nils-herrmann/clean_scirepeval huggingface dataset:
Age related changes in gut microbiota composition from newborn to centenarian: a cross sectional study
Venue: BMC Microbiology

BackgroundIt has been reported that the composition of human gut microbiota changes with age; however, few studies have used molecular techniques to investigate the long term, sequential changes in gut microbiota composition. In this study, we investigated the sequential changes in gut microbiota composition in newborn to centenarian Japanese subjects.ResultsFecal samples from 367 healthy Japanese subjects between the ages of 0 and 104 years were analyzed by high throughput sequencing of amplicons derived from the V3 V4 region of the 16S rRNA gene. Analysis based on bacterial co abundance groups (CAGs) defined by Kendall correlations between genera revealed that certain transition types of microbiota were enriched in infants, adults, elderly individuals and both infant and elderly subjects. More positive correlations between the relative abundances of genera were observed in the elderly associated CAGs compared with the infant and adult associated CAGs. Hierarchical Ward's linkage clustering based on the abundance of genera indicated five clusters, with median (interquartile range) ages of 3 (0 35) 33 (24 45) 42 (32 62) 77 (36 84) and 94 (86 98) years. Subjects were predominantly clustered with their matched age; however, some of them fell into mismatched age clusters. Furthermore, clustering based on the proportion of transporters predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) showed that subjects were divided into two age related groups, the adult enriched and infant/elderly enriched clusters. Notably, all the drug transporters based on Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology groups were found in the infant/elderly enriched cluster.ConclusionOur results indicate some patterns and transition points in the compositional changes in gut microbiota with age. In addition, the transporter property prediction results suggest that nutrients in the gut might play an important role in changing the gut microbiota composition with age.
Constant Composition Distribution Matching
Venue: IEEE Transactions on Information Theory

Distribution matching transforms independent and Bernoulli(1/2) distributed input bits into a sequence of output symbols with a desired distribution. Fixed to fixed length, invertible, and low complexity encoders and decoders based on constant composition and arithmetic coding are presented. The encoder achieves the maximum rate, namely, the entropy of the desired distribution, asymptotically in the blocklength. Furthermore, the normalized divergence of the encoder output and the desired distribution goes to zero in the blocklength.
High Persister Mutants in Mycobacterium tuberculosis
Venue: PloS one

Mycobacterium tuberculosis forms drug tolerant persister cells that are the probable cause of its recalcitrance to antibiotic therapy. While genetically identical to the rest of the population, persisters are dormant, which protects them from killing by bactericidal antibiotics. The mechanism of persister formation in M. tuberculosis is not well understood. In this study, we selected for high persister (hip) mutants and characterized them by whole genome sequencing and transcriptome analysis. In parallel, we identified and characterized clinical isolates that naturally produce high levels of persisters. We compared the hip mutants obtained in vitro with clinical isolates to identify candidate persister genes. Genes involved in lipid biosynthesis, carbon metabolism, toxin antitoxin systems, and transcriptional regulators were among those identified. We also found that clinical hip isolates exhibited greater ex vivo survival than the low persister isolates. Our data suggest that M. tuberculosis persister formation involves multiple pathways, and hip mutants may contribute to the recalcitrance of the infection.
Les poles de competitivite a l'epreuve de la regulation les conditions d'emergence d'un acteur collectif

Cet article examine l'emergence d'un pole de competitivite afin de comprendre comment des acteurs locaux se sont saisis d'un dispositif etatique pour donner naissance a un acteur collectif. Une etude de cas longitudinale conduit a envisager l'emergence du collectif comme un processus de regulation, destine a repondre aux problemes rencontres par les acteurs. L'intervention de la structure de pilotage du pole permet d'offrir une regulation conjointe, faisant advenir le pole en tant que collectif.
Molecular graph convolutions: moving beyond fingerprints
Venue: Journal of Computer Aided Molecular Design

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data driven decisions. We describe molecular graph convolutions, a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph atoms, bonds, distances, etc. which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint based methods, they (along with other graph based methods) represent a new paradigm in ligand based virtual screening with exciting opportunities for future improvement.
Architecture for in space robotic assembly of a modular space telescope

An architecture and conceptual design for a robotically assembled, modular space telescope (RAMST) that enables extremely large space telescopes to be conceived is presented. The distinguishing features of the RAMST architecture compared with prior concepts include the use of a modular deployable structure, a general purpose robot, and advanced metrology, with the option of formation flying. To demonstrate the feasibility of the robotic assembly concept, we present a reference design using the RAMST architecture for a formation flying 100 m telescope that is assembled in Earth orbit and operated at the Sun Earth Lagrange Point 2.
The effect of long term migration dynamics on population structure in England Wales and Scotland
Venue: Population studies

