bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic value of a deep learning-based hyoid bone tracking model for aspiration in patients with post-stroke dysphagia
Authors: Ryu Yeong Hwan , Kim Ji Hyun , Kim Dohhyung , Kim Seo Young , Lee Seong Jae 
Published: August 2024

Objective Hyoid bone movement is potentially related to aspiration risk in post-stroke dysphagia (PSD) patients but is difficult to assess quantitatively. This study aimed to measure the distance of hyoid bone movement more efficiently and accurately using a deep learning model and determine the clinical usefulness of the model in PSD patients. Methods This study included 85 patients with PSD within 6 months from onset. Patients were grouped into an aspiration group ( n = 35) and a non-aspiration group ( n = 50) according to the results of a videofluoroscopic swallowing study. Hyoid bone movement was tracked using a deep learning model constructed with the BiFPN-U-Net(T) architecture. The maximum distance of hyoid bone movement was measured horizontally ( Hmax), vertically ( Vmax), and diagonally ( Dmax). Results Compared with the non-aspiration group, the aspiration group showed significant decreases in hyoid bone movement in all directions. The area under the curve of Vmax was highest at 0.715 with a sensitivity of 0.680 and specificity of 0.743. The Vmax cutoff value for predicting aspiration risk was 1.61 cm. The success of oral feeding at the time of discharge was significantly more frequent when hyoid movement was equal to or larger than the cutoff value although no significant relationship was found between hyoid movement and other clinical characteristics. Conclusion Hyoid bone movement of PSD patients can be measured quantitatively and efficiently using a deep learning model. Deep learning model-based analysis of hyoid bone movement seems to be useful for predicting aspiration risk and the possibility of resuming oral feeding.
Proposals for revised International Working Group–European LeukemiaNet criteria for anemia response in myelofibrosis
Authors: Tefferi Ayalew , Barosi Giovanni , Passamonti Francesco , Hernandez-Boluda Juan-Carlos , Bose Prithviraj , Döhner Konstanze , Ellis Martin , Gangat Naseema , Garcia Jacqueline S. , Gisslinger Heinz , Gotlib Jason , Guglielmelli Paola , Gupta Vikas , Harrison Claire , Hexner Elizabeth O. , Hobbs Gabriela S. , Kiladjian Jean-Jacques , Koschmieder Steffen , Kroger Nicolaus , Kuykendall Andrew T. , Loscocco Giuseppe G. , Mascarenhas John , Masarova Lucia , Mesa Ruben , Mora Barbara , Odenike Olatoyosi , Oh Stephen T. , Pardanani Animesh , Patel Anand , Pemmaraju Naveen , Rambaldi Alessandro , Rampal Raajit , Sirhan Shireen , Szuber Natasha , Talpaz Moshe , Vachhani Pankit J. , Vannucchi Alessandro M. , Barbui Tiziano 
Published: August 2024

Abstract
With emerging new drugs in myelofibrosis (MF), a robust and harmonized framework for defining the severity of anemia and response to treatment will enhance clinical investigation and facilitate interstudy comparisons. Accordingly, the lead authors on the 2013 edition of the International Working Group–European LeukemiaNet (IWG-ELN) response criteria in MF were summoned to revise their document with the intent to (1) account for gender-specific differences in determining hemoglobin levels for eligibility criteria; (2) revise the definition of transfusion-dependent anemia (TDA) based on current restrictive transfusion practices; and (3) provide a structurally simple and easy to apply response criteria that are sensitive enough to detect efficacy signals (minor response) and also account for major responses. The initial draft of the 2024 IWG-ELN proposed criteria was subsequently circulated around a wider group of international experts and their feedback incorporated. The proposed articles include new definitions for TDA (≥3 units in the 12 weeks before study enrollment) and hemoglobin thresholds for eligibility criteria (&lt;10 g/dL for women and &lt;11 g/dL for men). The revised document also provides separate (TDA vs non-TDA) and graded (major vs minor response) response criteria while preserving the requirement for a 12-week period of screening and observation on treatment.
Activated platelets retain and protect most of their factor XIII-A cargo from proteolytic activation and degradation
Authors: Sang Yaqiu , Lee Robert H. , Luong Annie , Katona Éva , Whyte Claire S. , Smith Nicholas L. , Mast Alan E. , Flick Matthew J. , Mutch Nicola J. , Bergmeier Wolfgang , Wolberg Alisa S. 
Published: August 2024

