bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Musculoskeletal Pathologies Affecting Shoulder Girdle: A Systematic Review with Anatomical and Radiological Validation”
Authors: Charmode Sundip Hemant , Kushwaha Sudhir , Mishra Abhishek Kumar , Nimavat Nirav , Ratanpara Lalit , Mehra Simmi , Ravi Satish Kumar 
Published: January 2024

ABSTRACTIntroductionMusculoskeletal pathologies affecting shoulder girdle joints, other than gleno-humeral joint such as acromioclavicular joint arthritis, tendonitis, subacromial bursitis, subdeltoid bursitis, and osteochondritis dissecans, are relatively rare. In Middle East and Asian countries, public health services are generally availed by a large number of patients in primary health centres, rural hospitals, and district hospitals, but the scarcity of specialist orthopaedic surgeons in such hospitals usually leads to misdiagnosis of rare musculoskeletal pathologies, which may result in complications and morbidity. Objectives: To determine the presentation, progression, diagnostic evaluation, and treatment of musculoskeletal pathologies affecting the shoulder girdle and develop an algorithm to screen such pathologies.MethodsA systematic literature search of four medical databases (PubMed, Scopus, Web of Science and Google Scholar) was conducted, from 1stJanuary 1950 to 31stDecember 2022. Studies (case reports, prospective studies, review articles) reporting pathological conditions affecting shoulder girdles, with a focus on clinical presentation, physical examination tests required for diagnostic evaluation, and management, were included. The relevant data was extracted from the selected studies and tabulated for analysis.Results and DiscussionSeventeen studies were included in the final analysis. Several case reports, case series and review articles showed that very few musculoskeletal conditions can be correctly diagnosed based on only physical examination tests. Radiological and anatomical basis of each of the cases were discussed.ConclusionAn algorithm was prepared to help diagnose shoulder girdle pathologies based on clinical presentation and examination findings.Key messageAn algorithm was developed which will facilitate precise diagnosis of musculoskeletal conditions affecting shoulder girdle. The musculoskeletal pathologies of shoulder girdle were categorised based on the modalities that led to their confirmatory diagnosis, and the modes management that resulted in complete functional recovery.
ARYANA-BS: Context-Aware Alignment of Bisulfite-Sequencing Reads
Authors: Nikaein Hassan , Sharifi-Zarchi Ali , Afzal Afsoon , Ezzati Saeedeh , Rasti Farzane , Chitsaz Hamidreza , Kunde-Ramamoorthy Govindarajan 
Published: January 2024

AbstractMotivationDNA methylation plays a crucial role in biological processes, including imprinting, development, inflammation, and several disorders, such as cancer. Bisulfite sequencing (BS) is the gold standard for single-base resolution in measuring DNA methylation. This process involves treating genomic DNA with sodium bisulfite, followed by polymerase chain reaction (PCR), converting unmethylated cytosines to thymines (C to T) and guanines to adenines (G to A). However, aligning reads obtained through next-generation sequencing (NGS) of the converted DNA is challenging due to the high number of mismatches caused by these conversions.Various BS aligners aim to simplify BS read alignment to conventional DNA alignment by modifying the reference genome and/or reads. Methods include three-letter alignment and wild-card alignment, each with its limitations.This work introduces a novel BS aligner, ARYANA-BS, which departs from conventional DNA aligners by considering base alterations in BS reads within its alignment engine. Leveraging well-established DNA methylation patterns in different genomic contexts, ARYANA-BS generates five indexes from the reference, aligns each read to all indexes, and selects the hit with the minimum penalty. To further enhance alignment accuracy, an optional EM step has been developed, incorporating methylation probability information in the decision-making process for the index with the minimum penalty for each read. The presented approach seeks to improve the accuracy of BS read alignment by accounting for the intricacies of DNA methylation patterns in diverse genomic contexts.ResultsOur experimental results, based on both simulated and real data, demonstrate that ARYANA-BS achieves state-of-the-art accuracy while maintaining competitive speed and memory usage.AvailabilityThe source code of ARYANA and ARYANA-BS, the read simulator for both normal and bisulfite-treated reads, SAM file analyzer which is used for post processing of the alignment penalties, and test procedures for benchmarking different aligners using simulated and real data, are publicly available inhttps://github.com/hnikaein/aryana.Contactsharifi@sharif.eduSupplementary informationSupplementary data are available atJournal Nameonline.
Physical Effort Pre-Crastination Determines Preference in an Isometric Task
Authors: Healy Chadwick M. , Ahmed Alaa A. 
Published: January 2024