We investigated the effect of migration on population dynamics in England Wales and Scotland from the mid nineteenth century to the present by comparing actual population size and structure with estimates based on zero net migration from a range of starting dates. In this period, Scotland had the largest net outflow among countries in Europe for which detailed information is available, whereas overall net migration in England Wales was close to zero. In the absence of migration, population would have been over twice as large in Scotland in 2013 as the actual value, but similar to its actual value in England Wales. Levels and pace of population ageing have been broadly similar in both countries, so the major impact of differential migration has been on population size rather than structure. We discuss these findings in relation to the debate on migration policy between political parties supporting and opposing independence in the 2014 Scottish referendum.
A SDN Controller with Energy Efficient Routing in the Internet of Things (IoT)

Internet of things is a new paradigm that aids the communication between heterogeneous devices and objects. It provides a unified framework that allows interoperability across varied platforms. It has the ability of sharing the information globally be it with any device. By 2020, it is estimated that nearly about 50 billion of devices will be connected. By providing an exclusive and unique identity for each object, gives the privilege for any device to connect to the internet. The main focus is to permit 'anyone' or 'anything' at 'any time' to exchange information services from 'anywhere' 'anyplace' This emergence technology keeps the people connected with 'anything' and 'anyone' and be it 'anywhere' To achieve this, routing protocol is needed that will entail the transmission of data between heterogeneous devices. In this paper, a routing protocol is proposed that will take in consideration the energy consumption of the heterogeneous devices. A SDN controller is also introduced in the network that serves as a centralized manager providing a secure network by denying access to selfish nodes that are present in the network.
Assessing the Construct Validity and Internal Reliability of the Screening Tool Test Your Memory in Patients with Chronic Pain
Venue: PloS one

Patients with chronic pain often complain about cognitive difficulties, and since these symptoms represent an additional source of suffering and distress, evaluating the cognitive status of these patients with valid and reliable tests should be an important part of their overall assessment. Although cognitive impairment is a critical characteristic of pain, there is no specific measure designed to detect these effects in this population. The objective was to analyze the psychometric properties of the "Test Your Memory" (TYM) test in patients with chronic pain of three different origins. A cross sectional study was carried out on 72 subjects free of pain and 254 patients suffering from different types of chronic pain: neuropathic pain (104) musculoskeletal pain (99) and fibromyalgia (51) The construct validity of the TYM was assessed using the Mini Mental State Examination (MMSE) Hospital Anxiety and Depression Scale (HADs) Index 9 from MOS sleep, SF 12, and through the intensity (Visual Analogical Scale) and duration of pain. An exploratory factor analysis was also performed and internal reliability was assessed using Cronbach's alpha. After adjusting for potential confounders the TYM could distinguish between pain and pain free patients, and it was correlated with the: MMSE (0.89, p<0.001) HAD anxiety 0.50, p<0.001) and HAD depression scales 0.52, p<0.001) MOS sleep Index 9 0.49, p<0.001) and the physical (0.49, p .001) and mental components (0.55, p .001) of SF 12. The exploratory structure of the TYM showed an 8 factor solution that explained 53% of the variance, and Cronbach's alpha was 0.66. The TYM is a valid and reliable screening instrument to assess cognitive function in chronic pain patients that will be of particular value in clinical situations.
Effect of Silicon Fertilization on Growth, Yield, and Nutrient Uptake of Rice

A field experiment was conducted to study the effect of silicon (diatomaceous earth, DE) fertilization on growth, yield, and nutrient uptake of rice during the kharif season of 2012 and 2013 in the new alluvial zone of West Bengal, India. Results showed that application of silicon significantly increased grain and straw yield as well as yield attributing parameters such as plant height (cm) number of tillers m 2, number of panicle m 2, and 1000 grain weight (g) of rice. The greatest grain and straw yields were observed in the treatment T6 (DE at 600 kg ha 1 in combination with standard fertilizer practice (SFP) The concentration and uptake of silicon, nitrogen (N) phosphorus (P) and potassium (K) in grain and straw were also greater under this treatment compared to others. It was concluded that application of DE at 600 kg ha 1 along with SFP resulted increased grain, straw, and uptake of NPK.
Efficacies of designer biochars in improving biomass and nutrient uptake of winter wheat grown in a hard setting subsoil layer.
Venue: Chemosphere

