bluuebunny/crossref_metadata_2025_split huggingface dataset:
PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection
Authors: Zhang Fuhao , Shi Wenbo , Zhang Jian , Zeng Min , Li Min , Kurgan Lukasz 
Published: September 2020

AbstractMotivationKnowledge of protein-binding residues (PBRs) improves our understanding of protein−protein interactions, contributes to the prediction of protein functions and facilitates protein−protein docking calculations. While many sequence-based predictors of PBRs were published, they offer modest levels of predictive performance and most of them cross-predict residues that interact with other partners. One unexplored option to improve the predictive quality is to design consensus predictors that combine results produced by multiple methods.ResultsWe empirically investigate predictive performance of a representative set of nine predictors of PBRs. We report substantial differences in predictive quality when these methods are used to predict individual proteins, which contrast with the dataset-level benchmarks that are currently used to assess and compare these methods. Our analysis provides new insights for the cross-prediction concern, dissects complementarity between predictors and demonstrates that predictive performance of the top methods depends on unique characteristics of the input protein sequence. Using these insights, we developed PROBselect, first-of-its-kind consensus predictor of PBRs. Our design is based on the dynamic predictor selection at the protein level, where the selection relies on regression-based models that accurately estimate predictive performance of selected predictors directly from the sequence. Empirical assessment using a low-similarity test dataset shows that PROBselect provides significantly improved predictive quality when compared with the current predictors and conventional consensuses that combine residue-level predictions. Moreover, PROBselect informs the users about the expected predictive quality for the prediction generated from a given input protein.Availability and implementationPROBselect is available at http://bioinformatics.csu.edu.cn/PROBselect/home/index.Supplementary informationSupplementary data are available at Bioinformatics online.
At 50, Janzen–Connell Has Come of Age
Authors: Terborgh John 
Published: September 2020

AbstractFifty years ago, Janzen (1970) and Connell (1971) independently published a revolutionary idea to explain the hyperdiverse tree communities of the tropics. The essential observations were that seedfall is concentrated in the vicinity of fruiting trees, whereas saplings recruit at a distance from reproductive conspecifics. These observations were encapsulated in a simple focal-tree model constructed of intersecting curves for seedfall and escape from host-specific enemies postulated to attack propagules (seeds and seedlings) in the vicinity of reproductive conspecifics. In conflict with the thinking of the times, the mechanism operates from the top down rather than from the bottom up. A deterrent to broad acceptance has been the giant intuitive leap required to generalize the focal tree model to an entire forest community. Recent theoretical and empirical results have succeeded in bridging the gap between the focal tree model and its community-level implications. With these new findings, Janzen–Connell has come of age.
Comparison of Surface Area and Cortical Thickness Asymmetry in the Human and Chimpanzee Brain
Authors: Xiang Li , Crow Timothy J , Hopkins William D , Roberts Neil 
Published: September 2020

Abstract
Comparative study of the structural asymmetry of the human and chimpanzee brain may shed light on the evolution of language and other cognitive abilities in humans. Here we report the results of vertex-wise and ROI-based analyses that compared surface area (SA) and cortical thickness (CT) asymmetries in 3D MR images obtained for 91 humans and 77 chimpanzees. The human brain is substantially more asymmetric than the chimpanzee brain. In particular, the human brain has 1) larger total SA in the right compared with the left cerebral hemisphere, 2) a global torque-like asymmetry pattern of widespread thicker cortex in the left compared with the right frontal and the right compared with the left temporo-parieto-occipital lobe, and 3) local asymmetries, most notably in medial occipital cortex and superior temporal gyrus, where rightward asymmetry is observed for both SA and CT. There is also 4) a prominent asymmetry specific to the chimpanzee brain, namely, rightward CT asymmetry of precentral cortex. These findings provide evidence of there being substantial differences in asymmetry between the human and chimpanzee brain. The unique asymmetries of the human brain are potential neural substrates for cognitive specializations, and the presence of significant CT asymmetry of precentral gyrus in the chimpanzee brain should be further investigated.
Functional Connectivity Hypersynchronization in Relatives of Alzheimer’s Disease Patients: An Early E/I Balance Dysfunction?
Authors: Ramírez-Toraño F , Bruña R , de Frutos-Lucas J , Rodríguez-Rojo I C , Marcos de Pedro S , Delgado-Losada M L , Gómez-Ruiz N , Barabash A , Marcos A , López Higes R , Maestú F 
Published: September 2020

