bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of a Pragmatic Home-based Exercise Program Concurrent With Neoadjuvant Therapy on Physical Function of Patients With Pancreatic Cancer
Authors: Ngo-Huang An T. , Parker Nathan H. , Xiao Lianchun , Schadler Keri L. , Petzel Maria Q.B. , Prakash Laura R. , Kim Michael P. , Tzeng Ching-Wei D. , Lee Jeffrey E. , Ikoma Naruhiko , Wolff Robert A. , Javle Milind M. , Koay Eugene J. , Pant Shubham D. , Folloder Justin P. , Wang Xuemei , Cotto Alicia M. , Ju Ye Rang , Garg Naveen , Wang Huamin , Bruera Eduardo D. , Basen-Engquist Karen M. , Katz Matthew H.G. 
Published: April 2023

Objective:
To determine the effects of a preoperative, home-based exercise program on fitness and physical function in patients with pancreatic cancer.

Background:
We previously established a well-tolerated preoperative exercise program after finding a high frequency of sarcopenia and frailty in patients with pancreatic cancer.

Methods:
In this randomized, controlled trial (NCT03187951), patients with pancreatic cancer were randomized to Arm A: enhanced usual care or Arm B: prescribed aerobic and resistance exercise during neoadjuvant therapy. Patients received nutrition counseling and activity trackers. The primary endpoint was a 6-minute walk distance (6MWD; ≥14 meters improvement was clinically meaningful). Secondary endpoints included additional physical function tests, health-related quality of life, and clinical outcomes.

Results:
One hundred fifty-one patients participated. Objectively measured weekly activity (151.6±135.0 and 161.8±123.1 min in Arm A and B, respectively, P=0.5) and self-reported weekly moderate-to-strenuous physical activity (107.4±160.4 and 130.9±162.9 min in Arm A and Arm B, respectively, P=0.47) were similar, but weekly strength training sessions increased more in Arm B (by 1.8±1.8 vs 0.1±2.4 sessions, P<0.001). 6MWD improved in both Arm A (mean change 17.8±56.7 m, P=0.02) and Arm B (28.3±68.2 m, P=0.002). Quality of life and clinical outcomes did not significantly differ between arms. Pooling patients in both study groups, exercise, and physical activity was favorably associated with physical performance and clinical outcomes.

Conclusions:
In this randomized trial of prescribed exercise versus enhanced usual care during neoadjuvant therapy for pancreatic cancer, a high volume of physical activity and increased exercise capacity were observed in both arms, highlighting the importance of activity among patients preparing for surgery.
The Neuroanatomy of Poststroke Subjective Sensory Hypersensitivity
Authors: Thielen Hella , Tuts Nora , Lafosse Christophe , Gillebert Céline Raymond 
Published: April 2023

Background:
Although subjective sensory hypersensitivity is prevalent after stroke, it is rarely recognized by health care providers, and its neural mechanisms are largely unknown.

Objective:
To investigate the neuroanatomy of poststroke subjective sensory hypersensitivity as well as the sensory modalities in which subjective sensory hypersensitivity can occur by conducting both a systematic literature review and a multiple case study of patients with subjective sensory hypersensitivity.

Method:
For the systematic review, we searched three databases (Web of Science, PubMed, and Scopus) for empirical articles discussing the neuroanatomy of poststroke subjective sensory hypersensitivity in humans. We assessed the methodological quality of the included studies using the case reports critical appraisal tool and summarized the results using a qualitative synthesis. For the multiple case study, we administered a patient-friendly sensory sensitivity questionnaire to three individuals with a subacute right-hemispheric stroke and a matched control group and delineated brain lesions on a clinical brain scan.

Results:
Our systematic literature search resulted in four studies (describing eight stroke patients), all of which linked poststroke subjective sensory hypersensitivity to insular lesions. The results of our multiple case study indicated that all three stroke patients reported an atypically high sensitivity to different sensory modalities. These patients’ lesions overlapped with the right anterior insula, the claustrum, and the Rolandic operculum.

