bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of topical anesthesia on outcomes and glucose control in diabetic patients treated with split-thickness skin graft surgery
Authors: Chang Dun-Hao , Lin Shen-Che , Lin Yi-Ting , Chang Ke-Chung , Chan Chien-Lung 
Published: December 2022

Background:
Using split-thickness skin grafting to treat diabetic foot and leg ulcers is common. Diabetic patients usually exhibit multiple comorbidities and high risks of adverse responses to general and spinal anesthesia. Topical anesthesia can be an alternative to avoid these risks. In this study, the clinical experience of split-thickness skin grafting under topical anesthesia was demonstrated, to evaluate its effectiveness and benefits in diabetic patients.

Methods:
From 2018 to 2020, diabetic patients with foot or leg wounds undergoing split-thickness skin grafting were reviewed and categorized into two groups according to the anesthesia methods: topical anesthesia and general/spinal anesthesia. Patient demographics, wound characteristics and healing status, postoperative complications, and perioperative blood glucose levels were recorded and analyzed.

Results:
During the study period, 28 patients underwent split-thickness skin grafting under topical anesthesia and 46 under general/spinal anesthesia. The rate of complete wound healing in 4 weeks was similar in both the groups. The topical anesthesia group suffered fewer postoperative infections (3.6% vs 21.7%, p = 0.044), required shorter postoperative hospitalization (8.3 ± 6.2 vs 11.1 ± 7.2 days, p = 0.048), and exhibited lower mean blood glucose levels and less glucose variability than the general/spinal anesthesia group.

Conclusion:
Conducting split-thickness skin grafting under topical anesthesia was shown to be a safe and effective means of treating leg and foot wounds in diabetic patients.
Automated genome mining predicts combinatorial diversity and taxonomic distribution of peptide metallophore structures
Authors: Reitz Zachary L. , Butler Alison , Medema Marnix H. 
Published: December 2022

AbstractMicrobial competition for trace metals shapes their communities and interactions with humans and plants. Many bacteria scavenge trace metals with metallophores, small molecules that chelate environmental metal ions and transport them back into the cell. Our incomplete knowledge of metallophores diversity stymies our ability to fight infectious diseases and harness beneficial microbiome interactions. The majority of known metallophores are non-ribosomal peptides (NRPs), which feature metal-chelating moieties rarely found in other classes of natural products. NRP metallophore production may be predicted by genome mining, where genomes are scanned for homologs of known biosynthetic gene clusters (BGCs). However, accurately detecting NRP metallophore biosynthesis currently requires expert manual inspection. Here, we introduce automated identification of NRP metallophore BGCs through a comprehensive detection algorithm, newly implemented in antiSMASH. Custom-designed profile hidden Markov models detect genes encoding the biosynthesis of most known NRP metallophore chelating moieties (2,3-dihydroxybenzoate, hydroxamates, salicylate, β-hydroxyamino acids, graminine, Dmaq, and the pyoverdine chromophore), achieving 97% precision and 78% recall against manual curation. We leveraged the algorithm, in combination with transporter gene detection, to detect NRP metallophore BGCs in 15,562 representative bacterial genomes and predict that 25% of all non-ribosomal peptide synthetases encode metallophore production. BiG-SCAPE clustering of 2,562 NRP metallophore BGCs revealed that significant diversity remains unexplored, including new combinations of chelating groups. Additionally, we find that Cyanobacteria are severely understudied and should be the focus of more metallophore isolation efforts. The inclusion of NRP metallophore detection in antiSMASH version 7 will aid non-expert researchers and facilitate large-scale investigations into metallophore biology.
E(3) equivariant graph neural networks for robust and accurate protein–protein interaction site prediction
Authors: Roche Rahmatullah , Moussad Bernard , Shuvo Md Hossain , Bhattacharya Debswapna 
Published: December 2022