Abstract
Alzheimer’s disease (AD) studies on animal models, and humans showed a tendency of the brain tissue to become hyperexcitable and hypersynchronized, causing neurodegeneration. However, we know little about either the onset of this phenomenon or its early effects on functional brain networks. We studied functional connectivity (FC) on 127 participants (92 middle-age relatives of AD patients and 35 age-matched nonrelatives) using magnetoencephalography. FC was estimated in the alpha band in areas known both for early amyloid accumulation and disrupted FC in MCI converters to AD. We found a frontoparietal network (anterior cingulate cortex, dorsal frontal, and precuneus) where relatives of AD patients showed hypersynchronization in high alpha (not modulated by APOE-ε4 genotype) in comparison to age-matched nonrelatives. These results represent the first evidence of neurophysiological events causing early network disruption in humans, opening a new perspective for intervention on the excitation/inhibition unbalance.
Magnetic Polydopamine Modified with Choline-Based Deep Eutectic Solvent for the Magnetic Solid-Phase Extraction of Sulfonylurea Herbicides in Water Samples
Authors: Wang Dan-Dan , Lu Zhi-Heng , Guan Xiao-yu , Yang Mei-Nan Ou , Guo Hao-Ming , Yang Zhong-Hua 
Published: September 2020

Abstract
A novel magnetic solid-phase extraction technique coupled to ultraperformance liquid chromatography has been developed for separation and preconcentration of four sulfonylurea herbicides (sulfosulfuron, bensulfuron-methyl, pyrazosulfuron-ethyl and halosulfuro-methyl) in aqueous samples. The key point of this method was the application of a novel magnetic nanomaterial that composed of a low eutectic solvent as a shell coated on the magnetic core modified by polydopamine. The extensive active sites outside the low eutectic solvent can effectively adsorb the target herbicide in the extraction process. The obtained magnetic adsorbent was characterized with fourier transform infrared spectrometry, scanning electron microscopy and vibrating sample magnetometer. The influence parameters relevant to this method were optimized. Under the optimum conditions, good linearities could be obtained within the range of 1.0–200 μg L−1 for all analytes, with correlation coefficients ≥0.9908. The limit of detections of the method was between 0.0074 and 0.0100 μg L−1 and the relative standard deviations were 1.1–3.6%. The enrichment factor is 66.6. In the final experiment, the proposed method was successfully applied to the analysis of sulfonylurea herbicides residue in environment and drinking-water samples, and the obtained recoveries were between 70.6% and 109.4%.
Management of Drug Toxicity in Mycobacterium avium Complex Pulmonary Disease: An Expert Panel Survey
Authors: van Ingen Jakko , Aliberti Stefano , Andrejak Claire , Chalmers James D , Codecasa Luigi R , Daley Charles L , Hasegawa Naoki , Griffith David E , Hoefsloot Wouter , Huitt Gwen , Jarand Julie , Jhun Byung Woo , Loebinger Michael R , Marras Theodore K , Morimoto Kozo , Polverino Eva , Ringshausen Felix C , Santin Miguel , Thomson Rachel , Wagner Dirk , Wallace Richard J , Winthrop Kevin L , Yim Jae-Joon 
Published: September 2020

Abstract
Adverse events are frequent in nontuberculous mycobacteria pulmonary disease treatment, but evidence to support their management is scarce. An expert panel survey on management of adverse events shows consistent opinions on management of hepatoxicity, ocular toxicity, ototoxicity, tinnitus, and gastrointestinal upset. These opinions can provide assistance in individual patient management decisions.
The Conditional Reliability Evaluation of Data Center Network BCDC
Authors: Lv Mengjie , Cheng Baolei , Fan Jianxi , Wang Xi , Zhou Jingya , Yu Jia 
Published: September 2020

Abstract
As the number of servers in a data center network (DCN) increases, the probability of server failures is significantly increased. Traditional connectivity is an important metric to measure the reliability of DCN. However, the traditional connectivity of a DCN based on the condition of arbitrary faulty servers is generally lower. Therefore, it is important to increase the connectivity of a DCN by adding some limited conditions for the faulty server set. As a result, $g$-restricted connectivity and $h$-extra connectivity, which are two crucial subjects for a DCN’s ability to tolerate faulty servers, were proposed in the literature. In this paper, we study the $g$-restricted connectivity and $h$-extra connectivity of a new server-centric DCN, called BCDC, based on crossed cube with excellent performance. We prove that the $g$-restricted connectivity of BCDC is 4 for $n=3$ and $2n+g(n-2)-2$ for $n\geq 4$, where $0\leq g\leq n-3$, and the $h$-extra connectivity of BCDC is 4 for $n=3$ and $2n+h(n-2)-2$ for $n\geq 4$, where $0\leq h\leq n-3$.
Market heterogeneity and the distributional incidence of soft-drink taxes: evidence from France
Authors: Etilé Fabrice , Lecocq Sébastien , Boizot-Szantai Christine 
Published: September 2020