Conclusion:
Both our systematic literature review and our multiple case study provide preliminary evidence for a role of the insula in poststroke subjective sensory hypersensitivity and suggest that poststroke subjective sensory hypersensitivity can occur in different sensory modalities.
THAPBI PICT - a fast, cautious, and accurate metabarcoding analysis pipeline
Authors: Cock Peter J. A. , Cooke David E. L. , Thorpe Peter , Pritchard Leighton 
Published: April 2023

ABSTRACTTHAPBI PICT is an open source software pipeline for metabarcoding analysis with multiplexed Illumina paired-end reads, including where different amplicons are sequenced together. We demonstrate using worked examples with our own and public data sets how, with appropriate primer settings and a custom database, THAPBI PICT can be applied to other amplicons and organisms, and used for reanalysis of existing datasets. The core dataflow of the implementation is (i) data reduction to unique marker sequences, often called amplicon sequence variants (ASVs), (ii) dynamic thresholds for discarding low abundance sequences to remove noise and artifacts (rather than error correction by default), before (iii) classification using a curated reference database. The default classifier assigns a label to each query sequence based on a database match that is either perfect, or a single base pair edit away (substitution, deletion or insertion). Abundance thresholds for inclusion can be set by the user or automatically using per-batch negative or synthetic control samples. Output is designed for practical interpretation by nonspecialists and includes a read report (ASVs with classification and counts per sample), sample report (samples with counts per species classification), and a topological graph of ASVs as nodes with short edit distances as edges. Source code available fromhttps://github.com/peterjc/thapbi-pict/withdocumentation including installation instructions.
Comparative Phylogenomics and Phylotranscriptomics Provide Insights into the Genetic Complexity of Nitrogen Fixing Root Nodule Symbiosis
Authors: Zhang Yu , Fu Yuan , Xian Wenfei , Li Xiuli , Feng Yong , Bu Fengjiao , Shi Yan , Chen Shiyu , van Velzen Robin , Berry Alison M. , Salgado Marco G. , Liu Hui , Yi Tingshuang , Fournier Pascale , Alloisio Nicole , Pujic Petar , Boubakri Hasna , Schranz M. Eric , Delaux Pierre-Marc , Wong Gane Ka-shu , Hocher Valerie , Svistoonoff Sergio , Gherbi Hassen , Wang Ertao , Kohlen Wouter , Wall Luis G. , Parniske Martin , Pawlowski Katharina , Philippe Normand , Doyle Jeffrey J. , Cheng Shifeng 
Published: April 2023

AbstractPlant root nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. It is widely accepted that nodulation originated through the assembly of modules recruited from existing functions, such as mycorrhizal symbiosis, polar growth, and lateral root development. Because nodulating species are scattered within the NFNC, the number of times nodulation has evolved or has been lost has been a matter of considerable speculation. This interesting evolutionary question has practical implications concerning the ease with which nodulation might be engineered in non-nodulating crop plants. Nodulating species share many commonalities, due either to divergence from a common ancestor over 100 million years ago or to convergence or deep homology following independent origins over that same time period. In either case, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation—what must be acquired or cannot be lost for a functional symbiosis—and what the latitude is for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here we present new information across the spectrum of nodulating groups. We find no evidence for convergence at the level of amino acid residues or gene family expansion across the NFNC. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor, NIN, as a master regulator of nodulation, and identify key mutations affecting its function across the NFNC. We find that nodulation genes are over-represented among orthologous gene groups (OGs) present in the NFNC common ancestor, but that lineage-specific OGs play major roles in nodulation. We identified over 900,000 conserved noncoding elements (CNEs), of which over 300,000 were unique to NFNC species. A significant proportion of these are associated with nodulation-related genes and thus are candidates for transcriptional regulators.
DrBERT: A Robust Pre-trained Model in French for Biomedical and Clinical domains
Authors: Labrak Yanis , Bazoge Adrien , Dufour Richard , Rouvier Mickael , Morin Emmanuel , Daille Béatrice , Gourraud Pierre-Antoine 
Published: April 2023

