bluuebunny/crossref_metadata_2025_split huggingface dataset:
Boosting the analysis of protein interfaces with Multiple Interface String Alignment:illustration on the spikes of coronaviruses
Authors: Bereux S. , Delmas B. , Cazals F. 
Published: September 2020

AbstractWe introduceMultiple Interface String Alignment(MISA), a visualization tool to display coherently various sequence and structure based statistics at protein-protein interfaces (SSE elements, buried surface area, ΔASA, B factor values, etc). The amino-acids supporting these annotations are obtained from Voronoi interface models. The benefit of MISA is to collate annotated sequences of (homologous) chains found in different biological contextsi.e.bound with different partners or unbound. The aggregated views MISA/SSE, MISA/BSA, MISA/Δ ASAetc make it trivial to identify commonalities and differences between chains, to infer key interface residues, and to understand where conformational changes occur upon binding. As such, they should prove of key relevance for knowledge based annotations of protein databases such as the Protein Data Bank.Illustrations are provided on the receptor binding domain (RBD) of coronaviruses, in complex with their cognate partner or (neutralizing) antibodies. MISA computed with a minimal number of structures complement and enrich findings previously reported.The corresponding package is available from the Structural Bioinformatics Library (http://sbl.inria.fr)
Integrating GPU support for FreeSurfer with OpenACC
Authors: Shen Jingcheng , Mei Jie , Walldén Marcus , Ino Fumihiko 
Published: September 2020

AbstractFreeSurfer is among the most widely used suites of software for the study of cortical and subcortical brain anatomy. However, analysis using FreeSurfer can be time-consuming and it lacks support for the graphics processing units (GPUs) after the core development team stopped maintaining GPU-accelerated versions due to significant programming cost. As FreeSurfer is a large project with millions of source lines, in this work, we introduce and examine the use of a directive-based framework, OpenACC, in GPU acceleration of FreeSurfer, and we found the OpenACC-based approach significantly reduces programming costs. Moreover, because the overhead incurred by CPU-to-GPU data transfer is the major challenge in delivering GPU-based codes of high performance, we compare two schemes, copy- and-transfer and overlapped-fully-transfer, to reduce such data transfer overhead. Exper-imental results show that the target function we accelerated with overlapped-fully-transfer scheme ran 2.3 as fast as the original CPU-based function, and the GPU-accelerated program achieved an average speedup of 1.2 compared to the original CPU-based program. These results demonstrate the usefulness and potential of utilizing the proposed OpenACC-based approach to integrate GPU support for FreeSurfer which can be easily extended to other computationally expensive functions and modules of FreeSurfer to achieve further speedup.
Quantitative analysis of transporter activity biosensors
Authors: Park Jihyun , Chavez Taylor M. , Frommer Wolf B. , Cheung Lily S. 
Published: September 2020

AbstractThe allocation of sugars from photosynthetic leaves to storage tissues in seeds, fruits, and tubers is an important determinant of crop yields. Genetically guided selection and transgenic modification of plant membrane transporters can help enhance crop yields and increase pathogen resistance. Yet, quantitative, systems-level models to support this effort are lacking. Recently, biosensors gained popularity for collecting spatiotemporally resolved information on cell physiology and validating computational models. Here, we report the design and use of genetically-encoded biosensors to measure the activity of SWEETs, the only family of sugar transporters known to facilitate the cellular release of sugar in plants. We created SweetTrac sensors by inserting circularly-permutated GFP into SWEET transporters, resulting in chimeras that translate substrate-triggered conformational rearrangements during the transport cycle into detectable changes in fluorescence intensity. We demonstrate that a combination of cell sorting and bioinformatics can be applied as a general approach to accelerate the design of biosensors forin vivobiochemistry. Finally, mass action kinetics analysis of the biosensors’ response suggests that SWEETs are low-affinity, near-symmetric transporters that can rapidly equilibrate intra- and extracellular concentrations of sugars.Significance StatementTransporters are the gatekeepers of the cell. Transporters facilitate the exchange of ions and metabolites between cellular and subcellular compartments, thus controlling processes from bacterial chemotaxis to the release of neurotransmitters. In plants, transporters play critical roles in the allocation of carbon to different organs. Biosensors derived from transporters have been generated to monitor the activity of these proteins within the complex environment of the cell. However, a quantitative framework that reconciles molecular and cellular-level events to help interpret the response of biosensors is still lacking. Here, we created novel sugar transport biosensors and formulated a mathematical model to explain their response. These types of models can help realize multiscale, dynamic simulations of metabolite allocation to guide crop improvement.
A Novel Role for the Nuclear Receptor, NR4A1, inKlebsiella pneumoniaeLung Infection
Authors: Partyka Jessica , Henkel Matthew , Campfield Brian T. 
Published: September 2020