AbstractArtificial intelligence-powered protein structure prediction methods have led to a paradigm-shift in computational structural biology, yet contemporary approaches for predicting the interfacial residues (i.e., sites) of protein-protein interaction (PPI) still rely on experimental structures. Recent studies have demonstrated benefits of employing graph convolution for PPI site prediction, but ignore symmetries naturally occurring in 3-dimensional space and act only on experimental coordinates. Here we present EquiPPIS, an E(3) equivariant graph neural network approach for PPI site prediction. EquiPPIS employs symmetry-aware graph convolutions that transform equivariantly with translation, rotation, and reflection in 3D space, providing richer representations for molecular data compared to invariant convolutions. EquiPPIS substantially outperforms state-of-the-art approaches based on the same experimental input, and exhibits remarkable robustness by attaining better accuracy with predicted structural models from AlphaFold2 than what existing methods can achieve even with experimental structures. Freely available athttps://github.com/Bhattacharya-Lab/EquiPPIS, EquiPPIS enables accurate PPI site prediction at scale.
Ploidy effects on the relationship between floral phenotype, reproductive investment and fitness exhibited by an autogamous species complex
Authors: García-Muñoz Ana , Ferrón Camilo , Vaca-Benito Celia , Loureiro João , Castro Sílvia , Muñoz-Pajares A. Jesús , Abdelaziz Mohamed 
Published: December 2022

AbstractPremiseThe relationships between reproductive investment, phenotype and fitness have been broadly studied in cross-pollinated plants in contrast to selfing species, which are considered less interesting in this area because they are supposed to be a dead-end in any evolutionary pathway. Still, selfing plants are unique systems to study these questions since the position of reproductive structures and traits related to flower size play an important role in female and male pollination success.MethodErysimum incanum s.l. is a selfing species complex exhibiting three levels of ploidy: diploids, tetraploids and hexaploids. This species complex shows traits typically associated with the selfing syndrome. Here, we used 1609 plants belonging to these three ploidies to characterize floral phenotype and spatial configuration of reproductive structures, reproductive investment (pollen and ovules production) and plant fitness. Then, we explored the relationship between all these variables using structural equation modelling across ploidy levels.Key ResultsAn increase in ploidy level leads to bigger flowers with more exerted stamens and a greater amount of pollen and ovules. In addition, hexaploid plants exhibit higher absolute values for herkogamy which is positively correlated with fitness. Phenotypic traits and pollen production are indirectly selected by the relationship among ovules and fitness, maintained across ploidies.ConclusionsChanges in floral phenotypes, reproductive investment and fitness with the ploidy level suggests that genome duplication can be a driver for the reproductive strategy transitions by modifying the investment in pollen and ovules and linking them with plant phenotype and fitness.
Effect of Hydromethanolic Seed Extract of Garcinia Kola on Male Reproductive Hormones
Authors: Harry Tamunotonye 
Published: December 2022

ABSTRACTReproduction is central to the continued existence of mankind on earth, while infertility presents both a social and a public health concern, with male factor infertility present in 20% – 50% of all cases of infertility among couples. As part of the solution for male fertility disorders, drugs including those that are plant-based are being employed to address such issues. Hence, this study was focused on the effect of the administration of hydro-methanol seed extract ofG. kolaon the reproductive hormone of adult male Wistar rats. The plant material was procured, identified, and extracted while a total of 36 adult male rats were procured and distributed equally into three groups which were subdivided into two. Animals in group 1 served as the control while groups 2 and 3 served as the extract-treated groups which received 100 and 200 mg/kg BW of the extract respectively. Those in subgroups A and B were treated for 14 and 30 days respectively after which the animals were sacrificed and the blood collected via cardiac puncture into the appropriate bottles for hormonal profile assay. The result showed that the administration of the extract resulted in a reduction in the level of FSH and LH but increased the level of Testosterone, with a significant increase recorded in the 200 mg/kg group, while the level of prolactin was increased in the 100 mg/kg group but decreased in the 200mg/kg group. Hence, Garcinia kola might not be the best solution to aid fertility in males
Mirage2’s high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms
Authors: Nord Alex J. , Wheeler Travis J. 
Published: December 2022

