bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent progress in optoelectronic memristors for neuromorphic and in-memory computation
Authors: Pereira Maria Elias , Martins Rodrigo , Fortunato Elvira , Barquinha Pedro , Kiazadeh Asal 
Published: May 2023

Abstract
Neuromorphic computing has been gaining momentum for the past decades and has been appointed as the replacer of the outworn technology in conventional computing systems. Artificial neural networks (ANNs) can be composed by memristor crossbars in hardware and perform in-memory computing and storage, in a power, cost and area efficient way. In optoelectronic memristors (OEMs), resistive switching (RS) can be controlled by both optical and electronic signals. Using light as synaptic weigh modulator provides a high-speed non-destructive method, not dependent on electrical wires, that solves crosstalk issues. In particular, in artificial visual systems, OEMs can act as the artificial retina and combine optical sensing and high-level image processing. Therefore, several efforts have been made by the scientific community into developing OEMs that can meet the demands of each specific application. In this review, the recent advances in inorganic OEMs are summarized and discussed. The engineering of the device structure provides the means to manipulate RS performance and, thus, a comprehensive analysis is performed regarding the already proposed memristor materials structure and their specific characteristics. Moreover, their potential applications in logic gates, ANNs and, in more detail, on artificial visual systems are also assessed, taking into account the figures of merit described so far.
Impacts of droughts and floods on agricultural productivity in New Zealand as measured from space
Authors: Blanc Elodie , Noy Ilan 
Published: May 2023

Abstract
We estimate the impact of precipitation extremes on the productivity of agricultural land parcels in New Zealand using satellite data. This type of post-disaster damage assessment aims to allow for the quantification of disaster damage when an on-the-ground assessment of damage is too costly or too difficult to conduct. It can also serve as a retroactive data collection tool for disaster loss databases where data collection did not happen at the time. We use satellite-derived observations of terrestrial vegetation (the enhanced vegetation index (EVI)) over the growing season, with data at the land parcel level identifying five land use types (annual and perennial crops, and three types of pasture), and with precipitation records, which we use to identify both excessively dry (drought) and excessively wet (flood) episodes. Using regression analyses, we examine whether these precipitation extremes had an observable impact on agricultural productivity. We find statistically significant declines in agricultural productivity that are associated with both droughts and floods. The average impact of these events is usually less than 1%, but the impacts are quite heterogeneous across years and across regions, with some parcels experiencing a much more significant decline in the EVI. We also identify several impact patterns related to the varying drought and flood vulnerability of the analysed land use types.
Activation of the toll-like receptor 2 signaling pathway by GAPDH from bacterial strain RD055328
Authors: Kurata Atsushi , Takeuchi Shimpei , Fujiwara Ryo , Tamura Kento , Imai Tomoya , Yamasaki-Yashiki Shino , Onuma Hiroki , Fukuta Yasuhisa , Shirasaka Norifumi , Uegaki Koichi 
Published: May 2023

ABSTRACT
We characterized the membrane vesicle fraction (RD-MV fraction) from bacterial strain RD055328, which is related to members of the genus Companilactobacillus and Lactiplantibacillus plantarum. RD-MVs and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were detected in the RD-MV fraction. Immunoglobulin A (IgA) was produced by Peyer's patch cells following the addition of the RD-MV fraction. In the presence of the RD-MV fraction, RAW264 cells produced the pro-inflammatory cytokine IL-6. Recombinant GAPDH probably induced the production of IL-6 by RAW264 cells via superficial toll-like receptor 2 (TLR2) recognition. A confocal laser scanning microscopy image analysis indicated that RD-MVs and GAPDH were taken up by RAW264 cells. GAPDH wrapped around RAW264 cells. We suggest that GAPDH from strain RD055328 enhanced the production of IgA by acquired immune cells via the production of IL-6 by innate immune cells through TLR2 signal transduction.
(E)-7-phenyl-2-heptene-4,6-diyn-1-ol fromBidens pilosaas a repellent against isopods
Authors: Ishida Masashi , Yamaji Yuika , Isoda Wakana , Abe Haruki , Sato Masashi , Kariya Keisuke , Ishihara Atsushi , Tebayashi Shin-ichi , Sato Shu-ushi 
Published: May 2023

