bluuebunny/crossref_metadata_2025_split huggingface dataset:
A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer
Authors: Lapcik Petr , Synkova Klara , Janacova Lucia , Bouchalova Pavla , Potesil David , Nenutil Rudolf , Bouchal Pavel 
Published: July 2024

AbstractTriple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, and deeper proteome coverage is needed for its molecular characterization. We present comprehensive library of targeted mass spectrometry assays specific for TNBC and demonstrate its applicability. Proteins were extracted from 105 TNBC tissues and digested. Aliquots were pooled, fractionated using hydrophilic chromatography and analyzed by LC-MS/MS in data-dependent acquisition (DDA) parallel accumulation-serial fragmentation (PASEF) mode on timsTOF Pro LC-MS system. 16 individual lysates were analyzed in data-independent acquisition (DIA)-PASEF mode. Hybrid library was generated in Spectronaut software and covers 244,464 precursors, 168,006 peptides and 11,564 protein groups (FDR = 1%). Application of our library for pilot quantitative analysis of 16 tissues increased identification numbers in Spectronaut 18.5 and DIA-NN 1.8.1 software compared to library-free setting, with Spectronaut achieving the best results represented by 190,310 precursors, 140,566 peptides, and 10,463 protein groups. In conclusion, we introduce assay library that offers the deepest coverage of TNBC proteome to date. The TNBC library is available via PRIDE repository (PXD047793).
High-quality reference genome of cowpea beetle Callosobruchus maculatus
Authors: Lu Hao-Ran , Mao Chu-Yang , Zhang Li-Jie , He Jin-Wu , Wang Xie-Shuang , Zhang Xin-Ying , Fan Wei-Li , Huang Zheng-Zhong , Zong Le , Cui Chu-Han , Wu Feng-Ming , Wang Xue-Li , Zou Zhen , Li Xue-Yan , Ge Si-Qin 
Published: July 2024

AbstractCallosobruchus maculatus is one of the most competitive stored grain pests, which causes a great loss to agricultural economy. However, due to an inadequacy of high-quality reference genome, the molecular mechanisms for olfactory and hypoxic adaptations to stored environments are unknown and require to be revealed urgently, which will contribute to the detection and prevention of the invasive pests C. maculatus. Here, we presented a high-quality chromosome-level genome of C. maculatus based on Illumina, Nanopore and Hi-C sequencing data. The total size was 1.2 Gb, and 65.17% (797.47 Mb) of it was identified to be repeat sequences. Among assembled chromosomes, chromosome 10 was considered the X chromosome according to the evidence of reads coverage and homologous genes among species. The current version of high-quality genome provides preferable data resources for the adaptive evolution research of C. maculatus.
The effect of human albumin administration on postoperative renal function following major surgery: a systematic review and meta-analysis
Authors: Lee Kuen Su , Kim Ji Eun , Kang Giung , Won Young Ju , Choi Yoon Ji 
Published: July 2024

AbstractOptimal fluid management during major surgery is of considerable concern to anesthesiologists. Although crystalloids are the first choice for fluid management, the administration of large volumes of crystalloids is associated with poor postoperative outcomes. Albumin can be used for fluid management and may protect renal function. However, data regarding the effects of albumin administration on kidney function are conflicting. As such, the present study aimed to investigate the effect of albumin administration on renal function in patients undergoing major surgery and compare its effects with those of crystalloid fluid. The Embase, Medline, Web of Science, Cochrane Library, and KoreaMed databases were searched for relevant studies. The primary endpoint of the meta-analysis was the incidence of postoperative kidney injury, including acute kidney injury and renal replacement therapy. Twelve studies comprising 2311 patients were included; the primary endpoint was analyzed in four studies comprising 1749 patients. Perioperative albumin levels in patients undergoing major surgery did not significantly influence kidney dysfunction (p = 0.98). Postoperative fluid balance was less positive in patients who underwent major surgery and received albumin than in those who received crystalloids. Owing to the limitations of this meta-analysis, it remains unclear whether albumin administration during major surgery is better than crystalloid fluid for improving postoperative renal function.
Estimating infant age from skull X-ray images using deep learning
Authors: Lee Heui Seung , Kang Jaewoong , Kim So Eui , Kim Ji Hee , Cho Bum-Joo 
Published: July 2024