ABSTRACTHow the brain decides when to invest effort is a central question in neuroscience. When asked to walk a mile to a destination, would you choose a path with a hill at the beginning or the end? The traditional view of effort suggests we should be indifferent—all joules are equal so long as it does not interfere with accomplishing the goal. Yet when total joules are equal, the brain’s sensitivity to the temporal profile of effort investment throughout a movement remains poorly understood. Here, we sought to parse out the interaction of time and physical effort by comparing subjective preferences in an isometric arm-pushing task that varied the duration and timing of high and low effort. Subjects were presented with a series of two-alternative forced choices, where they chose the force profile they would rather complete. Subjects preferred to pre-crastinate physical effort but were idiosyncratic about preference for task timing. A model of subjective utility that includes physical effort costs, task costs, and independent temporal sensitivity factors described subject preferences best. Interestingly, deliberation time and response vigor are best described by the same subjective utility model that won for preference, further validating this model of subjective utility. These results suggest physical effort costs are temporally sensitive, with earlier investment of effort preferred to later investment. These findings demonstrate that the representation of effort is based not only on the total energy required but its timing as well, and offer an alternative hypothesis for why animals pre-crastinate in physical tasks.NEW & NOTEWORTHYThis research utilizes a novel paradigm that differentiates between physical effort costs, task costs, and time, where subjects choose between isometric arm-pushing tasks. Here, subjects prefer high physical effort earlier, independent of task timing. We find that deliberation time and response vigor reflect subjective preferences. This research proposes a generalizable subjective utility model that includes independent time-sensitivity factors on physical effort and task costs and offers an alternative hypothesis for why animals may pre-crastinate.
Genome-wide profiling of genetic variation at tandem repeat from long reads
Authors: Jam Helyaneh Ziaei , Zook Justin M. , Javadzadeh Sara , Park Jonghun , Sehgal Aarushi , Gymrek Melissa 
Published: January 2024

AbstractTandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve TR analysis, especially for long or complex repeats. Here we introduce LongTR, which accurately genotypes tandem repeats from high fidelity long reads available from both PacBio and Oxford Nanopore Technologies. LongTR is freely available athttps://github.com/gymrek-lab/longtr.
Engineering multivalent Fc display for FcγR blockade
Authors: Petrova Ekaterina , Kiriako Georges , Rebetz Johan , Johansson Karl , Wennmalm Stefan , Meijer Niels E.J. , Hällberg B. Martin , André Ingemar , Ambrosetti Elena , Semple John W. , Teixeira Ana I. 
Published: January 2024