Abstract
Market heterogeneity may affect the distributional incidence of nutritional taxes if households sort by income across markets with different characteristics. We use scanner data to analyse the distributional incidence of the 2012 French soda tax on Exact Price Indices that measure consumer welfare from the price and availability of soft-drinks at a local level. While the average pass-through was small—about 45 per cent—, tax incidence was significantly higher in low-income and less-competitive markets. Market heterogeneity ultimately has substantial distributional effects: it accounts for at least 33 per cent of the difference in welfare variation between low- and high-income consumers.
The domestic consumption of firewood in preindustrial Seville, 1518–1775. An intensive bias driven by the Mediterranean diet
Authors: Bartolomé Rodríguez Isabel , González-Mariscal Manuel 
Published: September 2020

AbstractFuelwood was the main domestic fuel in the Mediterranean Basin during the early modern age, although the consumption level was lower than in other latitudes. The calculation of annual real prices and per capita household consumption figures in Seville from 1518 to 1775 reveals a complex evolution connected to a European-wide scenario. As expected, low levels of domestic fuelwood use were maintained in accordance with climate and heating requirements, but contrary to prior assumptions, a substantial increase is evidenced as of 1630. The growing supply of firewood from tree-crops, leading to a decrease in real prices, ran parallel to an early diet shift to pulses and the corresponding extension of cooking times.
Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana
Authors: Hamilton John P , Godden Grant T , Lanier Emily , Bhat Wajid Waheed , Kinser Taliesin J , Vaillancourt Brieanne , Wang Haiyan , Wood Joshua C , Jiang Jiming , Soltis Pamela S , Soltis Douglas E , Hamberger Bjoern , Buell C Robin 
Published: September 2020

Abstract

Background
Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance.

Findings
We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs.

Conclusions
Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.
Water weaponization in the Syrian conflict: strategies of domination and cooperation
Authors: Daoudy Marwa 
Published: September 2020

Abstract
How do actors weaponize water in intrastate conflicts? Existing typologies of water weaponization make deterministic differentiations between state and non-state actors and invoke opaque labels like ‘terrorism’. Furthermore, these typologies ignore how various actors engaged in violent conflict also cooperate over water, and whether water weaponization occurs beyond war. I propose a new typology for water weaponization in an analysis of the case of Syria, drawing on the leaked ‘ISIS papers’ as well as primary sources and interviews. The study begins by charting how the Ba'athist regime used water as a weapon of domination and legitimacy against its Kurdish population with infrastructure that would later facilitate the Islamic State of Iraq and Syria's (ISIS) ability to take hold of northeast Syria. I then turn to how non-state armed groups like ISIS and the Kurdish Democratic Union Party (PYD) have adopted strategies of water weaponization similar to the Syrian government by targeting and channelling water systems with major tactical implications. Finally, I show how enemy parties such as ISIS and the al-Assad regime weaponized cooperative water agreements to advance their mutual interests with violent implications for civilians. As such, I sort strategies of water weaponization into four categories: domination and legitimacy, military tools, military targets, and cooperation. In doing so, this new typology makes three main contributions, by: 1) accounting for how water is weaponized in state-society relations outside conflict; 2) refining existing definitions of water as a military tool and target; and 3) appraising the weapon-like effects of water cooperation.
In situ calibration of observatory broadband echosounders
Authors: Ona Egil , Zhang Guosong , Pedersen Geir , Johnsen Espen 
Published: September 2020

Abstract
Today, numerous scientific echosounders are used as continuously monitoring systems in ocean observatories. These echosounders are usually calibrated in shallow water, either in laboratory tanks or at random ocean docks before deployments. If the systems are used for quantitative measurements by the observatories, they should be calibrated at the operating depths to consider the environmental effects on the calibration parameters. In this article, a simple in situ calibration method is presented, which was recently applied to one of the nodes of the Norwegian Lofoten-Vesterålen ocean observatory, when the research vessel with dynamic positioning system suspended and moved the calibration sphere between the vessel and the transducer. The calibration results of a 70-kHz split-beam echosounder demonstrate that this method can be applied to the cabled observatories.
Offering care for victims of torture among a migrant population in a transit country: a descriptive study in a dedicated clinic from January 2017 to June 2019
Authors: Keshk Manar , Harrison Rebecca , Kizito Walter , Psarra Christina , Owiti Phillip , Timire Collins , Camacho Mabel Morales , De Maio Gianfranco , Safwat Hadeel , Matboly Abeer , Van den Bergh Rafael 
Published: September 2020

Abstract

Background
Medecins Sans Frontieres set up a clinic to provide multidisciplinary care to a vulnerable migrant population experiencing torture. We describe the population accessing care, the characteristics of care provided and patient outcomes.