AbstractThe organization of homologous protein sequences into multiple sequence alignments (MSAs) is a cornerstone of modern analysis of proteins. Recent focus on the importance of alternatively-spliced isoforms in disease and cell biology has highlighted the need for MSA software that can appropriately account for isoforms and the exon-length insertions or deletions that isoforms may have relative to each other. We previously developedMirage, a software package for generating MSAs for isoforms spanning multiple species. Here, we presentMirage2, which retains the fundamental algorithms of the originalMirageimplementation while providing substantially improved translated mapping and improving several aspects of usability. We demonstrate thatMirage2is highly effective at mapping proteins to their encoding exons, and that these protein-genome mappings lead to extremely accurate intron-aware alignments. Additionally,Mirage2implements a number of engineering improvements that simplify installation and use.
Unsupervized identification of prognostic copy-number alterations using segmentation and lasso regularization
Authors: Cleynen Alice , Avet-Loiseau Hervé , Corre Jill 
Published: December 2022

AbstractIdentifying copy-number alteration with prognostic impact is typically done in a supervised approach, were candidate regions are user-selected (chomosome arms, oncogenes, etc). Yet CNA events may range from whole chromosome alterations to small focal amplifications or deletions, with no available approach to combine the potential prognostic impact of different aberration ranges. We propose and compare different statistical models to integrate the effects of multi-scale CNA events by exploiting the longitudinal structure of the genome, and assume that the survival distribution follows a Cox-proportional hazard model. These methods are adaptable to any cohorts screened for CNA by genome-wide assays such as CGH-array or whole-genome sequencing technologies, and with sufficient follow-up time. We show that combining a segmentation in the survival odds strategy with a lasso-regularization selection approach provides the best results in terms of recovering the true significant CNA regions as well as predicting survival outcomes. In particular, as shown on a 551 Multiple Myeloma patient cohort, this method allows to refine previously identified regions to exhibit potential novel driver genes.
Identifying indels from WGS short reads of haploid genomes distinguishes variant-calling algorithms
Authors: Seah Yee Mey , Stewart Mary K. , Hoogestraat Daniel , Ryder Molly , Cookson Brad T. , Salipante Stephen J. , Hoffman Noah G. 
Published: December 2022

AbstractIdentification of clinically relevant strains of bacteria increasingly relies on whole genome sequencing. The downstream bioinformatics steps necessary for calling variants from short read sequences are well-established but seldom validated against haploid genomes. We devised anin silicoworkflow to introduce single nucleotide polymorphisms (SNP) and indels into bacterial reference genomes, and computationally generate sequencing reads based on the mutated genomes. We then applied the method toMycobacterium tuberculosisH37Rv and used the synthetic reads as truth sets for evaluating several popular variant callers. Insertions proved especially challenging for most variant callers to correctly identify, relative to deletions and single nucleotide polymorphisms. With adequate read depth, however, variant callers that use high quality soft-clipped reads and base mismatches to perform local realignment consistently had the highest precision and recall in identifying medium-length insertions and deletions.
How do we explain painful chronic non-traumatic knee conditions to children and adolescents? A multiple-method study to develop credible explanations
Authors: Djurtoft C , Bruun MK , Riel H , Hoegh MS , Darlow B , Rathleff MS 
Published: December 2022

