional cooperativity, that are used to regulate cell growth and persistence. We also discuss the potential for targeting TA systems for antimicrobial drug discovery.
The Cell Cycle Arrest and Apoptotic Functions of p53 in Tumor Initiation and Progression.
Venue: Cold Spring Harbor perspectives in medicine

P53 is a transcription factor highly inducible by many stress signals such as DNA damage, oncogene activation, and nutrient deprivation. Cell cycle arrest and apoptosis are the most prominent outcomes of p53 activation. Many studies showed that p53 cell cycle and apoptosis functions are important for preventing tumor development. p53 also regulates many cellular processes including metabolism, antioxidant response, and DNA repair. Emerging evidence suggests that these noncanonical p53 activities may also have potent antitumor effects within certain context. This review focuses on the cell cycle arrest and apoptosis functions of p53, their roles in tumor suppression, and the regulation of cell fate decision after p53 activation.
Extracorporeal life support during cardiac arrest and cardiogenic shock: a systematic review and meta analysis
Venue: Intensive Care Medicine

PurposeVeno arterial extracorporeal life support (ECLS) is increasingly used in patients during cardiac arrest and cardiogenic shock, to support both cardiac and pulmonary function. We performed a systematic review and meta analysis of cohort studies comparing mortality in patients treated with and without ECLS support in the setting of refractory cardiac arrest and cardiogenic shock complicating acute myocardial infarction.MethodsWe systematically searched MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials and the publisher subset of PubMed updated to December 2015. Thirteen studies were included of which nine included cardiac arrest patients (n 3098) and four included patients with cardiogenic shock after acute myocardial infarction (n 235) Data were pooled by a Mantel Haenzel random effects model and heterogeneity was examined by the I2 statistic.ResultsIn cardiac arrest, the use of ECLS was associated with an absolute increase of 30 days survival of 13 compared with patients in which ECLS was not used [95 CI 6 20 p 0.001; number needed to treat (NNT) 7.7] and a higher rate of favourable neurological outcome at 30 days (absolute risk difference 14 95 CI 7 20 p 0.0001; NNT 7.1) Propensity matched analysis, including 5 studies and 438 patients (219 in both groups) showed similar results. In cardiogenic shock, ECLS showed a 33 higher 30 day survival compared with IABP (95 CI, 14 52 p 0.001; NNT 13) but no difference when compared with TandemHeart/Impella 3 95 CI 21 to 14 p 0.70; NNH 33).ConclusionsIn cardiac arrest, the use of ECLS was associated with an increased survival rate as well as an increase in favourable neurological outcome. In the setting of cardiogenic shock there was an increased survival with ECLS compared with IABP.
EFEKTIVITAS ALGORITMA CLARKE WRIGHT DAN SEQUENTIAL INSERTION DALAM PENENTUAN RUTE PENDISTRIBUSIAN TABUNG GAS LPG

Permasalahan rute pendistribusian termasuk dalam Vehicle Routing Problem (VRP) yaitu permasalahan penentuan rute kendaraan untuk melayani beberapa pelanggan. Jenis VRP di antaranya Capacitated Vehicle Routing Problem (CVRP) di mana setiap kendaraan mempunyai kapasitas yang terbatas. Permasalahan distribusi tabung gas LPG dari salah satu agen LPG di Blora yaitu PT. X ke beberapa sub agen/pangkalan merupakan contoh kasus permasalahan Capacitated Vehicle Routing Problem (CVRP) Dalam penelitian ini, yang menjadi permasalahan adalah bagaimana menyelesaikan masalah rute pendistribusian tabung gas LPG menggunakan algoritma Clarke Wright dan algoritma Sequential Insertion. Pencarian rute tersebut dilakukan secara hitungan manual dan dengan bantuan program Matlab R2014a. Selanjutnya akan ditentukan keefektifan dari penggunaan kedua algoritma tersebut. Pengambilan data dilakukan dengan metode observasi dan wawancara secara langsung dengan pegawai di PT. X. Data yang diambil berupa alamat alamat pelanggan dan jumlah permintaan setiap pelanggan pada bulan April 2016. Selanjutnya dilakukan pencarian jarak dari masing masing lokasi ke lokasi lain dengan bantuan google maps. PT. X Blora mendistribusikan gas LPG 3 kg ke 38 tempat di 7 kecamatan. PT. X biasanya mendistribusikan tabung gas ke pangkalan sebanyak 3 kali seminggu dengan menggunakan 3 kendaraan berkapasitas 560 tabung. Pada solusi algoritma Clarke Wright diperoleh penghematan jarak sebesar 146,2 km/minggu dan penghematan biaya transportasi sebesar Rp.94.116,25/minggu. Sedangkan pada solusi algoritma Sequential Insertion diperoleh penghematan jarak sebesar 160,2 km/minggu dan penghematan biaya transportasi sebesar Rp.103.128,75/minggu. Dengan demikian dapat disimpulkan bahwa rute yang dibentuk menggunakan algoritma Sequential Insertion pada kasus ini lebih efektif dibandingkan rute yang dibentuk menggunakan algoritma Clarke Wright. Dari hasil analisis, diharapkan PT. X menerapkan algoritma Sequential Insertion dalam proses pendistribusian tabung gas LPG 3 kg sehingga biaya yang dikeluarkan minimal.
Systemes d'Information et Management des Organisations 7eme edition