ABSTRACTThe development of repellents as alternatives to insecticides has expanded in recent years. However, their use in isopod pest control is limited. To develop an isopod repellent, a plant extract library from wild plants native to the Kochi Prefecture was screened for repellent activity against pillbugs, and 82 samples (87%) exhibited repellent activity. Among them, (E)-7-phenyl-2-heptene-4,6-diyn-1-ol was isolated and identified as a repellent from the root of Bidens pilosa. It had a half-maximal effective concentration of 0.20 µm, with a strong repellency. A study of the structure–activity relationship to (E)-7-phenyl-2-heptene-4,6-diyn-1-ol revealed that the presence of a hydroxyl group and an aromatic at both ends of the length of the seven-carbon chain is important for the expression of repellency. These results can potentially lead to a new repellent of phenylalkyl alcohol.
Aggression and spatial positioning of kin and non-kin fish in social groups
Authors: Bose Aneesh P H , Dabernig-Heinz Johanna , Oberkofler Jan , Koch Lukas , Grimm Jacqueline , Sefc Kristina M , Jordan Alex 
Published: May 2023

AbstractGroup-living animals are faced with the challenge of sharing space and local resources amongst group members who may be either relatives or non-relatives. Individuals may reduce the inclusive fitness costs they incur from competing with relatives by either reducing their levels of aggression toward kin, or by maintaining physical separation between kin. In this field study, we used the group-living cichlid Neolamprologus multifasciatus to examine whether within-group aggression is reduced among group members that are kin, and whether kin occupy different regions of their group’s territory to reduce kin competition over space and local resources. We determined the kinship relationships among cohabiting adults via microsatellite genotyping and then combined these with spatial and behavioral analyses of groups in the wild. We found that aggressive contests between group members declined in frequency with spatial separation between their shelters. Female kin did not engage in aggressive contests with one another, whereas non-kin females did, despite the fact these females lived at similar distances from one another on their groups’ territories. Contests within male–male and male–female dyads did not clearly correlate with kinship. Non-kin male-male and male–female dyads lived at more variable distances from one another on their territories than their corresponding kin dyads. Together, our study indicates that contests among group members can be mediated by relatedness in a sex-dependent manner. We also suggest that spatial relationships can play an important role in determining the extent to which group members compete with one another.
Efficient short read mapping to a pangenome that is represented by a graph of ED strings
Authors: Büchler Thomas , Olbrich Jannik , Ohlebusch Enno 
Published: May 2023

AbstractMotivationA pangenome represents many diverse genome sequences of the same species. In order to cope with small variations as well as structural variations, recent research focused on the development of graph-based models of pangenomes. Mapping is the process of finding the original location of a DNA read in a reference sequence, typically a genome. Using a pangenome instead of a (linear) reference genome can, e.g. reduce mapping bias, the tendency to incorrectly map sequences that differ from the reference genome. Mapping reads to a graph, however, is more complex and needs more resources than mapping to a reference genome. Reducing the complexity of the graph by encoding simple variations like SNPs in a simple way can accelerate read mapping and reduce the memory requirements at the same time.ResultsWe introduce graphs based on elastic-degenerate strings (ED strings, EDS) and the linearized form of these EDS graphs as a new representation for pangenomes. In this representation, small variations are encoded directly in the sequence. Structural variations are encoded in a graph structure. This reduces the size of the representation in comparison to sequence graphs. In the linearized form, mapping techniques that are known from ordinary strings can be applied with appropriate adjustments. Since most variations are expressed directly in the sequence, the mapping process rarely has to take edges of the EDS graph into account. We developed a prototypical software tool GED-MAP that uses this representation together with a minimizer index to map short reads to the pangenome. Our experiments show that the new method works on a whole human genome scale, taking structural variants properly into account. The advantage of GED-MAP, compared with other pangenomic short read mappers, is that the new representation allows for a simple indexing method. This makes GED-MAP fast and memory efficient.Availability and implementationSources are available at: https://github.com/thomas-buechler-ulm/gedmap.
Timing of rectal cancer surgery after short-course radiotherapy: national database study
Authors: Verweij Maaike E , Franzen Jolien , van Grevenstein Wilhelmina M U , Verkooijen Helena M , Intven Martijn P W 
Published: May 2023

Abstract

Background
Previous randomized trials found that a prolonged interval between short-course radiotherapy (SCRT, 25 Gy in 5 fractions) and surgery for rectal cancer (4–8 weeks, SCRT-delay) results in a lower postoperative complication rate and a higher pCR rate than SCRT and surgery within a week (SCRT-direct surgery). This study sought to confirm these results in a Dutch national database.