AbstractINTRODUCTIONPerceived diagnostic uncertainty can leave adolescents confused about their condition and impede their ability to understand“what’s wrong with me”. Our aim is to develop credible explanations (trustworthy and understandable explanation of the condition) for adolescents suffering from chronic non-traumatic knee pain.METHODSThis multiple-method study integrated findings from a systematic literature search of qualitative studies, an Argumentative Delphi with international experts (n=16) and think-aloud sessions with adolescents (n=7). Experts provided feedback with arguments on how to communicate credible explanations to meet adolescents’ needs. We analyzed feedback using thematic analysis before tailoring explanations to end-users.RESULTSWe screened 3.239 titles/abstracts and included 16 papers which explored diagnostic uncertainty from adolescents’ and parents’ perspectives. Five themes emerged: (1) Understanding causes and contributors to the pain experience, (2) Feeling stigmatized for having an invisible condition, (3) Having a name for pain, Controllability of pain, and (5) Worried about something being missed. The Argumentative Delphi revealed the following themes: (1) Multidimensional perspective, (2) Tailored to adolescents, (3) Validation and reassurance, and (4) Careful wording. Merging findings from the systematic search and the Delphi revealed three essential domains to address in credible explanations: “What is non-traumatic knee pain and what does it mean?”, “What is causing my knee pain?” and “How do I manage my knee pain?”.CONCLUSIONSSix credible explanations for the six most common diagnoses of chronic non-traumatic knee pain were developed. We identified three domains to consider when tailoring credible explanations to adolescents experiencing non-traumatic knee pain.
Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by epitope selection
Authors: Akiba Hiroki , Fujita Junso , Ise Tomoko , Nishiyama Kentaro , Miyata Tomoko , Kato Takayuki , Namba Keiichi , Ohno Hiroaki , Kamada Haruhiko , Nagata Satoshi , Tsumoto Kouhei 
Published: December 2022

AbstractConventional bivalent antibodies against cell surface receptors often initiate unwanted signal transduction by crosslinking two antigen molecules. Biparatopic antibodies (BpAbs) bind to two different epitopes on the same antigen, thus altering crosslinking ability. In this study, we developed BpAbs against tumor necrosis factor receptor 2 (TNFR2), which is an attractive immune checkpoint target. Using different pairs of variable regions specific to topographically distinct TNFR2 epitopes, we successfully regulated the size of BpAb-TNFR2 immunocomplexes to result in controlled agonistic activities. One particular antagonist BpAb bound TNFR2 in 1:1 ratio without unwanted signal transduction, with its structural basis revealed by cryo-electron microscopy. This antagonist suppressed the proliferation of regulatory T cells expressing TNFR2. Therefore, the BpAb format would be useful in designing specific and distinct antibody functions.
A pH-sensitive switch activates virulence inSalmonella
Authors: Shetty Dasvit , Kenney Linda J. 
Published: December 2022

ABSTRACTThe transcriptional regulator SsrB acts as a switch between virulent and biofilm lifestyles of non-typhoidalSalmonella entericaserovar Typhimurium. During infection, phosphorylated SsrB activates genes onSalmonellaPathogenicity Island-2 (SPI-2) essential for survival and replication within the macrophage. Low pH inside the vacuole is a key inducer of expression and SsrB activation. Previous studies demonstrated an increase in SsrB protein levels and DNA-binding affinity at low pH; the molecular basis was unknown (Liew et al., 2019). This study elucidates its underlying mechanism andin vivosignificance. Employing single-molecule and transcriptional assays, we report that the SsrB DNA binding domain alone (SsrBc) is insufficient to induce acid pH sensitivity. Instead, His12, a conserved residue in the receiver domain, confers pH sensitivity to SsrB allosterically. Acid-dependent DNA binding was highly cooperative, suggesting a new configuration of SsrB oligomers at SPI-2-dependent promoters. His12 plays a role in SsrB phosphorylation; substituting His12 reduced phosphorylation at neutral pH and abolished pH-dependent differences. Failure to flip the switch in SsrB rendersSalmonellaavirulent and represents a potential means of controlling virulence.
Presaccadic attention depends on eye movement direction and is related to V1 cortical magnification
Authors: Hanning Nina M. , Himmelberg Marc M. , Carrasco Marisa 
Published: December 2022