In the Coastal Plains region of the United States, the hard setting subsoil layer of Norfolk soils results in low water holding capacity and nutrient retention, which often limits root development. In this region, the Norfolk soils are under intensive crop production that further depletes nutrients and reduces organic carbon (C) Incorporation of pyrolyzed organic residues or "biochars" can provide an alternative recalcitrant C source. However, biochar quality and effect can be inconsistent and different biochars react differently in soils. We hypothesized that addition of different designer biochars will have variable effects on biomass and nutrient uptake of winter wheat. The objective of this study was to investigate the effects of designer biochars on biomass productivity and nutrient uptake of winter wheat (Triticum aestivum L. in a Norfolk's hard setting subsoil layer. Biochars were added to Norfolk's hard setting subsoil layer at the rate of 40 Mg ha( 1) The different sources of biochars were: plant based (pine chips, PC) animal based (poultry litter, PL) 50:50 blend (50% PC:50% PL) 80:20 blend (80% PC:20% PL) and hardwood (HW) Aboveground and belowground biomass and nutrient uptake of winter wheat varied significantly (p0.0001) with the different designer biochar applications. The greatest increase in the belowground biomass of winter wheat over the control was from 80:20 blend of PC:PL (81% followed by HW (76% PC (59% and 50:50 blend of PC:PL (9% However, application of PL resulted in significant reduction of belowground biomass by about 82% when compared to the control plants. The average uptake of P, K, Ca, Mg, Na, Al, Fe, Cu and Zn in both the aboveground and belowground biomass of winter wheat varied remarkably with biochar treatments. Overall, our results showed promising significance for the treatment of a Norfolk's hard setting subsoil layer since designer biochars did improve both aboveground/belowground biomass and nutrient uptake of winter wheat.
Contribution of the computed tomography of the anatomical aspects of the sphenoid sinuses to forensic identification.
Venue: Journal of neuroradiology. Journal de neuroradiologie

Body identification is the cornerstone of forensic investigation. It can be performed using radiographic techniques, if antemortem images are available. This study was designed to assess the value of visual comparison of the computed tomography (CT) anatomical aspects of the sphenoid sinuses, in forensic individual identification, especially if antemortem dental records, fingerprints or DNA samples are not available.  This retrospective work took place in a French university hospital. The supervisor of this study randomly selected from the picture archiving and communication system (PACS) 58 patients who underwent one (16 patients) or two (42 patients) head CT in various neurological contexts. To avoid bias, those studies were prepared (anonymized, and all the head structures but the sphenoid sinuses were excluded) and used to constitute two working lists of 50 (42+8) CT studies of the sphenoid sinuses. An anatomical classification system of the sphenoid sinuses anatomical variations was created based on the anatomical and surgical literature. In these two working lists, three blinded readers had to identify, using the anatomical system and subjective visual comparison, 42 pairs of matched studies, and 16 unmatched studies. Readers were blinded from the exact numbers of matching studies.  Each reader correctly identified the 42 pairs of CT with a concordance of 100% [97.5% confidence interval: 91 100% and the 16 unmatched CT with a concordance of 100% [97.5% confidence interval: 79 100% Overall accuracy was 100%  Our study shows that establishing the anatomical concordance of the sphenoid sinuses by visual comparison could be used in personal identification. This easy method, based on a frequently and increasingly prescribed exam, still needs to be assessed on a postmortem cohort.
Purkinje Cell Collaterals Enable Output Signals from the Cerebellar Cortex to Feed Back to Purkinje Cells and Interneurons
Venue: Neuron

Purkinje cells (PCs) provide the sole output from the cerebellar cortex. Although PCs are well characterized on many levels, surprisingly little is known about their axon collaterals and their target neurons within the cerebellar cortex. It has been proposed that PC collaterals transiently control circuit assembly in early development, but it is thought that PC to PC connections are subsequently pruned. Here, we find that all PCs have collaterals in young, juvenile, and adult mice. Collaterals are restricted to the parasagittal plane, and most synapses are located in close proximity to PCs. Using optogenetics and electrophysiology, we find that in juveniles and adults, PCs make synapses onto other PCs, molecular layer interneurons, and Lugaro cells, but not onto Golgi cells. These findings establish that PC output can feed back and regulate numerous circuit elements within the cerebellar cortex and is well suited to contribute to processing in parasagittal zones.
Purkinje Cells Directly Inhibit Granule Cells in Specialized Regions of the Cerebellar Cortex
Venue: Neuron

Inhibition of granule cells plays a key role in gating the flow of signals into the cerebellum, and it is thought that Golgi cells are the only interneurons that inhibit granule cells. Here we show that Purkinje cells, the sole output neurons of the cerebellar cortex, also directly inhibit granule cells via their axon collaterals. Anatomical and optogenetic studies indicate that this non canonical feedback is region specific: it is most prominent in lobules that regulate eye movement and process vestibular information. Collaterals provide fast, slow, and tonic inhibition to granule cells, and thus allow Purkinje cells to regulate granule cell excitability on multiple timescales. We propose that this feedback mechanism could regulate excitability of the input layer, contribute to sparse coding, and mediate temporal integration.
Stereotyped spatial patterns of functional synaptic connectivity in the cerebellar cortex
Venue: eLife