ABSTRACTAutoimmune diseases, driven by Fcγ receptor (FcγR) activation through autoantibody immune complexes (IC), present a complex therapeutic challenge of achieving pharmacological blockade of FcγR without triggering receptor activation. The assembly of ICs into polydisperse, higher-order structures is required for FcγR activation. However, engineered multimeric, monodisperse Fc assemblies have been reported to prevent FcγR activation, suggesting that Fc spatial organization determines FcγR activation. In this study, we engineered a functional single-chain Fc domain protein (scFc) for unidirectional, multivalent presentation by virus-like particles (VLPs), used as a display platform. We found that the multivalent display of scFc on the VLPs elicited distinct cellular responses compared with monovalent scFc, highlighting the importance of the structural context of scFc on its function. scFc-VLPs had minimal impact on the nanoscale spatial organization of FcγR at the cell membrane and caused limited receptor activation and internalization. In contrast, the monovalent scFc acted as an FcγR agonist, inducing receptor clustering, activation, and internalization. Increasing scFc valency in scFc-VLPs was associated with increased binding to monocytes, reaching a plateau at high valencies. Notably, the ability of scFc-VLPs to block IC-mediated phagocytosisin vitroincreased with scFc valency. In a murine model of passive immune thrombocytopenia (ITP), a high valency scFc-VLP variant with a desirable immunogenicity profile induced attenuation of thrombocytopenia. Here we show that multivalent presentation of an engineered scFc on a display platform can be tailored to promote suppression of IC-mediated phagocytosis while preventing FcγR activation. This work introduces a new paradigm that can contribute to the development of therapies for autoimmune diseases.
Black Soldier Fly Bioconversion to Cultivated Meat Media Components Using Blue Catfish Gut Microbiome
Authors: Timoneda Alfonso , Amirvaresi Arian , Ovissipour Reza 
Published: January 2024

AbstractDeveloping low-cost media is one of the major challenges in the cellular agriculture domain. Thus, this study aimed to develop low-cost media for cell-cultivated seafood using gut-microbial community-assisted fermentation. Black soldier fly larvae (Hermetia illucens) were used as the substrate and exposed to gut microbial communities isolated from Blue catfish (Ictalurus furcatus). In the first step, BSFL slurry was subjected to enzymatic digestion, using pepsin and trypsin to mimic animal digestive processes. The results showed a 2.8% degree of hydrolysis after digestion with pepsin and an additional 5.9% after digestion with trypsin. In the second step, two fermentation approaches were tested, including the direct addition of gut homogenate to the hydrolysates (fermentation A) and the establishment of microbial cultures from the gut homogenate before fermentation (fermentation B). Both fermentations resulted in similar protein content and degree of hydrolysis. Fermentation led to a decrease in species richness, with the loss of important chitinase and protease-producing genera such asPseudomonasand Clostridiaceae. However, there was an increase inParaclostridiumand members of the Enterobacteriaceae. In addition, the effect of fermented hydrolysates from BSFL on the proliferation of zebrafish embryo fibroblasts was tested in comparison to fetal bovine serum (FBS) in in vitro cell cultivation. Lower concentrations of FBS resulted in decreased cell density and altered cell morphology. The supplementation of hydrolysate B at high peptide concentrations had cytotoxic effects on the cells, while at lower peptide concentrations, it improved cell proliferation only in cultures with 2.5% FBS.
Infralimbic activity during REM sleep facilitates fear extinction memory
Authors: Hong Jiso , Choi Kyuhyun , Fuccillo Marc V. , Chung Shinjae , Weber Franz 
Published: January 2024

ABSTRACTRapid eye movement (REM) sleep is known to facilitate fear extinction and play a protective role against fearful memories. Consequently, disruption of REM sleep after a traumatic event may increase the risk for developing PTSD. However, the underlying mechanisms by which REM sleep promotes extinction of aversive memories remain largely unknown. The infralimbic cortex (IL) is a key brain structure for the consolidation of extinction memory. Using calcium imaging, we found in mice that most IL pyramidal neurons are intensively activated during REM sleep. Optogenetically suppressing the IL activity during REM sleep within a 4-hour window after auditory-cued fear conditioning impaired extinction memory consolidation. In contrast, REM-specific inhibition of the IL cortex after extinction learning did not affect the extinction memory. Whole-cell patch-clamp recordings demonstrated that inactivating IL neurons during REM sleep depresses their excitability. Together, our findings demonstrate that REM sleep after fear conditioning facilitates fear extinction by enhancing IL excitability, and highlight the importance of REM sleep in the aftermath of traumatic events for protecting against traumatic memories.
Bioengineering a plant NLR immune receptor with a robust binding interface towards a conserved fungal pathogen effector
Authors: Zdrzałek Rafał , Xi Yuxuan , Langner Thorsten , Bentham Adam R. , Petit-Houdenot Yohann , De la Concepcion Juan Carlos , Harant Adeline , Shimizu Motoki , Were Vincent , Talbot Nicholas J. , Terauchi Ryohei , Kamoun Sophien , Banfield Mark J. 
Published: January 2024

