bluuebunny/crossref_metadata_2025_split huggingface dataset:
The cell biology of HIV-1 latency and rebound
Authors: Mbonye Uri , Karn Jonathan 
Published: April 2024

AbstractTranscriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells—the “Shock and Kill” strategy. For “Shock and Kill” to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
Brain–machine interface based on deep learning to control asynchronously a lower-limb robotic exoskeleton: a case-of-study
Authors: Ferrero Laura , Soriano-Segura Paula , Navarro Jacobo , Jones Oscar , Ortiz Mario , Iáñez Eduardo , Azorín José M. , Contreras-Vidal José L. 
Published: April 2024

Abstract
Background
This research focused on the development of a motor imagery (MI) based brain–machine interface (BMI) using deep learning algorithms to control a lower-limb robotic exoskeleton. The study aimed to overcome the limitations of traditional BMI approaches by leveraging the advantages of deep learning, such as automated feature extraction and transfer learning. The experimental protocol to evaluate the BMI was designed as asynchronous, allowing subjects to perform mental tasks at their own will.

Methods
A total of five healthy able-bodied subjects were enrolled in this study to participate in a series of experimental sessions. The brain signals from two of these sessions were used to develop a generic deep learning model through transfer learning. Subsequently, this model was fine-tuned during the remaining sessions and subjected to evaluation. Three distinct deep learning approaches were compared: one that did not undergo fine-tuning, another that fine-tuned all layers of the model, and a third one that fine-tuned only the last three layers. The evaluation phase involved the exclusive closed-loop control of the exoskeleton device by the participants’ neural activity using the second deep learning approach for the decoding.

Results
The three deep learning approaches were assessed in comparison to an approach based on spatial features that was trained for each subject and experimental session, demonstrating their superior performance. Interestingly, the deep learning approach without fine-tuning achieved comparable performance to the features-based approach, indicating that a generic model trained on data from different individuals and previous sessions can yield similar efficacy. Among the three deep learning approaches compared, fine-tuning all layer weights demonstrated the highest performance.

Conclusion
This research represents an initial stride toward future calibration-free methods. Despite the efforts to diminish calibration time by leveraging data from other subjects, complete elimination proved unattainable. The study’s discoveries hold notable significance for advancing calibration-free approaches, offering the promise of minimizing the need for training trials. Furthermore, the experimental evaluation protocol employed in this study aimed to replicate real-life scenarios, granting participants a higher degree of autonomy in decision-making regarding actions such as walking or stopping gait.
Space-efficient computation of k-mer dictionaries for large values of k
Authors: Díaz-Domínguez Diego , Leinonen Miika , Salmela Leena 
Published: April 2024

AbstractComputing k-mer frequencies in a collection of reads is a common procedure in many genomic applications. Several state-of-the-art k-mer counters rely on hash tables to carry out this task but they are often optimised for small k as a hash table keeping keys explicitly (i.e., k-mer sequences) takes $$O(N\frac{k}{w})$$

O
(
N

k
w

)

computer words, N being the number of distinct k-mers and w the computer word size, which is impractical for long values of k. This space usage is an important limitation as analysis of long and accurate HiFi sequencing reads can require larger values of k. We propose , a space-efficient hash table for k-mers using $$O(N+u\frac{k}{w})$$

O
(
N
+
u

k
w

)

words of space, where u is the number of reads. Our framework exploits the fact that consecutive k-mers overlap by $$k-1$$

k
-
1

symbols. Thus, we only store the last symbol of a k-mer and a pointer within the hash table to a previous one, which we can use to recover the remaining $$k-1$$

k
-
1

symbols. We adapt to compute canonical k-mers as well. This variant also uses pointers within the hash table to save space but requires more work to decode the k-mers. Specifically, it takes $$O(\sigma ^{k})$$

O
(

σ
k

)

time in the worst case, $$\sigma$$
σ
being the DNA alphabet, but our experiments show this is hardly ever the case. The canonical variant does not improve our theoretical results but greatly reduces space usage in practice while keeping a competitive performance to get the k-mers and their frequencies. We compare canonical to a regular hash table storing canonical k-mers explicitly as keys and show that our method uses up to five times less space while being less than 1.5 times slower. We also show that canonical uses significantly less memory than state-of-the-art k-mer counters when they do not resort to disk to keep intermediate results.
Circ_0001786 facilitates gefitinib resistance and malignant progression in non-small cell lung cancer via miR-34b-5p/SRSF1
Authors: Ouyang Kaobin , Xie Dan , Liao Haojie , He Ying , Xiong Hailin 
Published: April 2024

Abstract
Background
Non-small cell lung cancer (NSCLC) is a widespread cancer and gefitinib is a primary therapy for NSCLC patients. Nevertheless, the underlying mechanisms for the progression of acquired drug resistance have not been clarified. The aim of this study was to investigate the role of circular RNA (circ_0001786) in gefitinib-resistant NSCLC.