Abstract
Platelet factor XIII-A (FXIII-A) is a major cytoplasmic protein (∼3% of total), representing ∼50% of total circulating FXIII. However, mobilization of FXIII-A during platelet activation is not well defined. To determine mechanisms mediating the retention vs release of platelet FXIII-A, platelets from healthy humans and mice (F13a1−/−, Fga−/−, Plg−/−, Stim1fl/flPf4-Cre, and respective controls) were stimulated with thrombin, convulxin plus thrombin, or calcium ionophore (A23187), in the absence or presence of inhibitors of transglutaminase activity, messenger RNA (mRNA) translation, microtubule rearrangement, calpain, and Rho GTPase. Platelet releasates and pellets were separated by (ultra)centrifugation. FXIII-A was detected by immunoblotting and immunofluorescence microscopy. Even after strong dual agonist (convulxin plus thrombin) stimulation of human platelets, &gt;80% platelet FXIII-A remained associated with the platelet pellet. In contrast, essentially all tissue factor pathway inhibitor, another cytoplasmic protein in platelets, was released to the supernatant. Pellet-associated FXIII-A was not due to de novo synthesis via platelet F13A1 mRNA. The proportion of platelet FXIII-A retained by vs released from activated platelets was partly dependent on STIM1 signaling, microtubule rearrangement, calpain, and RhoA activation but did not depend on the presence of fibrinogen or plasminogen. Immunofluorescence microscopy confirmed the presence of considerable FXIII-A within the activated platelets. Although released FXIII-A was cleaved to FXIII-A∗ and could be degraded by plasmin, platelet-associated FXIII-A remained uncleaved. Retention of substantial platelet-derived FXIII-A by activated platelets and its reduced susceptibility to thrombin- and plasmin-mediated proteolysis suggest platelet FXIII-A is a protected pool with biological role(s) that differs from plasma FXIII.
Value of elastography in characterization of solid renal masses
Authors: Abbassy Ahmed Hazem , Emara Ayah Adel , Barsoum Nadine Rashad , El Shorbagy Galal Mohamed 
Published: August 2024

Abstract
Background
Solid renal masses often come to light as incidental findings during abdominal ultrasound examinations. Once detected, determining whether a renal mass is benign or malignant becomes imperative for informed decision-making regarding management and treatment strategies. In this investigation, the aim was to explore the diagnostic efficacy of real-time strain sonoelastography in assessing solid renal masses.

Methods
This prospective research was steered on 26 individuals diagnosed with a solid renal mass, as endorsed by pathological analysis after surgical removal or biopsy. Elastography was performed on all patients. The measurement of strain index values for tissues was achieved by placing regions of interest of equal or near-equal size on both the tumor (A) and the adjacent normal renal cortex (B).

Results
Strain elastography showed no correlation with patient’s age, size of mass and probe to mass distance with p > 0.05 all. Sensitivity analysis showed that strain index can significantly predict malignant renal masses (P = 0.003) using a cut-off point 2, with 92.9% area under curve, 95.2% sensitivity, 80% specificity, 80% negative predictive value, 95.2% positive predictive value, and overall diagnostic accuracy 92.3%. Strain index > 2 was an independent predictor for malignant renal masses (P = 0.025), odds ratio 7.29 when adjusting for other risk factors. Malignant renal masses were significantly higher strain index compared to benign lesions with (P = 0.001).

Conclusions
Strain elastography is a valuable technique for distinguishing between malignant and benign solid renal tumors. Benign lesions have lower strain index values compared to malignant ones, making the strain index a useful screening tool for distinguishing between benign and malignant renal masses using cut-off point 2.
Maptcha: an efficient parallel workflow for hybrid genome scaffolding
Authors: Bhowmik Oieswarya , Rahman Tazin , Kalyanaraman Ananth 
Published: August 2024

Abstract
Background
Genome assembly, which involves reconstructing a target genome, relies on scaffolding methods to organize and link partially assembled fragments. The rapid evolution of long read sequencing technologies toward more accurate long reads, coupled with the continued use of short read technologies, has created a unique need for hybrid assembly workflows. The construction of accurate genomic scaffolds in hybrid workflows is complicated due to scale, sequencing technology diversity (e.g., short vs. long reads, contigs or partial assemblies), and repetitive regions within a target genome.