AbstractBioengineering of plant immune receptors has emerged as a key strategy for generating novel disease resistance traits to counteract the expanding threat of plant pathogens to global food security. However, current approaches are limited by rapid evolution of plant pathogens in the field and may lack durability when deployed. Here, we show that the rice nucleotide-binding, leucine-rich repeat (NLR) immune receptor Pik-1 can be engineered to respond to a conserved family of effectors from the multihost blast fungus pathogenMagnaporthe oryzae. We switched the effector binding and response profile of the Pik NLR from its cognate rice blast effector AVR-Pik to the host-determining factor Pwl2 by installing a putative host target, OsHIPP43, in place of the native integrated HMA domain (generating Pikm-1OsHIPP43). This chimeric receptor also responded to other PWL alleles from diverse blast isolates. The crystal structure of the Pwl2/OsHIPP43 complex revealed a multifaceted, robust interface that cannot be easily disrupted by mutagenesis, and may therefore provide durable, broad resistance to blast isolates carrying PWL effectors in the field. Our findings highlight how the host targets of pathogen effectors can be used to bioengineer new recognition specificities that have more robust properties compared to naturally evolved disease resistance genes.
Epigenetic reprogramming driving successful and failed repair in acute kidney injury
Authors: Muto Yoshiharu , Dixon Eryn E. , Yoshimura Yasuhiro , Ledru Nicolas , Kirita Yuhei , Wu Haojia , Humphreys Benjamin D. 
Published: January 2024

ABSTRACTAcute kidney injury (AKI) causes epithelial damage followed by subsequent repair. While successful repair restores kidney function, this process is often incomplete and can lead to chronic kidney disease (CKD) in a process called failed repair. To better understand the epigenetic reprogramming driving this AKI-to-CKD transition we generated a single nucleus multiomic atlas for the full mouse AKI time course, consisting of ∼280,000 single nucleus transcriptomes and epigenomes. We reveal cell-specific dynamic alterations in gene regulatory landscapes reflecting especially activation of proinflammatory pathways. We further generated single nucleus multiomic data from four human AKI samples including validation by genome-wide identification of NF-kB binding sites. A regularized regression analysis identifies key regulators involved in both successful and failed repair cell fate, identifying the transcription factor CREB5 as a regulator of both successful and failed tubular repair that also drives proximal tubule cell proliferation after injury. Our interspecies multiomic approach provides a foundation to comprehensively understand cell states in AKI.
Learned response dynamics reflect stimulus timing and encode temporal expectation violations in superficial layers of mouse V1
Authors: Knudstrup Scott G. , Martinez Catalina , Gavornik Jeffrey P. 
Published: January 2024

AbstractThe ability to recognize ordered event sequences is a fundamental component of sensory cognition and underlies the capacity to generate temporally specific expectations of future events based on previous experience. Various lines of evidence suggest that the primary visual cortex participates in some form of predictive processing, though many details remain ambiguous. Here we use two-photon calcium imaging in layer 2/3 (L2/3) of the mouse primary visual cortex (V1) to study changes in neural activity under a multi-day sequence learning paradigm with respect to prediction error responses, stimulus encoding, and time. We find increased neural activity at the time an expected, but omitted, stimulus would have occurred but no significant prediction error responses following an unexpected stimulus substitution. Sequence representations became sparser and less correlated with training, although these changes had no effect on decoding accuracy of stimulus identity or timing. Additionally, we find that experience modifies the temporal structure of stimulus responses to produce a bias towards predictive stimulus-locked activity. Finally, we observe significant temporal structure during intersequence rest periods that was largely unchanged by training.
Dispersion-free inertial focusing (DIF) for high-yield polydisperse micro-particles filtration and analysis
Authors: Lee Kelvin C. M. , Chung Bob M. F. , Siu Dickson M. D. , Ho Sam C. K. , Ng Daniel K. H. , Tsia Kevin K. 
Published: January 2024