AbstractThis study constructed deep learning models using plain skull radiograph images to predict the accurate postnatal age of infants under 12 months. Utilizing the results of the trained deep learning models, it aimed to evaluate the feasibility of employing major changes visible in skull X-ray images for assessing postnatal cranial development through gradient-weighted class activation mapping. We developed DenseNet-121 and EfficientNet-v2-M convolutional neural network models to analyze 4933 skull X-ray images collected from 1343 infants. Notably, allowing for a ± 1 month error margin, DenseNet-121 reached a maximum corrected accuracy of 79.4% for anteroposterior (AP) views (average: 78.0 ± 1.5%) and 84.2% for lateral views (average: 81.1 ± 2.9%). EfficientNet-v2-M reached a maximum corrected accuracy 79.1% for AP views (average: 77.0 ± 2.3%) and 87.3% for lateral views (average: 85.1 ± 2.5%). Saliency maps identified critical discriminative areas in skull radiographs, including the coronal, sagittal, and metopic sutures in AP skull X-ray images, and the lambdoid suture and cortical bone density in lateral images, marking them as indicators for evaluating cranial development. These findings highlight the precision of deep learning in estimating infant age through non-invasive methods, offering the progress for clinical diagnostics and developmental assessment tools.
Prediction of freak waves from buoy measurements
Authors: Breunung Thomas , Balachandran Balakumar 
Published: July 2024

AbstractFreak or rogue waves are a danger to ships, offshore infrastructure, and other maritime equipment. Reliable rogue wave forecasts could mitigate this risk for operations at sea. While the occurrence of oceanic rogue waves at sea is generally acknowledged, reliable rogue wave forecasts are unavailable. In this paper, the authors seek to overcome this shortcoming by demonstrating how rogue waves can be predicted from field measurements. An extensive buoy data set consisting of billions of waves is utilized to parameterize neural networks. This network is trained to distinguish waves prior to an extreme wave from waves which are not followed by an extreme wave. With this approach, three out of four rogue waves are correctly predicted 1 min ahead of time. When the advance warning time is extended to 5 min, it is found that the ratio of accurate predictions is reduced to seven out of ten rogue waves. Another strength of the trained neural networks is their capabilities to extrapolate. This aspect is verified by obtaining forecasts for a buoy location that is not included in the networks’ training set. Furthermore, the performance of the trained neural network carries over to realistic scenarios where rogue waves are extremely rare.
Down syndrome and postoperative hemodynamics in patients undergoing surgery for congenital cardiac communications
Authors: Carvalho Eloisa Sassá , Penha Juliano Gomes , Maeda Nair Yukie , Abud Kelly Cristina O. , Souza Maria Francilene S. , Castro Claudia R. P. , dos Santos Johnny X. , Pereira Juliana , Lopes Antonio Augusto 
Published: July 2024

AbstractAlthough Down syndrome (DS) is considered a risk factor for hemodynamic instabilities (mainly pulmonary hypertension–PH) following surgery for congenital cardiac communications, many DS patients do surprising well postoperatively. We prospectively analyzed perioperative factors for a possible correlation with post-cardiopulmonary bypass (CPB) inflammatory reaction and postoperative PH in pediatric subjects. Sixty patients were enrolled (age 3 to 35 months), 39 of them with DS. Clinical and echocardiographic parameters (anatomical and hemodynamic) were computed preoperatively. Pulmonary and systemic mean arterial pressures (PAP and SAP) were assessed invasively intra and postoperatively. Immediate postoperative PAP/SAP ratio (PAP/SAPIPO) and the behavior of pressure curves were selected as primary outcome. Serum levels of 36 inflammatory proteins were measured by chemiluminescence preoperatively and 4 h post CPB. Of all factors analyzed, peripheral oxygen saturation (O2Sat, bedside assessment) was the only preoperative predictor of PAP/SAPIPO at multivariate analysis (p = 0.007). Respective values in non-DS, DS/O2Sat ≥ 95% and DS/O2Sat < 95% subgroups were 0.34 (0.017), 0.40 (0.027) and 0.45 (0.026), mean (SE), p = 0.004. The difference between non-DS and DS groups regarding postoperative PAP curves (upward shift in DS patients, p = 0.015) became nonsignificant (p = 0.114) after adjustment for preoperative O2Sat. Post-CPB levels of at least 5 cytokines were higher in patients with O2Sat < 95% versus those at or above this level, even within the DS group (p < 0.05). Thus, a baseline O2Sat < 95% representing pathophysiological phenomena in the airways and the distal lung, rather than DS in a broad sense, seems to be associated with post-CPB inflammation and postoperative PH in these patients.
Metagenomic next-generation sequencing for the diagnosis of invasive pulmonary aspergillosis in type 2 diabetes mellitus patients
Authors: Liu Zhiyun , Chen Hengxin , Chen Dubo , Wu Xianjin , Xu Hongxu , Chen Peisong , Wang Ruizhi , Chen Yili 
Published: July 2024