Results
In this paper, we present a new parallel workflow for hybrid genome scaffolding that would allow combining pre-constructed partial assemblies with newly sequenced long reads toward an improved assembly. More specifically, the workflow, called , is aimed at generating long scaffolds of a target genome, from two sets of input sequences—an already constructed partial assembly of contigs, and a set of newly sequenced long reads. Our scaffolding approach internally uses an alignment-free mapping step to build a $$\langle $$
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contig,contig$$\rangle $$
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graph using long reads as linking information. Subsequently, this graph is used to generate scaffolds. We present and evaluate a graph-theoretic “wiring” heuristic to perform this scaffolding step. To enable efficient workload management in a parallel setting, we use a batching technique that partitions the scaffolding tasks so that the more expensive alignment-based assembly step at the end can be efficiently parallelized. This step also allows the use of any standalone assembler for generating the final scaffolds.

Conclusions
Our experiments with on a variety of input genomes, and comparison against two state-of-the-art hybrid scaffolders demonstrate that is able to generate longer and more accurate scaffolds substantially faster. In almost all cases, the scaffolds produced by are at least an order of magnitude longer (in some cases two orders) than the scaffolds produced by state-of-the-art tools. runs significantly faster too, reducing time-to-solution from hours to minutes for most input cases. We also performed a coverage experiment by varying the sequencing coverage depth for long reads, which demonstrated the potential of to generate significantly longer scaffolds in low coverage settings ($$1\times $$

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–$$10\times $$

10
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).
The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus
Authors: Blumstein Danielle , MacManes Matthew 
Published: August 2024

AbstractThe harsh and dry conditions of desert environments have resulted in genomic adaptations, allowing for desert organisms to withstand prolonged drought, extreme temperatures, and limited food resources. Here, we present a comprehensive exploration of gene expression across five tissues (kidney, liver, lung, gastrointestinal tract, and hypothalamus) and 19 phenotypic measurements to explore the whole-organism physiological and genomic response to water deprivation in the desert-adapted cactus mouse (Peromyscus eremicus). The findings encompass the identification of differentially expressed genes and correlative analysis between phenotypes and gene expression patterns across multiple tissues. Specifically, we found robust activation of the vasopressin renin-angiotensin-aldosterone system (RAAS) pathways, whose primary function is to manage water and solute balance. Animals reduced food intake during water deprivation, and upregulation ofPCK1highlights the adaptive response to reduced oral intake via its actions aimed at maintained serum glucose levels. Even with such responses to maintain water balance, hemoconcentration still occurred, prompting a protective downregulation of genes responsible for the production of clotting factors while simultaneously enhancing angiogenesis which is thought to maintain tissue perfusion. In this study, we elucidate the complex mechanisms involved in water balance in the desert-adapted cactus mouse,P. eremicus. By prioritizing a comprehensive analysis of whole-organism physiology and multi-tissue gene expression in a simulated desert environment, we describe the complex response of regulatory processes.
A simple and effective method for simulating nested exchangeable correlated binary data for longitudinal cluster randomised trials
Authors: Bowden Rhys A. , Kasza Jessica , Forbes Andrew B. 
Published: August 2024

Abstract
Background
Simulation is an important tool for assessing the performance of statistical methods for the analysis of data and for the planning of studies. While methods are available for the simulation of correlated binary random variables, all have significant practical limitations for simulating outcomes from longitudinal cluster randomised trial designs, such as the cluster randomised crossover and the stepped wedge trial designs. For these trial designs as the number of observations in each cluster increases these methods either become computationally infeasible or their range of allowable correlations rapidly shrinks to zero.