ABSTRACTKlebsiella pneumoniaeis a Gram-negative bacterial pathogen and common cause of pneumonia and bacteremia. Increasingly,K. pneumoniaehas become a public health concern due to its rate of nosocomial infection and emerging, broad-spectrum antibiotic resistance. The nuclear receptor NR4A1 exhibits functionality in a multitude of organ systems and is implicated as having a role in the immune response to bacterial infection, though its role inK. pneumoniaeinfection is unknown. To determine ifNr4a1functions in response toK. pneumoniaepulmonary disease, we infected wild-type andNr4a1−/−mice withK. pneumoniaeand assessed bacterial growth, immune cell recruitment and function, and cytokine production. We found thatNr4a1−/−mice had increased bacterial burden in the lungs and spleen, though no differences in cell recruitment. Pro-inflammatory cytokines,Il1βandIl6, as well as chemokine,Cxcl2, were significantly decreased in the BAL fluid cells ofNr4a1−/−mice 5 hours post-infection. Additionally,Nr4a1−/−mice had reduced IL-1β and myeloperoxidase protein production. We then examined the bactericidal function of macrophages and neutrophils from WT andNr4a1−/−mice. We identified thatNr4a1−/−neutrophils had decreased bactericidal function compared to wild-type neutrophils, which was associated with reduced expression ofIl1β,Lcn2,Mpo, andLyz2. These data suggestNr4a1plays a novel and essential role in neutrophil function during the host immune response toK. pneumoniaepulmonary infection.
Representative bubbles and deleveraging
Authors: Strati Francesco 
Published: September 2020

PurposeThe causes for the formation of a bubble in the collateral market when agents are provided with homogeneous expectations are explored. This bubbly dynamics will define a sufficient condition for deleveraging.Design/methodology/approachTheoretical approach with neutral deleveraging.FindingsFindings of the study are defined sufficient conditions for a behavioral rational bubble's formation in a market of collateral and the subsequent deleveraging. The crowd-in effect of the representative bubble is caused by errors in extrapolating information and thus by representativeness, while the crowd-out effect of deleveraging is set off by reverting to a rational heuristic.Research limitations/implicationsThe limit is that it is a homogeneous expectations approach, the implication is that cannot be rational speculation.Practical implicationsEven in a simple model of homogeneous expectations a bubble may arise with serious effect on the demand side: models that detect just rational mispricings cannot account for behavioral components that have financial and real effects.Originality/valueThe paper defines how deleveraging may occur even in case of homogeneous expectations. The latter should not be seen just as a limit but also as a signal of the importance of being aware of behavioral components.
Growth of private university business following “oligopoly” and “SME” approaches: an impact on the concept of university and on society
Authors: Alam Gazi Mahabubul , Parvin Morsheda , Roslan Samsilah 
Published: September 2020

Purpose
Universally, university is considered as the apex body which is ethically obliged to present a substantial society. In doing so, universities often innovate dynamic business models and theories. Ideally, the countries whose universities contribute for better and sustainable business growth are the advanced one. However, universities themselves should be the business organisation – an argument is yet to receive attention. Although literature lacks in the area of education business especially university provision, the sector behaves as business entity after the inception of private sector. Therefore, this paper aims to explore the paradigm transformation of university sector and its impact on the society.