Methods
Firstly, the expression of circ_0001786, miR-34b-5p and SRSF1 were assayed using qRT-PCR. Subsequently, CCK-8 test was utilized to measure the semi-inhibitory concentration (IC50) of cellular gefitinib. Apoptosis was identified by flow cytometry. At last, dual luciferase assay was applied to prove the binding association between miR-34b-5p, circ_0001786 or SRSF1.

Results
Our research disclosed that circ_0001786 was heightened in gefitinib-resistant NSCLC cells and tissues. Knockdown of circ_0001786 restrained IC50 values of gefitinib, attenuated the clonogenic ability and facilitated apoptosis in HCC827-GR and PC9-GR. In addition, circ_0001786 was a molecular sponge for miR-34b-5p. Silencing miR-34b-5p rescued the inhibitory impact of circ_0001786 knockdown on IC50 and cell cloning ability. Moreover, miR-34b-5p directly targeted SRSF1. Importantly, circ_0001786 enhanced gefitinib tolerance and malignant development in NSCLC through miR-34b-5p/SRSF1 pathway.

Conclusion
This research revealed a novel mechanism by which circ_0001786 enhanced NSCLC resistance to gefitinib by sponging miR-34b-5p and upregulating SRSF1. circ_0001786 was a potential target for improving the treatment of gefitinib-resistant NSCLC patients.
Association study of FLT4 and HYDIN single nucleotide polymorphisms with atrial septal defect susceptibility in the Han Chinese population of Southwest China
Authors: Jin Ye , Zhao Miao , Guo Qiuzhe , Zhao Wanyu , Lei Min , Zhang Yifei , zhang Yunhan , Shen Yan , Lin Keqin , Yang Zhaoqing , Chu Jiayou , Sun Hao , Luo Zhiling 
Published: April 2024

Abstract
Background
Atrial septal defect (ASD) is a common form of congenital heart disease. Although several genes related to ASD have been found, the genetic factors of ASD remain unclear. This study aimed to evaluate the correlation between 10 candidate single nucleotide polymorphisms (SNPs) and sporadic atrial septal defects.

Methods
Based on the results of 34 individual whole exome sequences, 10 candidate SNPs were selected. In total, 489 ASD samples and 420 normal samples were collected. The 10 SNPs in the case group and the control group were identified through Snapshot genotyping technology. The χ2-test and unconditional regression model were used to evaluate the relationship between ASD and each candidate SNP. Haploview software was used to perform linkage disequilibrium and haplotype analysis.

Results
The χ2 results showed that the FLT4 rs383985 (P = 0.003, OR = 1.115–1.773), HYDIN rs7198975 (P = 0.04621, OR = 1.003–1.461), and HYDIN rs1774266 (P = 0.04621, OR = 1.003–1.461) alleles were significantly different between the control group and the case group (P < 0.05). Only the association with the FLT4 polymorphism was statistically significant after adjustment for multiple comparisons.

Conclusion
These findings suggest that a possible molecular pathogenesis associated with sporadic ASD is worth exploring in future studies.
GFAP point-of-care measurement for prehospital diagnosis of intracranial hemorrhage in acute coma
Authors: Zylyftari Sabina , Luger Sebastian , Blums Kristaps , Barthelmes Stephan , Humm Sebastian , Baum Hannsjörg , Meckel Stephan , Braun Jörg , Lichy Gregor , Heilgeist Andreas , Kalra Love-Preet , Foerch Christian 
Published: April 2024

Abstract
Background
Prehospital triage and treatment of patients with acute coma is challenging for rescue services, as the underlying pathological conditions are highly heterogenous. Recently, glial fibrillary acidic protein (GFAP) has been identified as a biomarker of intracranial hemorrhage. The aim of this prospective study was to test whether prehospital GFAP measurements on a point-of-care device have the potential to rapidly differentiate intracranial hemorrhage from other causes of acute coma.

Methods
This study was conducted at the RKH Klinikum Ludwigsburg, a tertiary care hospital in the northern vicinity of Stuttgart, Germany. Patients who were admitted to the emergency department with the prehospital diagnosis of acute coma (Glasgow Coma Scale scores between 3 and 8) were enrolled prospectively. Blood samples were collected in the prehospital phase. Plasma GFAP measurements were performed on the i-STAT Alinity® (Abbott) device (duration of analysis 15 min) shortly after hospital admission.