Veritable classique du domaine, ce manuel complet est concu pour preparer des responsables a la gestion des systemes d'information. Labellise par la FNEGE. Ce manuel de reference propose une analyse complete des systemes d'information et permet de resoudre les principaux problemes lies a l'usage des technologies de l'information. A l'heure du cloud computing, de l'explosion des reseaux sociaux, de la croissance du commerce en ligne et des applications mobiles, cette 7e edition se situe dans une perspective resolument manageriale.
Open educational resources and college textbook choices: a review of research on efficacy and perceptions

Textbooks are a vital component in many higher education contexts. Increasing textbook prices, coupled with general rising costs of higher education have led some instructors to experiment with substituting open educational resources (OER) for commercial textbooks as their primary class curriculum. This article synthesizes the results of 16 studies that examine either (1) the influence of OER on student learning outcomes in higher education settings or (2) the perceptions of college students and instructors of OER. Results across multiple studies indicate that students generally achieve the same learning outcomes when OER are utilized and simultaneously save significant amounts of money. Studies across a variety of settings indicate that both students and faculty are generally positive regarding OER.
(Re)Searching culture in foreign language textbooks, or the politics of hide and seek

Textbooks are curriculum artefacts that embody particular ideologies and legitimise specific types of knowledge [Apple, M. W. (1982) Education and power.  Routledge Kegan Paul; Apple, M. W. Christian Smith, L. K. (1991) The politics of the textbook. In M. W. Apple L. K. Christian Smith (Eds. The politics of the textbook (pp. 1 21) London, NY: Routledge] As the general public tends to associate them with truth rather than opinion [Meyer, C. J. Rosenblatt, P. C. (1987) Feminist analysis of family textbooks. Journal of Family Issues, 8(2) 247 252.  http:/jfi.sagepub.com/ textbooks can contribute to the circulation of particular representations and stereotypes. In the past decades, there has been an increasing interest in analysing the ways in which textbooks (re)produce representations of history, ethnic groups, minorities and gender differences, to name a few. Foreign language research has focused on the representation of foreign and native culture(s) given that this term has been central in debates in the areas of second and foreign language theories [Weninger, C. Kiss, T. (2013) Culture in English as a Foreign Language (EFL) textbooks: A semiotic approach. TESOL Quarterly, 47(4) 694 716. Retrieved from http:/www.tesol.org/read and publish/journals/tesol quarterly] Using a qualitative synthesis research approach, this paper analyses a pool of studies on the representation of culture in foreign language textbooks to answer a main question: How do language textbooks represent foreign culture? Findings will contribute to understanding how textbook discourse favours some representations of culture and why it does so. In turn, they may also inform teaching and learning practices, such as the actual use of language textbooks in the classroom, in which teachers' and students' agency is undeniable.
Consecuencias de la violencia domestica contra la mujer en el progreso escolar de los ninos y ninas del Peru

La violencia contra la mujer es un gran problema que no solo tiene enormes consecuencias en las victimas directas. Ademas, perturba todo el ambito familiar, y atenta contra el desarrollo integral de los ninos y las ninas. Utilizando datos de la Encuesta Demografica y de Salud Familiar (ENDES) este estudio estima el efecto que tiene la violencia de genero sobre la probabilidad de que los ninos y las ninas repitan el ano escolar. La violencia en el hogar genera un clima de tension que impide el normal desarrollo cognitivo y de habilidades de los ninos y las ninas. Al mismo tiempo, las madres victimas de violencia tienen menos capacidad de brindar a sus hijos el cuidado y la atencion que necesitan, lo cual contribuye a reducir el desarrollo de las habilidades de los ninos y las ninas. Estos dos efectos suelen reflejarse en un desempeno escolar mas pobre en comparacion con el de sus pares que no sufren este problema. Por otra parte, el estudio no encuentra evidencia de que la violencia domestica contra la madre tenga un efecto diferenciado entre las ninas y los ninos.
The effect of magnetite on the start up and N2O emission reduction of the anammox process

In order to observe the effect of magnetite during anammox start up and stabilization stages, a novel up flow anaerobic sludge blanket reactor using magnetite as a functional bio carrier was designed and operated. Continuous experiments indicated that magnetite could shorten the endogenous denitrification stage and improve the nitrogen removal rate. The nitrogen removal performance increased from 0.06 to 1.17 kg N per m3 per d of R1 and from 0.08 to 1.18 kg N per m3 per d of R0 (as control reactor) on day 150. Analysis of variance (ANOVA) results of NRR during days 90 150 showed that R1 was statistically different from R0 (p 0.045 0.05) The corresponding quantitative polymerase chain reaction results of nirS and nirK, fluorescence in situ hybridization results and Illumina MiSeq sequencing showed that proliferation of the anammox bacteria was promoted by magnetite with an increase of the nitrogen loading rate. The reduced N2O emission (25.06 15.27 mmol L 1) combined with the reduced nosZ qPCR results (2.26 0.029 x 106 copies per ng) revealed that this magnetite anammox reactor also can serve as an ideal alternative for N2O emission reduction in ammonium rich wastewater treatment.