Design/methodology/approach
Given the differentiated nature of research questions, multiple techniques are used to collect the data. However, this research adopts the norms of qualitative methods. Both secondary and primary data are used. While secondary data are collected by University Grants Commission (UGC), primary data are collected through interviews.

Findings
Findings show that the development of university sector started following monopoly model. More than half a century, the same model was continued. Thereafter, duopoly model was introduced which carried until the inception of private sector. The growth of private sector followed oligopoly model which was further extended to small and medium enterprises (SMEs). These days, society compares university with “diploma mill”, as production of knowledge and civic society is longer than the part of the core business of university. Consequently, compromising with research is to be judged as a threat to overall development that includes business and social development.

Originality/value
A few studies have been published in the area of private university. To the best of the authors’ knowledge, none covers the oligopoly-ism and SME-ism behaviour of university and its impact on the concept of university and on the society. Therefore, this project aims to understand the norms of university business and its substantial contribution on the social change.
Chlorogenic acid: A comprehensive review of the dietary sources, processing effects, bioavailability, beneficial properties, mechanisms of action, and future directions
Authors: Lu Huijie , Tian Zhimei , Cui Yiyan , Liu Zhichang , Ma Xianyong 
Published: September 2020

AbstractChlorogenic acids (CGAs), a group of hydroxycinnamates, are generally abundant in everyday foods and beverages, most prominently in certain coffee drinks. Among them, the chlorogenic acid (CGA), also termed as 5‐O‐caffeoylquinic acid (5‐CQA), is one of the most abundant, highly functional polyphenolic compounds in the human diet. The evidence of its health benefits obtained from clinical studies, as well as basic research, indicates an inverse correlation between 5‐CQA consumption and a lower risk of metabolic syndromes and chronic diseases. This review focuses on the beneficial properties for health and mechanisms of action of 5‐CQA, starting with its history, isomers, dietary sources, processing effects, preparation methods, pharmacological safety evaluation, and bioavailability. It also provides the possible molecular mechanistic bases to explain the health beneficial effects of 5‐CQA including neuroprotective, cardiovascular protective, gastrointestinal protective, renoprotective, hepatoprotective, glucose and lipid metabolism regulatory, and anticarcinogenic effects. The information summarized here could aid in the basic and clinical research on 5‐CQA as a natural dietary additive, potential drug candidate, as well as a natural health promoter.
Development of insect‐proof starch adhesive containing encapsulated cinnamon oil for paper box adhesion to inhibit Plodia interpunctella larvae infestation
Authors: Kim Jungheon , Yoon Chan Suk , Lee Sang‐eun , Na Ja Hyun , Han Jaejoon 
Published: September 2020

AbstractThe objectives of this study were to develop insect‐resistant adhesives and apply them to a cardboard packaging system for preventing Plodia interpunctella (Hübner) (Lepidoptera: Pyralidae) larvae infestation. Cinnamon essential oil (CO), an insecticide, was encapsulated with maltodextrin (CS/MD/CO), β‐cyclodextrin (CS/β‐CD/CO), and polyvinyl alcohol (CS/PVA/CO) in corn starch (CS) paste. This resulted in a sustained and gradual release of CO from the starch‐based insect‐proof adhesives. Penetration pathways of insects into corrugated cardboard boxes were investigated through the use of a screening test for infestation profiling. Microscopic images of encapsulated CO in an oil in water (O/W) emulsion were observed to confirm the morphology of the adhesives. Adhesion forces of CS, CS/CO, CS/MD/CO, CS/β‐CD/CO, and CS/PVA/CO were determined to be 6.2 N, 4.0 N, 3.1 N, 6.0 N, and 5.8 N, respectively. Consequently, significant decreases of adhesion force in the CS/CO and CS/MD/CO were found to be due to the presence of the surfactant (Span® 80) and the low adhesive properties of MD. The duration of the insecticidal activities of the developed adhesives was evaluated by measuring their release rates for 14 days and repellent profiles up to 24 hr and 40 days. As a result, CS/β‐CD/CO and CS/PVA/CO were found to have an inhibited rapid release and sustained repellent profiles. In conclusion, CS/β‐CD/CO and CS/PVA/CO were determined to be suitable for encapsulation models and could be applied to industrial cardboard containers to prevent cases of insect invasion.Practical ApplicationCorn starch‐based natural adhesives with an insect‐proof property were applied to food containers consisted of corrugated cardboard boxes. Cornflake cereal packaging using insect‐proof corrugated cardboard successfully prohibited pest invasion in commercial food distribution simulation model. Developed insecticidal adhesives are able to control insect penetration in distribution and storage steps.
Ultrasonographic evaluation of shoulder tendons in patients with Hashimoto's disease
Authors: Buyuksireci Dilek Eker , Tecer Duygu , Bolayir Basak , Yon Merve Ecem Erdogan , Akturk Mujde , Gunendi Zafer , Gogus Feride 
Published: September 2020