Methods
In this paper we present a simple method for simulating binary random variables with a specified vector of prevalences and correlation matrix. This method allows for the outcome prevalence to change due to treatment or over time, and for a ‘nested exchangeable’ correlation structure, in which observations in the same cluster are more highly correlated if they are measured in the same time period than in different time periods, and where different individuals are measured in each time period. This means that our method is also applicable to more general hierarchical clustered data contexts, such as students within classrooms within schools. The method is demonstrated by simulating 1000 datasets with parameters matching those derived from data from a cluster randomised crossover trial assessing two variants of stress ulcer prophylaxis.

Results
Our method is orders of magnitude faster than the most well known general simulation method while also allowing a much wider range of correlations than alternative methods. An implementation of our method is available in an R package .

Conclusions
This simulation method is the first to allow for practical and efficient simulation of large datasets of binary outcomes with the commonly used nested exchangeable correlation structure. This will allow for much more effective testing of designs and inference methods for longitudinal cluster randomised trials with binary outcomes.
On-admission serum 25(OH)D level and mortality within one year in older patients
Authors: Abel Nadav , Stern Felicia , Tal Sari 
Published: August 2024

Abstract
Background
Mounting evidence suggests that vitamin D deficiency is associated with a higher risk of many chronic non-skeletal, age-associated diseases as well as mortality.

Aim
To determine, in older patients aged ≥ 80, the prevalence of vitamin D deficiency and its association with comorbidity, laboratory tests, length of stay and mortality within one year from blood withdrawal on admission to acute geriatrics ward.

Methods
We retrospectively surveyed electronic hospital health records of 830 older patients. The recorded data included patient demographics (e.g., age, sex, stay duration, readmissions number, death within one year from blood withdrawal on admission), medical diagnoses, laboratory results, including 25-hydroxyvitamin D [25(OH)D], and medications. We compared the characteristics of the patients who survived to those who died within one year.

Results
On admission, in 53.6% patients, vitamin D levels were lower than 50 nmol/L, and in 32%, the levels were ≤ 35 nmol/L. Persons who died were likely to be older, of male sex, were likely to be admitted for pneumonia or CHF, were likely to have lower level of albumin or hemoglobin, lower level of vitamin D or higher vitamin B12 and higher level of creatinine, were also likely to have had a lengthier hospitalization stay, a greater number of hospitalizations in the last year, a higher number of comorbidities, to have consumption of ≥5 drugs or likely to being treated with insulin, diuretics, antipsychotics, anticoagulants or benzodiazepines. Higher age, male sex, on-admission CHF, higher number of drugs, lower albumin, higher vitamin B12, vitamin D < 50 nmol/L, and consumption of antipsychotics and anticoagulants – were predictors of mortality.

Conclusion
Hypovitaminosis D is predictive of mortality in older patients within one year from hospitalization in the acute geriatric ward, but a causal relationship cannot be deduced. Nevertheless, older patients in acute care settings, because of their health vulnerability, should be considered for vitamin D testing. In the acutely ill patients, early intervention with vitamin D might improve outcomes. Accurate evaluation of mortality predictors in this age group patients may be more challenging and require variables that were not included in our study.
Exploring the relationship between gut microbiota and breast cancer risk in European and East Asian populations using Mendelian randomization
Authors: Lin Wei , Gu Chenghao , Chen Zheyin , Xue Shihang , Wu Haiyan , Zeng Liuhai 
Published: August 2024

Abstract
Background
Several studies have explored the potential link between gut microbiota and breast cancer; nevertheless, the causal relationship between gut microbiota and breast cancer remains unclear.

Methods
We utilized summary statistics from genome-wide association studies (GWAS) of the gut microbiome from the MiBioGen project with summary data from GWAS on breast cancer from the FinnGen consortium and the IEU database, with the IEU data sourced from the Biobank Japan. Preliminary statistical analyses were conducted using inverse variance weighting (IVW), supplemented by various sensitivity analysis methods, including MR-Egger regression, weighted median, weighted mode, simple median, and simple mode, to ensure the robustness of our findings. Heterogeneity and pleiotropy were assessed to avoid misleading conclusions caused by unconsidered confounders or non-specific effects of genetic variants, ensuring that the results reflect a genuine causal relationship.