AbstractWith every saccadic eye movement, humans bring new information into their fovea to be processed with high visual acuity. Notably, perception is enhanced already before a relevant item is foveated: During saccade preparation,presaccadic attentionshifts to the upcoming fixation location, which can be measured via behavioral correlates such as enhanced visual performance or modulations of sensory feature tuning. The coupling between saccadic eye movements and attention is assumed to be robust and mandatory, and considered a mechanism facilitating the integration of pre- and post-saccadic information. However, until recently it had not been investigated as a function of saccade direction. Here, we measured contrast response functions during fixation and saccade preparation in male and female observers and found that the pronounced response gain benefit typically elicited by presaccadic attention is selectively lacking before upward saccades at the group level – some observers even showed a cost. Individual observers’ sensitivity before upward saccades was negatively related to their amount of surface area in primary visual cortex representing the saccade target, suggesting a potential compensatory mechanism that optimizes the use of the limited neural resources processing the upper vertical meridian. Our results raise the question how perceptual continuity is achieved and upward saccades can be accurately targeted despite the lack of – theoretically required– presaccadic attention.Significance StatementWhen we make a saccadic eye movement to a target location in the visual field, perception improves at the saccade target, already before the eyes start moving. This benefit afforded by presaccadic attention is thought to be mandatory and independent of eye movement direction. We show that this is not the case; moving our eyes horizontally or downwards, but not upwards, enhances contrast sensitivity. At the neural level, however, humans with less V1 cortical tissue representing the target location for upwards saccades have some presaccadic enhancement. The finding that presaccadic attention is dependent upon eye movement direction challenges the view that the presaccadic benefit is automatic and mandatory in nature.
Steric Communication between Dynamic Components on DNA nanodevices
Authors: Wang Y. , Sensale S. , Pedrozo M. , Huang C-M. , Poirier M.G. , Arya G. , Castro C.E. 
Published: December 2022

ABSTRACTBiomolecular nanotechnology has helped emulate basic robotic capabilities such as defined motion, sensing, and actuation in synthetic nanoscale systems. DNA origami is an attractive approach for nanorobotics, as it enables creation of devices with complex geometry, programmed motion, rapid actuation, force application, and various kinds of sensing modalities. Advanced robotic functions like feedback control, autonomy, or programmed routines also require the ability to transmit signals among sub-components. Prior work in DNA nanotechnology has established approaches for signal transmission, for example through diffusing strands or structurally coupled motions. However, soluble communication is often slow and structural coupling of motions can limit the function of individual components, for example to respond to the environment. Here, we introduce a novel approach inspired by protein allostery to transmit signals between two distal dynamic components through steric interactions. These components undergo separate thermal fluctuations where certain conformations of one arm will sterically occlude conformations of the distal arm. We implement this approach in a DNA origami device consisting of two stiff arms each connected to a base platform via a flexible hinge joint. We demonstrate the ability for one arm to sterically regulate both the range of motion as well as the conformational state (latched or freely fluctuating) of the distal arm, results that are quantitatively captured by mesoscopic simulations using experimentally informed energy landscapes for hinge-angle fluctuations. We further demonstrate the ability to modulate signal transmission by mechanically tuning the range of thermal fluctuations and controlling the conformational states of the arms. Our results establish a communication mechanism well-suited to transmit signals between thermally fluctuating dynamic components and provide a path to transmitting signals where the input is a dynamic response to parameters like force or solution conditions.
Explicit and implicit motor simulations are impaired in individuals with aphantasia
Authors: Dupont W. , Papaxanthis C. , Madden-Lombardi C. , Lebon F. 
Published: December 2022

AbstractIndividuals with aphantasia report having difficulties or an inability to generate visual images of objects or events. So far, there is no evidence showing that this condition also impacts the motor system and the generation of motor simulations. We probed the neurophysiological marker of aphantasia during explicit and implicit forms of motor simulation, i.e., motor imagery and action observation, respectively. We tested a group of individuals without any reported imagery deficits (phantasics) as well as a group of individuals self-reporting the inability to form mental images (aphantasics). We instructed the participants to explicitly imagine a maximal pinch movement in the visual and kinesthetic modalities and to observe a video showing a pinch movement. By means of transcranial magnetic stimulation, we triggered motor-evoked potentials (MEP) in the target right index finger. As expected, MEP amplitude, a marker of corticospinal excitability, increased for phantasics during kinaesthetic motor imagery and action observation relative to rest but not during visual motor imagery. Interestingly, MEP amplitude did not increase in either form of motor simulation for the group of aphantasics. This result provides neurophysiological evidence that individuals living with aphantasia have a real deficit in activating the motor system during motor simulations.