AbstractObjectivesTo investigate the thickness of the shoulder tendons and the measurement of acromiohumeral distance (AHD) in patients with Hashimoto's disease (HD).Material and MethodsTwenty‐eight patients with subclinical hypothyroid HD, 40 patients with euthyroid HD, and 51 healthy subjects were included. The thicknesses of biceps brachii, subscapularis, supraspinatus, infraspinatus tendons at both shoulders were evaluated with ultrasonography. Serum levels of thyroid stimulated hormone (TSH), free tri‐iodothyronine, free thyroxine (FT4), anti‐thyroid peroxidase (TPO) and anti‐thyroglobulin (anti‐TG) antibodies levels were measured.ResultsHeight, weight, body mass index (BMI), free T3 and free T4 levels were similar between the three groups (P = .839, P = .205, P = .374, P = .430 and P = .497, respectively). Biceps brachii, supraspinatus and infraspinatus tendon thicknesses in dominant arm and biceps brachii, subscapularis and infraspinatus tendon thicknesses in non‐dominant arm were significantly increased in euthyroid HD compared to healthy controls (P = .003, P = .030, P < .001; P = .035, P = .042, P < .001, respectively). Biceps brachii tendon thickness in dominant arm and subscapularis and supraspinatus tendon thicknesses in non‐dominant arms were significantly increased in subclinical hypothyroid HD compared to healthy controls (P = .025; P = .046, P = .017, respectively). However there was no such difference between euthyroid HD and subclinical hypothyroid HD groups (P < .05). There was low correlation between biceps brachii tendon thickness and free T4 level in non‐dominant shoulder in patients with HD (r = .272 P = .030). For the rest of the tendons, there was no correlation between TSH, anti‐TPO, anti‐TG levels and tendon thicknesses in patients with HD.ConclusionsThis study suggests that thyroid autoimmunity in HD may lead to an increase in thickness of shoulder tendons.
Long‐term observational study on 6223 survivors of arsenic poisoning due to contaminated milk powder during infancy
Authors: Liu Rong , Tabuchi Takahiro , Kitamura Tetsuhisa , Miyashiro Isao , Sobue Tomotaka 
Published: September 2020