Results
In European populations, four types of gut microbiota were associated with breast cancer. The genus Erysipelatoclostridium was positively associated with the risk of breast cancer, with an odds ratio (OR) of 1.21 (95% confidence interval [CI] 1.083–1.358), false discovery rate (FDR) = 0.0039. The class Coriobacteriia, order Coriobacteriales, and family Coriobacteriaceae, which belong to the same phylogenetic system, showed a consistent inversely association with breast cancer risk, with an OR of 0.757 (95% CI 0.616–0.930), FDR = 0.0281. In East Asian populations, three types of gut microbiota were related to breast cancer. The Eubacterium ruminantium group was positively associated with breast cancer risk, with an OR of 1.259 (95% CI 1.056–1.499), FDR = 0.0497. The families Porphyromonadaceae and Ruminococcaceae were inversely associated with breast cancer risk, with ORs of 0.304 (95% CI 0.155–0.596), FDR = 0.0005, and 0.674 (95% CI 0.508–0.895), FDR = 0.03173, respectively. However, these two taxa had limited instrumental variables, restricting the statistical power and potentially affecting the interpretation of the results.

Conclusion
This MR analysis demonstrated a probable causal link between specific gut microbiota and breast cancer. This study, through Mendelian randomization analysis comparing European and East Asian populations, reveals that gut microbiota may influence breast cancer risk differently across populations, providing potential directions for developing targeted prevention and treatment methods.
Diagnostic efficacy of [99mTc]Tc-PSMA SPECT/CT for prostate cancer: a meta-analysis
Authors: Wang Qi , Ketteler Svea , Bagheri Shamim , Ebrahimifard Ali , Luster Markus , Librizzi Damiano , Yousefi Behrooz H. 
Published: August 2024

Abstract
Background
Prompt and accurate diagnosis of prostate cancer (PCa) is of paramount importance for effective treatment planning. While Gallium-68 labeled prostate-specific membrane antigen (PSMA) positron emission tomography (PET)/computed tomography (CT) has proven efficacy in detecting PCa, limited availability poses challenges. As a potential alternative, [99mTc]Tc-PSMA single photon emission computed tomography (SPECT)/computed tomography (CT) holds promise. This systematic review and meta-analysis aimed to evaluate the diagnostic value of [99mTc]Tc-PSMA SPECT/CT for prostate cancer.

Methods
A comprehensive search of PubMed, Cochrane, EMBASE, Scopus, Ovid, and Web of Science databases was conducted until July 2024. Sensitivity and specificity data were extracted to assess the diagnostic accuracy of [99mTc]Tc-PSMA SPECT/CT, while the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool was used to evaluate study quality. Statistical analyses were performed using STATA 18, with MetaDisc 1.4 employed to detect threshold effects. Diagnostic accuracy indicators, including sensitivity, specificity, diagnostic odds ratio (DOR), negative likelihood ratio (LR-), and positive likelihood ratio (LR+), were pooled. The area under the curve (AUC) of the combined model was calculated using summary receiver-operating characteristic (SROC) curves.

Results
Seven studies meeting the inclusion criteria were identified from an initial pool of 1467 articles, with no publication bias observed. The pooled sensitivity, specificity, and AUC of [99mTc]Tc-PSMA SPECT/CT were found to be 0.89 (95% CI, 0.84–0.93), 0.92 (95% CI, 0.67–0.99), and 0.93 (95% CI, 0.90–0.95), respectively. Additionally, the comprehensive diagnostic odds ratio, diagnostic score, positive likelihood ratio, and negative likelihood ratio were calculated as 95.24 (95% CI, 17.30-524.41), 4.56 (95% CI, 2.85–6.26), 11.35 (95% CI, 2.31–55.71), and 0.12 (95% CI, 0.08–0.18), respectively.

Conclusions
In conclusion, our findings demonstrate that [99mTc]Tc-PSMA SPECT/CT exhibits favorable diagnostic performance for prostate cancer and can provide valuable supplementary information, particularly in regions and settings where [68Ga]Ga-PSMA PET/CT availability is limited, such as remote areas. These results highlight the potential of [99mTc]Tc-PSMA SPECT/CT as a valuable tool in the diagnosis and management of prostate cancer, warranting further investigation and validation in larger patient cohorts.