Results
143 patients were enrolled (mean age 65 ± 20 years, 42.7% female). GFAP plasma concentrations were strongly elevated in patients with intracranial hemorrhage (n = 51) compared to all other coma etiologies (3352 pg/mL [IQR 613–10001] vs. 43 pg/mL [IQR 29–91.25], p < 0.001). When using an optimal cut-off value of 101 pg/mL, sensitivity for identifying intracranial hemorrhage was 94.1% (specificity 78.9%, positive predictive value 71.6%, negative predictive value 95.9%). In-hospital mortality risk was associated with prehospital GFAP values.

Conclusion
Increased GFAP plasma concentrations in patients with acute coma identify intracranial hemorrhage with high diagnostic accuracy. Prehospital GFAP measurements on a point-of-care platform allow rapid stratification according to the underlying cause of coma by rescue services. This could have major impact on triage and management of these critically ill patients.

Graphical Abstract
Effect of prebiotic oligosaccharides on bowel habit and the gut microbiota in children with functional constipation (Inside study): study protocol for a randomised, placebo-controlled, multi-centre trial
Authors: Wegh Carrie A. M. , Schoterman Margriet H. C. , Vaughan Elaine E. , van der Zalm Sofie C. C. , Smidt Hauke , Belzer Clara , A. Benninga Marc 
Published: April 2024

Abstract
Background
Functional constipation (FC) in children is a common gastrointestinal disorder with a worldwide-pooled prevalence of 9.5%. Complaints include infrequent bowel movements, painful defecation due to hard and/or large stools, faecal incontinence, and abdominal pain. Prebiotic oligosaccharides have been shown to relieve constipation symptoms in young adults and elderly. However, sufficient evidence is lacking linking additional prebiotic intake to improve symptoms in children with FC. We hypothesise that prebiotic oligosaccharides are able to relieve symptoms of constipation in young children as well.

Methods
In the present randomised, double-blind, placebo-controlled, multi-centre study, we will study the effects of two prebiotic oligosaccharides in comparison to placebo on constipation symptoms in children of 1–5 years (12 to 72 months) of age diagnosed with FC according to the Rome IV criteria for functional gastrointestinal disorders. The primary outcome measure will be change in stool consistency. Secondary outcomes include stool frequency and stool consistency in a number of cases (%). Tertiary outcomes include among others painful defecation, use of rescue medication, and quality of life. In addition, the impact on gut microbiome outcomes such as faecal microbiota composition and metabolites will be investigated. Participants start with a run-in period, after which they will receive supplements delivered in tins with scoops for 8 weeks, containing one of the two prebiotic oligosaccharides or placebo, followed by a 4-week wash-out period.

Discussion
This randomised double-blind, placebo-controlled multi-centre study will investigate the effectiveness of prebiotic oligosaccharides in children aged 1–5 years with FC.

Trial registration
ClinicalTrials.gov NCT04282551. Registered on 24 February 2020.
Impact of environmental factors on Biomphalaria pfeifferi vector capacity leading to human infection by Schistosoma mansoni in two regions of western Côte d'Ivoire
Authors: Sokouri Edwige A. , Ahouty Ahouty Bernardin , N’Djetchi Martial , Abé Innocent A. , Yao Ble Gbacla Flora Dominique , Konan Thomas Konan , MacLeod Annette , Noyes Harry , Nyangiri Oscar , Matovu Enock , Koffi Mathurin ,   the TrypanoGEN+ Research Group of the H3Africa Consortium
Published: April 2024

A﻿bstract
Background
Intestinal schistosomiasis remains a worrying health problem, particularly in western Côte d'Ivoire, despite control efforts. It is therefore necessary to understand all the factors involved in the development of the disease, including biotic and abiotic factors. The aim of this study was to examine the factors that could support the maintenance of the intermediate host and its vectorial capacity in western Côte d'Ivoire.

Methods
Data on river physicochemical, microbiological, and climatic parameters, the presence or absence of snails with Schistosoma mansoni, and human infections were collected between January 2020 and February 2021. Spearman rank correlation tests, Mann–Whitney, analysis of variance (ANOVA), and an appropriate model selection procedure were used to analyze the data.

Results
The overall prevalence of infected snails was 56.05%, with infection reaching 100% in some collection sites and localities. Of 26 sites examined, 25 contained thermophilic coliforms and 22 contained Escherichia coli. Biomphalaria pfeifferi was observed in environments with lower land surface temperature (LST) and higher relative air humidity (RAH), and B. pfeifferi infection predominated in more acidic environments. Thermal coliforms and E. coli preferred higher pH levels. Lower maximum LST (LST_Max) and higher RAH and minimum LST (LST_Min) were favorable to E. coli, and lower LST_Max favored coliforms. The presence of B. pfeifferi was positively influenced by water temperature (T °C), LST_Min, RAH, and precipitation (Pp) (P < 0.05) and negatively influenced by pH, total dissolved solids (TDS), electrical conductivity (EC), LST_Max, and mean land surface temperature (LST). The parameters pH, TDS, EC, LST_Min, LST, and Pp had a positive impact on snail infection, while LST_Max had a negative impact on infection. Only pH had a positive effect on coliform and E. coli abundance. Of the 701 people examined for human schistosomiasis, 73.13% were positive for the point-of-care circulating cathodic antigen (POC-CCA) test and 12.01% for the Kato–Katz (KK) test. A positive correlation was established between human infections and the abundance of Biomphalaria (r2 = 0.879, P = 0.04959).