AbstractIn 1955, an outbreak of arsenic poisoning caused by the ingestion of arsenic‐contaminated Morinaga Dry Milk occurred in western Japan. This study aimed to assess the mortality and cancer incidence risk among Japanese individuals who were poisoned during this time as infants. In total, 6223 survivors (mean age at enrollment, 27.5 y) who had ingested contaminated milk when they were aged ≤ 2 y participated in this study. Follow‐up was conducted from 1982 to 2018 (mean follow‐up duration, 30.3 y). Standardized mortality ratio (SMR) and standardized incidence ratio (SIR) were used to compare mortality and cancer incidence rates of subjects with the respective Japanese population rates, and 95% confidence intervals (95% CIs) of the SMR and SIR were also calculated. In total, 561 deaths and 524 new cancer cases were observed. A statistically significant increase in mortality rate was observed for all causes (SMR, 1.15; 1.01‐1.19), nervous system disease (2.83, 1.62‐4.19), respiratory disease (2.02, 1.37‐2.62), genitourinary system disease (2.25, 1.10‐3.73), and traffic accident (2.03, 1.14‐3.04). In contrast, a significant decrease in cancer incidence rate was observed for all cancers (SIR, 0.96; 0.84‐0.99), stomach cancer (0.77, 0.57‐0.92), colon cancer (0.63, 0.41‐0.85), rectum cancer (0.69, 0.43‐0.95), and breast cancer (0.72, 0.52‐0.89). Liver cancer showed a high mortality rate (SMR, 1.68; 1.06‐2.31). In this study, after the long‐term follow‐up we revealed overall and cause‐specific mortality and cancer incidence risk among survivors who ingested arsenic‐contaminated dry milk as infants.
An economic evaluation framework for land‐use‐based conservation policy instruments in a changing climate
Authors: Gerling Charlotte , Wätzold Frank 
Published: September 2020

AbstractClimate change is a key threat to biodiversity. To conserve species under climate change, ecologists and conservation scientists suggest 2 main conservation strategies regarding land use: supporting species’ range shifts to enable it to follow its climatic requirements by creating migration pathways, such as corridors and stepping stones, and conserving climate refugia (i.e., existing habitat areas that are somewhat buffered from climate change). The policy instruments that could be used to implement these conservation strategies have yet to be evaluated comprehensively from an economic perspective. The economic analyses of environmental policy instruments are often based on ecological effectiveness and cost‐effectiveness criteria. We adapted these general criteria to evaluate policy instruments for species’ conservation under climate change and applied them to a conceptual analysis of land purchases, offsets, and conservation payments. Depending on whether the strategy supporting species’ range shifts or conserving climate refugia is selected, the evaluation of the policy instruments differed substantially. For example, to ensure ecological effectiveness, habitat persistence over time was especially important for climate refugia and was best achieved by a land‐purchase policy instrument. In contrast, for the strategy supporting range shifts to be ecologically effective, a high degree of flexibility in the location of conserved sites was required to ensure that new habitat sites can be created in the species’ new range. Offset programs were best suited for that because the location of conservation sites can be chosen comparatively freely and may also be adapted over time.
CD8‐positive cutaneous lymphoproliferation associated with large granular lymphocyte leukemia in a patient with X‐linked agammaglobulinemia
Authors: Daou Hala , Hatch Leigh A. , Weinkle Allison , Morey Gabriel Eli , Messina Jane , Zhang Xiaohui , Sokol Lubomir , Seminario‐Vidal Lucia 
Published: September 2020

AbstractPatients with primary immunodeficiency are at increased risk for malignancy, especially hematologic neoplasms. This paper reports a unique case of a 47‐year‐old man with X‐linked agammaglobulinemia who presented with progressive asymptomatic violaceous papules and plaques on his face, hands, and trunk for 1 year. Skin biopsies revealed deep, nodular infiltrates of histiocytes and CD8‐positive lymphocytes, with a CD4:CD8 ratio of 1:10. Laboratory studies showed cytopenias. Flow cytometry in the skin, blood, and bone marrow (BM) showed a CD3+/CD8+/CD57+ large granular lymphocyte population. BM biopsy showed 30% involvement with these atypical T‐cells. T‐cell gene rearrangement studies of skin, blood, and BM revealed identical T‐cell clones. He was diagnosed with T‐large granular lymphocyte leukemia (T‐LGLL) with an associated CD8+ cutaneous lymphoproliferation. Skin involvement was suspected to represent infiltration by T‐LGLL. However, co‐existence of two lymphoproliferative disorders (LPDs), T‐LGLL and CD8+ granulomatous LPD, remains a possibility. In general, cutaneous infiltrates associated with LGLL are rare and poorly understood. It has been suggested that they are markers of poor prognosis. Our case report describes skin, blood, and BM findings in an immunosuppressed patient with T‐LGLL in detail. These findings have not yet been reported and their significance requires further investigation.