AbstractIn recent years, pre-trained language models (PLMs) achieve the best performance on a wide range of natural language processing (NLP) tasks. While the first models were trained on general domain data, specialized ones have emerged to more effectively treat specific domains. In this paper, we propose an original study of PLMs in the medical domain on French language. We compare, for the first time, the performance of PLMs trained on both public data from the web and private data from healthcare establishments. We also evaluate different learning strategies on a set of biomedical tasks. In particular, we show that we can take advantage of already existing biomedical PLMs in a foreign language by further pre-train it on our targeted data. Finally, we release the first specialized PLMs for the biomedical field in French, called DrBERT, as well as the largest corpus of medical data under free license on which these models are trained.
Protein language model powers accurate and fast sequence search for remote homology
Authors: Liu Wei , Wang Ziye , You Ronghui , Xie Chenghan , Wei Hong , Xiong Yi , Yang Jianyi , Zhu Shanfeng 
Published: April 2023

AbstractHomologous protein search is one of the most commonly used methods for protein annotation and analysis. Compared to structure search, detecting distant evolutionary relationships from sequences alone remains challenging. Here we propose PLMSearch (ProteinLanguageModel), a homologous protein search method with only sequences as input. With deep representations from a pre-trained protein language model to predict similarity, PLMSearch can capture the remote homology information hidden behind the sequences. Extensive experimental results show that PLMSearch can search millions of query-target protein pairs in seconds like MMseqs2 while increasing the sensitivity by more than threefold, and is comparable to state-of-the-art structure search methods. In particular, unlike traditional sequence search methods, PLMSearch can recall most remote homology pairs with low sequence similarity but sharing similar structures. PLMSearch is freely available athttps://dmiip.sjtu.edu.cn/PLMSearch.
Elevated glycolytic metabolism of monocytes limits the generation of HIF-1α-driven migratory dendritic cells in tuberculosis
Authors: Maio Mariano , Barros Joaquina , Joly Marine , Vahlas Zoi , Franco José Luis Marín , Genoula Melanie , Monard Sarah , Vecchione María Belén , Fuentes Federico , Polo Virginia Gonzalez , Quiroga María Florencia , Vermeulen Mónica , Manh Thien-Phong Vu , Argüello Rafael J , Inwentarz Sandra , Musella Rosa , Ciallella Lorena , Montaner Pablo González , Palmero Domingo , Villarino Geanncarlo Lugo , Sasiain María del Carmen , Neyrolles Olivier , Verollet Christel , Balboa Luciana 
Published: April 2023

AbstractDuring tuberculosis, migration of dendritic cells (DCs) from the site of infection to the draining lymph nodes is known to be impaired, hindering the rapid development of protective T-cell mediated immunity. However, the mechanisms involved in the delayed migration of DCs during tuberculosis (TB) are still poorly defined. Here, we found that infection of DCs withMycobacterium tuberculosis(Mtb) triggers HIF-1α-mediated aerobic glycolysis in a TLR2-dependent manner, and that this metabolic profile is essential for DC migration. In particular, the lactate dehydrogenase (LDH) inhibitor oxamate and the HIF-1α inhibitor PX-478 abrogated Mtb-induced DC migrationin vitroto the lymphoid tissue-specific chemokine CCL21, andin vivoto lymph nodes in mice. Strikingly, we found that although monocytes from TB patients are inherently biased toward glycolysis metabolism, they differentiate into poorly glycolytic and poorly migratory DCs, compared with healthy subjects. Taken together, these data suggest that because of their preexisting glycolytic state, circulating monocytes from TB patients are refractory to differentiation into migratory DCs, which may explain the delayed migration of these cells during the disease and opens avenues for host-directed therapies for TB.Graphical Abstract
Conditional Generative Learning for Medical Image Imputation
Authors: Raad Ragheb , Ray Deep , Varghese Bino , Hwang Darryl , Gill Inderbir , Duddalwar Vinay , Oberai Assad A. 
Published: April 2023