Methods
Patients with intermediate-risk rectal cancer (T3(mesorectal fascia (MRF)–) N0 M0 and T1–3(MRF–) N1 M0) treated with either SCRT-delay (4–12 weeks) or SCRT-direct surgery in 2018–2021 were selected from a Dutch national colorectal cancer database. Confounders were adjusted for using inverse probability of treatment weighting (IPTW). The primary endpoint was the 90-day postoperative complication rate. Secondary endpoints included the pCR rate. Endpoints were compared using log-binomial and Poisson regression.

Results
Some 664 patients were included in the SCRT-direct surgery and 238 in the SCRT-delay group. After IPTW, the 90-day postoperative complication rate was comparable after SCRT-direct surgery and SCRT-delay (40.1 versus 42.3 per cent; risk ratio (RR) 1.1, 95 per cent c.i. 0.9 to 1.3). A pCR occurred more often after SCRT-delay than SCRT-direct surgery (10.7 versus 0.4 per cent; RR 39, 11 to 139).

Conclusion
There was no difference in surgical complication rates between SCRT-delay and SCRT-direct, but SCRT-delay was associated with more patients having a pCR.
Computational studies on glycosaminoglycan recognition of sialyl transferases
Authors: Sankaranarayanan Nehru Viji , Sistla Srinivas , Nagarajan Balaji , Chittum John E , Lau Joseph T Y , Desai Umesh R 
Published: May 2023

Abstract
Despite decades of research, glycosaminoglycans (GAGs) have not been known to interact with sialyl transferases (STs). Using our in-house combinatorial virtual library screening (CVLS) technology, we studied seven human isoforms, including ST6GAL1, ST6GAL2, ST3GAL1, ST3GAL3, ST3GAL4, ST3GAL5, and ST3GAL6, and predicted that GAGs, especially heparan sulfate (HS), are likely to differentially bind to STs. Exhaustive CVLS and molecular dynamics studies suggested that the common hexasaccharide sequence of HS preferentially recognized ST6GAL1 in a site overlapping the binding site of the donor substrate CMP-Sia. Interestingly, CVLS did not ascribe any special role for the rare 3-O-sulfate modification of HS in ST6GAL1 recognition. The computational predictions were tested using spectrofluorimetric studies, which confirmed preferential recognition of HS over other GAGs. A classic chain length-dependent binding of GAGs to ST6GAL1 was observed with polymeric HS displaying a tight affinity of ~65 nM. Biophysical studies also confirmed a direct competition between CMP-Sia and an HS oligosaccharide and CS polysaccharide for binding to ST6GAL1. Overall, our novel observation that GAGs bind to ST6GAL1 with high affinity and compete with the donor substrate is likely to be important because modulation of sialylation of glycan substrates on cells has considerable physiological/pathological consequences. Our work also brings forth the possibility of developing GAG-based chemical probes of ST6GAL1.
Serious Infections in Offspring Exposed in Utero to Vedolizumab
Authors: Gorodensky Jonah H , Bernatsky Sasha , Afif Waqqas , St-Pierre Yvan , Filion Kristian B , Vinet Évelyne 
Published: May 2023

Lay Summary
Controlling IBD during pregnancy is important for maternal and fetal outcomes. We created a cohort of children born to mothers with IBD, comparing the risk of infections in those exposed to vedolizumab vs unexposed. We detected no increased risk.
Whole-body perfusion improves intraoperative transfusions in neonatal aortic arch surgery
Authors: Sandoval Boburg Rodrigo , Berger Rafal , Mustafi Migdat , Faust Charlotte , Magunia Harry , Neunhoeffer Felix , Hofbeck Michael , Rosenberger Peter , Schlensak Christian 
Published: May 2023

Abstract

OBJECTIVES
Whole-body perfusion is the combination of lower body perfusion and antegrade cerebral perfusion. This perfusion technique is used in some centres when performing aortic arch reconstruction surgery in neonates and infants. Several studies have shown intra- and postoperative benefits of this technique. However, no studies have analysed the impact it may have on the transfusion of blood products and coagulation factors.