AbstractInvasive pulmonary aspergillosis (IPA) in patients with diabetes mellitus has high incidence, especially in Type 2 diabetes mellitus (T2DM). The aim of this study was to evaluate the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) for IPA in patients with T2DM. A total of 66 patients with T2DM were included, including 21 IPA and 45 non-IPA patients, from January 2022 to December 2022. The demographic characteristics, comorbidities, laboratory test results, antibiotic treatment response, and 30-day mortality rate of patients were analyzed. The diagnostic accuracy of mNGS and conventional methods was compared, including sensitivity, specificity, positive predictive value and negative predictive value. The sensitivity and specificity of mNGS were 66.7% and 100.0%, respectively, which were significantly higher than those of fluorescence staining (42.1% and 100%), serum 1,3-β-D-glucan detection (38.1% and 90.9%), serum galactomannan detection (14.3% and 94.9%) and BALF galactomannan detection (47.3% and 70.7%). Although the sensitivity of BALF culture (75.0%) was higher than that of mNGS (66.7%), the turnover time of mNGS was significantly shorter than that of traditional culture (1.6 days vs. 5.0 days). The sensitivity of mNGS combined with BALF culture reached 100.0%. In addition, mNGS has a stronger ability to detect co-pathogens with IPA. 47.6% of T2DM patients with IPA were adjusted the initial antimicrobial therapy according to the mNGS results. This is the first study to focus on the diagnostic performance of mNGS in IPA infection in T2DM patients. MNGS can be used as a supplement to conventional methods for the diagnosis of IPA in patients with T2DM.
Effects of blood flow restriction training on physical fitness among athletes: a systematic review and meta-analysis
Authors: Yang Kun , Chee Chen Soon , Abdul Kahar Johan , Tengku Kamalden Tengku Fadilah , Li Rui , Qian Shaowen 
Published: July 2024

AbstractBlood flow restriction training (BFRT) is an effective, scientific and safe training method, but its effect on the overall quality of athletes remains unclear. The aim of this systematic review with meta-analysis was to clarify the effects of BFRT on the physical fitness among athletes. Based on the PRISMA guidelines, searches were performed in PubMed, Web of Science, SPORTDiscus, and SCOUPS, the Cochrane bias risk assessment tool was used to assess methodological quality, and RevMan 5.4 and STATA 15.0 software were used to analyze the data. A meta-analysis of 28 studies with a total sample size of 542 athletes aged 14–26 years and assessed as low risk for quality was performed. Our results revealed that the BFRT intervention had small to large improvements in the athletes' strength (ES = 0.74–1.03), power (ES = 0.46), speed (ES = 0.54), endurance (ES = 1.39–1.40), body composition (ES = 0.28–1.23), while there was no significant effect on body mass (p > 0.05). Subgroup analyses revealed that moderator variables (training duration, frequency, load, cuff pressure, and pressurization time) also had varying degrees of effect on athletes' physical fitness parameters. In conclusion, BFRT had a positive effect on the physical fitness parameters of the athletes, with significantly improved strength, power, speed, endurance and body composition, but not body mass parameters. When the training frequency ≥ 3 times/week, cuff pressure ≥ 160 mmHg, and pressurization time ≥ 10 min, the BFRT group was more favorable for the improvement of physical fitness parameters.
Expecting to integrate additional information improves averaging of experience
Authors: Grinfeld Guy , Usher Marius , Liberman Nira 
Published: July 2024

AbstractHumans learn both directly, from own experience, and via social communication, from the experience of others. They also often integrate these two sources of knowledge to make predictions and choices. We hypothesized that when faced with the need to integrate communicated information into personal experience, people would represent the average of experienced exemplars with greater accuracy. In two experiments, Mturk users estimated the mean of consecutively and rapidly presented number sequences that represented bonuses ostensibly paid by different providers on a crowdsource platform. Participants who expected integrating these values with verbal information about possible change in bonuses were more accurate in extracting the means of the values compared to participants who did not have such expectation. While our study focused on socially communicated information, the observed effect may potentially extend to other forms of information integration. We suggest that expected integration of experience with additional information facilitates an abstract representation of personal experiences.
Long-term renal outcome of Cryopyrin-associated periodic syndrome (CAPS) under anti-Interleukin-1 therapy
Authors: Russwurm Martin , Johannsen Sophia , Kortus-Götze Birgit , Haas Christian S. 
Published: July 2024