AbstractImage imputation refers to the task of generating a type of medical image given images of another type. This task becomes challenging when the difference between the available images, and the image to be imputed is large. In this manuscript, one such application, derived from the dynamic contrast enhanced computed tomography (CECT) imaging of the kidneys, is considered: given an incomplete sequence of three CECT images, we are required to the impute the missing image. This task is posed as one of probabilistic inference and a generative algorithm to generate samples of the imputed image, conditioned on the available images, is developed, trained, and tested. The output of this algorithm is the “best guess” of the imputed image, and a pixel-wise image of variance in the imputation. It is demonstrated that this best guess is more accurate than those generated by other, deterministic deep-learning based algorithms, including ones which utilize additional information and more complex loss terms. It is also shown the pixel-wise variance image, which quantifies the confidence in the reconstruction, can be used to determine whether the result of the imputation meets a specified accuracy threshold and is therefore appropriate for a downstream task.
Aged Breast Matrix Bound Vesicles Promote Breast Cancer Invasiveness
Authors: Yang Jun , Bahcecioglu Gokhan , Ronan George , Zorlutuna Pinar 
Published: April 2023

AbstractAging is one of the inherent risk factors for breast cancer. Although the influence of age-related cellular alterations on breast cancer development has been extensively explored, little is known about the alterations in the aging breast tissue microenvironment, specifically the extracellular matrix (ECM). Here, for the first time in literature, we have identified tissue resident matrix bound vesicles (MBVs) within the healthy mouse breast ECM, investigated and compared their characteristics in young and aged healthy breast tissues, and studied the effects of these MBVs on normal (KTB21) and cancerous (MDA-MB-231) human mammary epithelial cells with respect to the tissue age that they are extracted from. Using vesicle labeling technology, we were able to visualize cellular uptake of the MBVs directly from the native decellularized tissue sections, showing that these MBVs have regulatory roles in the tissue microenvironment. We mimicked the ECM by embedding the MBVs in collagen gels, and showed that MBVs could be taken up by the cells. The miRNA and cytokine profiling showed that MBVs shifted towards a more tumorigenic and invasive phenotype with age, as evidenced by the more pronounced presence of cancer-associated cytokines, and higher expression levels of oncomiRs miR-10b, miR-30e, and miR-210 in MBVs isolated from aged mice. When treated with MBVs or these upregulated factors, KTB21 and MDA-MB-231 cells showed significantly higher motility and invasion compared to untreated controls. Treatment of cells with a cocktail of miRNAs (miR-10b, miR-30e, and miR-210) or with the agonist of adiponectin (AdipoRon), which both were enriched in the aged MBVs, recapitulated the effect of aged MBVs on cells. This study shows for the first time that the MBVs have a regulatory role in the tissue microenvironment and that the MBV contents change towards cancer-promoting upon aging. Studying the effects of MBVs and their cargos on cellular behavior could lead to a better understanding of the critical roles of MBVs played in breast cancer progression and metastasis.
Lessons from relatives: C4 photosynthesis enhances CO2assimilation during the low-light phase of fluctuations
Authors: Arce Cubas Lucίa , Rodrigues Gabriel Sales Cristina , Vath Richard L. , Bernardo Emmanuel L. , Burnett Angela C. , Kromdijk Johannes 
Published: April 2023