METHODS
We retrospectively analysed 65 consecutive neonates and infants who underwent aortic arch reconstruction surgery from January 2014 to July 2020. Patients operated from 2014 to 2017 underwent surgery with antegrade cerebral perfusion; in patients who underwent surgery from 2017 to 2020 a whole-body perfusion strategy was used. Demographic, intra- and postoperative parameters were compared as well as intraoperative blood product and coagulation factor transfusions, chest-tube output in the first 24 h and postoperative bleeding complications.

RESULTS
Both groups required intraoperative transfusion of red blood cells, fresh frozen plasma, and platelets, as well as substitution of coagulation factors. The amount of transfused volumes of red blood cells, fresh frozen plasma and platelets (P-values 0.01, &lt;0.01 and &lt;0.01) and intraoperative transfusions of fibrinogen and von Willebrand factor were significantly lower in the whole-body perfusion group (P-value 0.04 and &lt;0.01).

CONCLUSIONS
A whole-body perfusion strategy may lead to fewer intraoperative blood product and coagulation factor transfusions when compared to antegrade cerebral perfusion alone in neonates and infants undergoing complex aortic arch reconstruction surgery.
Occult Hepatitis B Virus Infection and Liver Fibrosis in Chinese Patients
Authors: Tang Xi , Yang Liu , Zhang Panli , Wang Cong , Luo Shengxue , Liu Bochao , Fu Yongshui , Candotti Daniel , Allain Jean-Pierre , Zhang Ling , Li Chengyao , Li Tingting 
Published: May 2023

Abstract

Background
The impact of hepatitis B surface antigen (HBsAg)–negative/hepatitis B virus (HBV) DNA–positive occult HBV infection (OBI) on the severity of liver fibrosis remains unclear.

Methods
A total of 1772 patients negative for HBsAg but positive for antibody to hepatitis B core antigen (HBcAg), stratified by the presence or absence of OBI, were selected for long-term carriage leading to elevation of ≥2 of 4 liver fibrosis indexes—hyaluronic acid (HA), laminin, type III procollagen peptide (PCIII), and type IV collagen (CIV)—at testing in a Chinese hospital. Patients were tested for serum viral load, HBV markers, and histopathological changes in liver biopsy specimens.

Results
OBI was identified in 148 patients with liver fibrosis (8.4%), who had significantly higher levels of HA, laminin, PCIII, and CIV than 1624 fibrotic patients without OBI (P &lt; .05). In 36 patients with OBI who underwent liver biopsy, significant correlations were observed between OBI viral load and serum HA levels (P = .01), PCIII levels (P = .01), and pathological histological activity index (HAI) scores (P &lt; .001), respectively; HAI scores and PCIII levels (P = .04); HBcAg immunohistochemical scores and HA levels (P &lt; .001); and HBcAg immunohistochemical scores and PCIII levels (P = .03). Positive fluorescent in situ hybridization results were significantly more frequent in patients with OBIs (80.6% vs 37.5% in those without OBIs). Among patients with OBIs, HBcAg was detected in the liver tissue in 52.8% and HBsAg in 5.6%.