Motor coordination is supported by an array of highly organized heterogeneous modules in the cerebellum. How incoming sensorimotor information is channeled and communicated between these anatomical modules is still poorly understood. In this study, we used transgenic mice expressing GFP in specific subsets of Purkinje cells that allowed us to target a given set of cerebellar modules. Combining in vitro recordings and photostimulation, we identified stereotyped patterns of functional synaptic organization between the granule cell layer and its main targets, the Purkinje cells, Golgi cells and molecular layer interneurons. Each type of connection displayed position specific patterns of granule cell synaptic inputs that do not strictly match with anatomical boundaries but connect distant cortical modules. Although these patterns can be adjusted by activity dependent processes, they were found to be consistent and predictable between animals. Our results highlight the operational rules underlying communication between modules in the cerebellar cortex.
Mechanisms for motor timing in the cerebellar cortex
Venue: Current Opinion in Behavioral Sciences

In classical eyeblink conditioning a subject learns to blink to a previously neutral stimulus. This conditional response is timed to occur just before an air puff to the eye. The learning is known to depend on the cerebellar cortex where Purkinje cells respond with adaptively timed pauses in their spontaneous firing. The pauses in the inhibitory Purkinje cells cause disinhibition of the cerebellar nuclei, which elicit the overt blinks. The timing of a Purkinje cell response was previously thought to require a temporal code in the input signal but recent work suggests that the Purkinje cells can learn to time their responses through an intrinsic mechanism that is activated by metabotropic glutamate receptors (mGluR7)
Victims of Bullying in Schools

This article provides an overview of current research on bullying (peer victimization, peer harassment) in school, with a focus on victims of such bullying. The 1st section provides a working definition of bullying and its many forms. The 2nd section describes some of the known consequences of being bullied for mental health, physical health, and academic achievement. The 3rd section turns to individual characteristics that might place children at risk for being bullied. The 4th section describes school based interventions to reduce bullying and its negative effects. The final section considers implications of research on school bullying for teacher practice.
Learning Crosslingual Word Embeddings without Bilingual Corpora
Venue: EMNLP

Crosslingual word embeddings represent lexical items from different languages in the same vector space, enabling transfer of NLP tools. However, previous attempts had expensive resource requirements, difficulty incorporating monolingual data or were unable to handle polysemy. We address these drawbacks in our method which takes advantage of a high coverage dictionary in an EM style training algorithm over monolingual corpora in two languages. Our model achieves state of the art performance on bilingual lexicon induction task exceeding models using large bilingual corpora, and competitive results on the monolingual word similarity and cross lingual document classification task.
Association between energy drink intake, sleep, stress, and suicidality in Korean adolescents: energy drink use in isolation or in combination with junk food consumption
Venue: Nutrition Journal

BackgroundA considerable amount of research suggests that the frequent use of caffeinated energy drinks may be associated with undesirable effects, particularly so in children and adolescents. This study aimed to investigate the associations between energy drink intake and mental health problems, in isolation or in combination with junk food consumption, in a nationally representative sample of Korean adolescents.MethodsData from the 2015 Korean Youth Risk Behavior Web Based Survey, collected from 68,043 adolescents aged 12 18 years (mean age 15.09 1.72 years) were analyzed. Questionnaires were administered to collect information related to dietary behavior including energy drink intake and junk food consumption. Single item measures of sleep dissatisfaction, stress, depression, suicidal ideation, suicide plan, and suicide attempt were also administered. Associations between energy drink intake and sleep dissatisfaction, perceived severe stress, persistent depressive mood, and suicidality were investigated, and a multivariate approach was taken so that additional variance from demographic and lifestyle factors could be controlled for statistically.ResultsEnergy drink intake was significantly associated with sleep dissatisfaction (adjusted odd ratios [AORs] 1.64 and 1.25) severe stress (AORs 2.23 and 1.38) depressive mood (AOR 2.59 and 1.51) suicidal ideation (AORs 3.14 and 1.43) suicide plan (AORs 4.65 and 1.78) and suicide attempt (AORs 6.79 and 1.91) with a higher risk for more frequent use of energy drinks =5 times/wk) than for less frequent use (1 4 times/wk) The detrimental effect of energy drinks on mental health was particularly prominent in frequent junk food consumers.ConclusionsOur data suggest that energy drink intake had detrimental effects related to stress, sleep dissatisfaction, mood, and suicidality, in isolation or in combination with junk food consumption, in Korean adolescents. However, the cross sectional study design prevents our ability to assess causal relationships.