AbstractDespite the global importance of species with C4photosynthesis, there is a lack of consensus regarding C4performance under fluctuating light. Contrasting hypotheses and experimental evidence suggest that C4photosynthesis is either less, or more efficient in fixing carbon under fluctuating light than the ancestral C3form. Two main issues were identified that may underly the lack of consensus: neglect of evolutionary distance between selected C3and C4species and use of contrasting fluctuating light treatments. To circumvent these issues, we compared photosynthetic responses to fluctuating light across three independent phylogenetically controlled comparisons between C3and C4species fromAlloteropsis,Flaveria, andCleomegenera under 21% and 2% O2. Leaves were subjected to repetitive stepwise changes in light intensity (800 and 100 µmol m-2s-1PFD) with three contrasting durations: 6, 30 and 300 seconds. These experiments reconcile the opposing results found across previous studies showing that 1) stimulation of CO2assimilation in C4species during the low light phase was both stronger and more sustained than in C3species; 2) CO2assimilation patterns during the high light phase were genus-specific rather than impacted by photosynthetic pathway; and 3) the duration of each light step in the fluctuation regime can strongly influence experimental outcomes.One sentence significance statementComparing photosynthesis in three pairs of closely related C3and C4species across three fluctuating light regimes showed that C4photosynthesis has a systematic advantage under the low light phase not related to suppression of photorespiration, while the comparative efficiency under the high light phase was not determined by photosynthetic pathway.
Qualitatively different delay-dependent working memory distortions in people with schizophrenia and healthy control subjects
Authors: Bansal Sonia , Bae Gi-Yeul , Robinson Benjamin M , Dutterer Jenna , Hahn Britta , Luck Steven J , Gold James M 
Published: April 2023

ABSTRACTBackgroundImpairments in working memory(WM) have been well-documented in people with schizophrenia(PSZ). However, thesequantitativeWM impairments can often be explained by nonspecific factors, such as impaired goal maintenance. Here, we used a spatial orientation delayed-response task to explore aqualitativedifference in WM dynamics between PSZ and healthy control subjects(HCS). Specifically, we took advantage of the discovery that WM representations may drift either toward or away from previous-trial targets(serial dependence). We tested the hypothesis that WM representations drift toward the previous-trial target in HCS but away from the previous-trial target in PSZ.MethodsWe assessed serial dependence in PSZ(N=31) and HCS(N=25), using orientation as the to-be-remembered feature and memory delays from 0 to 8s. Participants were asked to remember the orientation of a teardrop-shaped object and reproduce the orientation after a varying delay period.ResultsConsistent with prior studies, we found that current-trial memory representations were less precise in PSZ than in HCS. We also found that WM for the current-trial orientation driftedtowardthe previous-trial orientation in HCS(representational attraction) but driftedawayfrom the previous-trial orientation in PSZ(representational repulsion).ConclusionsThese results demonstrate a qualitative difference in WM dynamics between PSZ and HCS that cannot easily be explained by nuisance factors such as reduced effort. Most computational neuroscience models also fail to explain these results, because they maintain information solely by means of sustained neural firing, which does not extend across trials. The results suggest a fundamental difference between PSZ and HCS in longer-term memory mechanisms that persist across trials, such as short-term potentiation and neuronal adaptation.
N-cadherin dynamically regulates pediatric glioma cell migration in complex environments
Authors: Kim Dayoung , Olson James M , Cooper Jonathan A 
Published: April 2023

AbstractPediatric high-grade gliomas are highly invasive and essentially incurable. Glioma cells migrate between neurons and glia, along axon tracts, and through extracellular matrix surrounding blood vessels and underlying the pia. Mechanisms that allow adaptation to such complex environments are poorly understood. N-cadherin is highly expressed in pediatric gliomas and associated with shorter survival. We found that inter-cellular homotypic N-cadherin interactions differentially regulate glioma migration according to the microenvironment, stimulating migration on cultured neurons or astrocytes but inhibiting invasion into reconstituted or astrocyte-deposited extracellular matrix. N-cadherin localizes to filamentous connections between migrating leader cells but to epithelial-like junctions between followers. Leader cells have more surface and recycling N-cadherin, increased YAP1/TAZ signaling, and increased proliferation relative to followers. YAP1/TAZ signaling is dynamically regulated as leaders and followers change position, leading to altered N-cadherin levels and organization. Together, the results suggest that pediatric glioma cells adapt to different microenvironments by regulating N-cadherin dynamics and cell-cell contacts.SummaryPediatric gliomas invade the brain by migrating between nerve cells or exploiting extracellular matrix along blood vessels. This research reveals cross-talk between YAP1/TAZ signaling and N-cadherin that regulates leader-follower cell phenotypes and migration efficiency in neural and extracellular matrix environments.