Conclusions
OBI status appears to be associated with liver fibrosis severity.
A Highly Attenuated Panfilovirus VesiculoVax Vaccine Rapidly Protects Nonhuman Primates Against Marburg Virus and 3 Species of Ebola Virus
Authors: Woolsey Courtney , Borisevich Viktoriya , Agans Krystle N , O’Toole Rachel , Fenton Karla A , Harrison Mack B , Prasad Abhishek N , Deer Daniel J , Gerardi Cheryl , Morrison Nneka , Cross Robert W , Eldridge John H , Matassov Demetrius , Geisbert Thomas W 
Published: May 2023

Abstract

Background
The family Filoviridae consists of several virus members known to cause significant mortality and disease in humans. Among these, Ebola virus (EBOV), Marburg virus (MARV), Sudan virus (SUDV), and Bundibugyo virus (BDBV) are considered the deadliest. The vaccine, Ervebo, was shown to rapidly protect humans against Ebola disease, but is indicated only for EBOV infections with limited cross-protection against other filoviruses. Whether multivalent formulations of similar recombinant vesicular stomatitis virus (rVSV)–based vaccines could likewise confer rapid protection is unclear.

Methods
Here, we tested the ability of an attenuated, quadrivalent panfilovirus VesiculoVax vaccine (rVSV-Filo) to elicit fast-acting protection against MARV, EBOV, SUDV, and BDBV. Groups of cynomolgus monkeys were vaccinated 7 days before exposure to each of the 4 viral pathogens. All subjects (100%) immunized 1 week earlier survived MARV, SUDV, and BDBV challenge; 80% survived EBOV challenge. Survival correlated with lower viral load, higher glycoprotein-specific immunoglobulin G titers, and the expression of B-cell–, cytotoxic cell–, and antigen presentation–associated transcripts.

Conclusions
These results demonstrate multivalent VesiculoVax vaccines are suitable for filovirus outbreak management. The highly attenuated nature of the rVSV-Filo vaccine may be preferable to the Ervebo “delta G” platform, which induced adverse events in a subset of recipients.
Size And Locomotor Ecology Have Differing Effects on the External and Internal Morphologies of Squirrel (Rodentia: Sciuridae) Limb Bones
Authors: Rickman J , Burtner A E , Linden T J , Santana S E , Law C J 
Published: May 2023

SynopsisMammals exhibit a diverse range of limb morphologies that are associated with different locomotor ecologies and structural mechanics. Much remains to be investigated, however, about the combined effects of locomotor modes and scaling on the external shape and structural properties of limb bones. Here, we used squirrels (Sciuridae) as a model clade to examine the effects of locomotor mode and scaling on the external shape and structure of the two major limb bones, the humerus and femur. We quantified humeral and femoral morphologies using 3D geometric morphometrics and bone structure analyses on a sample of 76 squirrel species across their four major ecotypes. We then used phylogenetic generalized linear models to test how locomotor ecology, size, and their interaction influenced morphological traits. We found that size and locomotor mode exhibit different relationships with the external shape and structure of the limb bones, and that these relationships differ between the humerus and femur. External shapes of the humerus and, to a lesser extent, the femur are best explained by locomotor ecology rather than by size, whereas structures of both bones are best explained by interactions between locomotor ecology and scaling. Interestingly, the statistical relationships between limb morphologies and ecotype were lost when accounting for phylogenetic relationships among species under Brownian motion. That assuming Brownian motion confounded these relationships is not surprising considering squirrel ecotypes are phylogenetically clustered; our results suggest that humeral and femoral variation partitioned early between clades and their ecomorphologies were maintained to the present. Overall, our results show how mechanical constraints, locomotor ecology, and evolutionary history may enact different pressures on the shape and structure of limb bones in mammals.
A Step-by-Step Guide to Writing a Scientific Review Article
Authors: Bahl Manisha 
Published: May 2023

Abstract
Scientific review articles are comprehensive, focused reviews of the scientific literature written by subject matter experts. The task of writing a scientific review article can seem overwhelming; however, it can be managed by using an organized approach and devoting sufficient time to the process. The process involves selecting a topic about which the authors are knowledgeable and enthusiastic, conducting a literature search and critical analysis of the literature, and writing the article, which is composed of an abstract, introduction, body, and conclusion, with accompanying tables and figures. This article, which focuses on the narrative or traditional literature review, is intended to serve as a guide with practical steps for new writers. Tips for success are also discussed, including selecting a focused topic, maintaining objectivity and balance while writing, avoiding tedious data presentation in a laundry list format, moving from descriptions of the literature to critical analysis, avoiding simplistic conclusions, and budgeting time for the overall process.