AbstractInertial focusing excels at the precise spatial ordering and separation of microparticles by size within fluid flows. However, this advantage, brought by its inherent size-dependent dispersion, could turn into a drawback that challenges applications requiring consistent and uniform positioning of polydisperse particles, such as microfiltration and flow cytometry. To overcome this fundamental challenge, we introduce Dispersion-Free Inertial Focusing (DIF). This new method minimizes particle size-dependent dispersion while maintaining the high throughput and precision of standard inertial focusing, even in a highly polydisperse scenario. We demonstrate a rule-of-thumb principle to reinvent inertial focusing system and achieve an efficient focusing of particles ranging from 6 to 30 µm in diameter onto a single plane with less than 3 µm variance and over 95% focusing efficiency at highly scalable throughput (2.4-30 mL/hr) – a stark contrast to existing technologies that struggle with polydispersity. We demonstrated that DIF could be applied in a broad range of applications, particularly enabling high-yield continuous microparticle filtration and large-scale high-resolution single-cell morphological analysis of heterogeneous cell populations. This new technique is also readily compatible with the existing inertial microfluidic design and thus could unleash more diverse systems and applications.
Automated Cell Lineage Reconstruction using Label-Free 4D Microscopy
Authors: Waliman Matthew , Johnson Ryan L , Natesan Gunalan , Tan Shiqin , Santella Anthony , Hong Ray L , Shah Pavak K 
Published: January 2024

AbstractHere we describe embGAN, a deep learning pipeline that addresses the challenge of automated cell detection and tracking in label-free 3D time lapse imaging. embGAN requires no manual data annotation for training, learns robust detections that exhibits a high degree of scale invariance and generalizes well to images acquired in multiple labs on multiple instruments.
Transcranial Focused Ultrasound Remotely Modulates Extrastriate Visual Cortex with Subregion Specificity
Authors: Yu Kai , Schmitt Samantha , Ni Yunruo , Crane Emily C. , Smith Matthew A. , He Bin 
Published: January 2024

AbstractLow-intensity transcranial focused ultrasound (tFUS) has emerged as a powerful neuromodulation tool characterized by its deep penetration and precise spatial targeting to influence neural activity. Our study directed low-intensity tFUS stimulation onto a region of prefrontal cortex (the frontal eye field, or FEF) of a rhesus macaque to examine its impact on a remote site, the extrastriate visual cortex (area V4). This pair of cortical regions form a top-down modulatory circuit that has been studied extensively with electrical microstimulation. To measure the impact of tFUS stimulation, we recorded local field potentials (LFPs) and multi-unit spiking activities from a multi-electrode array implanted in the visual cortex. To deliver tFUS stimulation, we leveraged a customized 128-element random array ultrasound transducer with improved spatial targeting. We observed that tFUS stimulation in FEF produced modulation of V4 neuronal activity, either through enhancement or suppression, dependent on the pulse repetition frequency of the tFUS stimulation. Electronically steering the transcranial ultrasound focus through the targeted FEF cortical region produced changes in the level of modulation, indicating that the tFUS stimulation was spatially targeted within FEF. Modulation of V4 activity was confined to specific frequency bands, and this modulation was dependent on the presence or absence of a visual stimulus during tFUS stimulation. A control study targeting the insula produced no effect, emphasizing the region-specific nature of tFUS neuromodulation. Our findings shed light on the capacity of tFUS to modulate specific neural pathways and provide a comprehensive understanding of its potential applications for neuromodulation within brain networks.