Conclusions
The results obtained reflect the environmental conditions that are conducive to the maintenance of S. mansoni infection in this part of the country. To combat this infection as effectively as possible, it will be necessary not only to redouble efforts but also to prioritize control according to the level of endemicity at the village level.

Graphical Abstract
Case report: Aberrant fecal microbiota composition of an infant diagnosed with prolonged intestinal botulism
Authors: Douillard François P. , Derman Yağmur , Jian Ching , Korpela Katri , Saxén Harri , Salonen Anne , de Vos Willem M. , Korkeala Hannu , Lindström Miia 
Published: April 2024

Abstract
Background
Intestinal botulism is primarily reported in small babies as a condition known as infant botulism. The condition results from the ingestion of environmental or foodborne spores of botulinum neurotoxin (BoNT) producing Clostridia, usually Clostridium botulinum, and subsequent spore germination into active botulinum neurotoxinogenic cultures in the gut. It is generally considered that small babies are susceptible to C. botulinum colonization because of their immature gut microbiota. Yet, it is poorly understood which host factors contribute to the clinical outcome of intestinal botulism. We previously reported a case of infant botulism where the infant recovered clinically in six weeks but continued to secrete C. botulinum cells and/or BoNT in the feces for seven months.

Case presentation
To further understand the microbial ecology behind this exceptionally long-lasting botulinum neurotoxinogenic colonization, we characterized the infant fecal microbiota using 16S rRNA gene amplicon sequencing over the course of disease and recovery. C. botulinum could be detected in the infant fecal samples at low levels through the acute phase of the disease and three months after recovery. Overall, we observed a temporal delay in the maturation of the infant fecal microbiota associated with a persistently high-level bifidobacterial population and a low level of Lachnospiraceae, Bacteroidaceae and Ruminococcaceae compared to healthy infants over time.

Conclusion
This study brings novel insights into the infant fecal composition associated with intestinal botulism and provides a basis for a more systematic analysis of the gut microbiota of infants diagnosed with botulism. A better understanding of the gut microbial ecology associated with infant botulism may support the development of prophylactic strategies against this life-threatening disease in small babies.
Vascular dysfunction in sporadic bvFTD: white matter hyperintensity and peripheral vascular biomarkers
Authors: Chu Min , Jiang Deming , Nan Haitian , Wen Lulu , Liu Li , Qu Miao , Wu Liyong 
Published: April 2024

AbstractBackgroundVascular dysfunction was recently reported to be involved in the pathophysiological process of neurodegenerative diseases, but its role in sporadic behavioral variant frontotemporal dementia (bvFTD) remains unclear. The aim of this study was to systematically explore vascular dysfunction, including changes in white matter hyperintensities (WMHs) and peripheral vascular markers in bvFTD.MethodsThirty-two patients with bvFTD who with no vascular risk factors were enrolled in this cross-sectional study and assessed using positron emission tomography/magnetic resonance (PET/MRI) imaging, peripheral plasma vascular/inflammation markers, and neuropsychological examinations. Group differences were tested using Student’st-tests and Mann–Whitney U tests. A partial correlation analysis was implemented to explore the association between peripheral vascular markers, neuroimaging, and clinical measures.ResultsWMH was mainly distributed in anterior brain regions. All peripheral vascular factors including matrix metalloproteinases-1 (MMP-1), MMP-3, osteopontin, and pentraxin-3 were increased in the bvFTD group. WMH was associated with the peripheral vascular factor pentraxin-3. The plasma level of MMP-1 was negatively correlated with the gray matter metabolism of the frontal, temporal, insula, and basal ganglia brain regions. The WMHs in the frontal and limbic lobes were associated with plasma inflammation markers, disease severity, executive function, and behavior abnormality. Peripheral vascular markers were associated with the plasma inflammation markers.ConclusionsWMHs and abnormalities in peripheral vascular markers were found in patients with bvFTD. These were found to be associated with the disease-specific pattern of neurodegeneration, indicating that vascular dysfunction may be involved in the pathogenesis of bvFTD. This warrants further confirmation by postmortem autopsy. Targeting the vascular pathway might be a promising approach for potential therapy.