Methods
A descriptive retrospective cohort study of patients enrolled in care during January 2017–June 2019 was conducted.

Results
Of 2512 victims of torture cases accessing the clinic, the male: female ratio was 1:1. About 67% of patients received medical care, mostly for chronic pain treatment. About 73% of patients received mental healthcare, 37% received physiotherapy and 33% received social support care; 49% came to the clinic upon the recommendation of a friend or family member. The discharge with improvement rate ranged from 23% in the mental health service to 9% in the sociolegal service. Patients retained in care had a median IQR of 3 (2–4) follow-up visits for medical care, 4 (2–7) for mental health, 6 (3–10) for physiotherapy and 2 (1–4) for sociolegal.

Conclusion
Care for victims of torture cases among vulnerable migrants is complex. For those who did receive care that led to an improvement in their condition, their care models have been described, to allow its implementation in other non-specialised settings.
AMBRA1 controls antigen-driven activation and proliferation of naive T cells
Authors: Masuhara Kaori , Akatsuka Hisako , Tokusanai Mizuki , Li Chenyang , Iida Yumi , Okada Yoshinori , Suzuki Takahiro , Ohtsuka Masato , Inoue Ituro , Kimura Minoru , Hosokawa Hiroyuki , Hozumi Katsuto , Sato Takehito 
Published: September 2020

Abstract
AMBRA1 (activating molecule in Beclin1-regulated autophagy) is a member of the BECN1 (BECLIN1) protein complex, and it plays a role in autophagy, cell death, tumorigenesis and proliferation. We recently reported that on T-cell receptor (TCR) stimulation, AMBRA1 controlled both autophagy and the cell cycle with metabolic regulation. Accumulating evidence has shown that autophagy and metabolic control are pivotal for T-cell activation, clonal expansion and effector/memory cell fate decision. However, it is unknown whether AMBRA1 is involved in T-cell function under physiological conditions. We found that T cells in Ambra1-conditional knockout (cKO) mice induced an exacerbated graft versus host response when they were transplanted into allogeneic BALB/c mice. Furthermore, Ambra1-deficient T cells showed increased proliferation and cytotoxic capability toward specific antigens in response to in vivo stimulation using allogeneic spleen cells. This enhanced immune response mainly contributed to naive T-cell hyperactivity. The T-cell hyperactivity observed in this study was similar to those in some metabolic factor-deficient mice, but not those in other pro-autophagic factor-deficient mice. Under the static condition, however, naive T cells were reduced in Ambra1-cKO mice, the same as in pro-autophagic factor-deficient mice. Collectively, these results suggested that AMBRA1 was involved in regulating T cell-mediated immune responses through autophagy-dependent and -independent mechanisms.
Fetal programming in sheep: effects on pre- and postnatal development in lambs
Authors: Sartori Everton D , Sessim Amir G , Brutti Danielle D , Lopes Jusecléia F , McManus Concepta M , Barcellos Júlio O J 
Published: September 2020

Abstract
This systematic review and meta-analysis aim to summarize the effects of maternal undernutrition or overnutrition during pregnancy on fetal weight and morphometric measurements during pregnancy, at birth, and postnatal period in sheep. After completing the search, selection, and data extraction steps, the measure of effect was generated by the individual comparison of each indicator with the average of the control and treated group (undernutrition or overnutrition) using the DerSimonian and Laird method for random effects. Subgroup analyses were also performed for lambing order, litter size, sex, as well as level, timing, and duration of the intervention. Fetal weight during the first third of pregnancy was not affected by maternal undernutrition or overnutrition. On the other hand, undernutrition in the second and last third of gestation reduces the weight of the lamb both during pregnancy, at birth, and during the postnatal period, requiring at least 120 postnatal days to achieve the same weight as its contemporaries in the control treatment. However, this reduction in weight is not accompanied by reductions in morphometric measurements, demonstrating that the animals were lighter, but of equal size. In overnutrition, there is an increase in fetal weight in the second third of gestation. However, in the last third of the gestational period, there are no differences in fetal weight for the multiparous subgroup, but it was reduced in primiparous ewes. There are no effects of overnutrition on birth weight; however, this result is highly heterogeneous. Thus, maternal nutrition of ewe during pregnancy has effects on fetal and postnatal weight, but not on size. Furthermore, the effects of undernutrition are more homogeneous while overnutrition showed heterogeneous responses.