AbstractCryopyrin-associated periodic syndromes (CAPS) are orphan hereditary auto-inflammatory diseases with various phenotypes, including chronic kidney disease (CKD). Current therapies inhibit interleukin-1 (IL-1) to achieve clinical and serological remission; however, the effect on kidney involvement remains unclear. The objective of this study was to investigate the long-term efficacy of anti-IL-1 treatment with special emphasis on renal outcome. We retrospectively analysed clinical, genetic and laboratory data of patients with CAPS under anti-IL-1 therapy from a single-centre university outpatient clinic. Patients with CAPS (n = 28) were followed for a median of 11 (IQR 8.5–13) years. Four patients at various ages (19%), bearing the most common CAPS mutation R260W, had significant CKD at presentation. All affected patients were related; however, other family members with the same genetic variant did not develop CKD. While anti-IL-1 therapy was effective in lowering symptom burden and inflammatory parameters in all CAPS patients, two of the four individuals with significant CKD had persistent proteinuria and worsening kidney function. None of the patients without renal affection at therapy initiation developed relevant CKD in the follow-up period. We showed that in patients with CAPS: (1) CKD is a common complication; (2) renal involvement shows familial predisposition beyond the mutational status and is independent of age; (3) anti-IL-1 therapy results in sustained improvement of inflammatory parameters and symptom load and (4) may prevent development of CAPS-associated CKD but not affect kidney involvement when already present. Overall, early therapy initiation might sufficiently prevent renal disease manifestation and attenuate progression.
Pituitary-derived small extracellular vesicles promote liver repair by its cargo miR-143-3p
Authors: Xiong Jia-Li , Wang Yu-Xuan , Luo Jun-Yi , Wang Shu-Meng , Sun Jia-Jie , Xi Qian-Yun , Chen Ting , Zhang Yong-Liang 
Published: July 2024

AbstractThe small Extracellular vesicles (sEV) has been recognized to be significant for intercellular communication due to their ability to transfer important cellular cargoes like miRNAs through circulation. The pituitary gland has not been clearly known about the role of its secreted sEV under normal physiological conditions. And Liver disease is a global public health burden. The present study is the first to investigate the effect of pituitary sEV on the liver. Sequencing and qRT-PCR revealed miR-143-3p is one of the richest in the pituitary sEV. MiR-143 Knockout (KO) mice resulted in a remarkable decrease in insulin-like growth factor 1 (IGF-1) levels and a significant increase in insulin-like growth factor binding protein 5 (IGFBP5) levels along with a reduction in liver primary cell growth. More importantly, compared with miR-143-KO-sEV, WT-sEV possesses a more robust capacity to improve miR-143 KO mice liver repair through the Wnt/β-catenin pathway after an acute injury caused by carbon tetrachloride (CCl4). Our results indicate that pituitary-derived sEV promotes hepatocyte proliferation and liver repair by its cargo miR-143-3p and provides new insight into the regulation mechanism of the pituitary-liver axis, and open a new window for endocrine regulation by using sEV.
Evolution of C-point singularities and polarization coverage of Poincaré–Bessel beam in self-healing process
Authors: Kumar Subith , Pal Anupam , Shiri Arash , Samanta G. K. , Gbur Greg 
Published: July 2024

AbstractAs a vector version of scalar Bessel beams, Poincaré–Bessel beams (PBBs) have attracted a great deal of attention due to their non-diffracting and self-healing properties as well as the presence of polarization singularities. Previous studies of PBBs have focused on cases that consist of a superposition of Bessel beams in orthogonal circular polarization states; here, we present a theoretical and experimental study of PBBs for which the polarization states are taken to be linear, which we call a linear PBB. Using a mode transformation of a full Poincaré beam constructed from linear polarization states, we observe the linear PBB as providing an in-principle infinite number of covers of the Poincaré sphere in the transverse plane and with an infinite number of C-points with positive and negative topological indices. We also study the dynamics of C-point singularities in a linear PBB in the process of self-healing after being obstructed by an obstacle, providing insight into “Hilbert Hotel” style evolution of singularities in light beams. The present study can be useful for imaging in the presence of depolarizing surroundings, studying turbulent atmospheric channels, and exploring the rich mathematical concepts of transfinite numbers.
Extended X-ray absorption spectroscopy using an ultrashort pulse laboratory-scale laser-plasma accelerator
Authors: Kettle Brendan , Colgan Cary , Los Eva E. , Gerstmayr Elias , Streeter Matthew J. V. , Albert Felicie , Astbury Sam , Baggott Rory A. , Cavanagh Niall , Falk Kateřina , Hyde Timothy I. , Lundh Olle , Rajeev P. Pattathil , Riley Dave , Rose Steven J. , Sarri Gianluca , Spindloe Chris , Svendsen Kristoffer , Symes Dan R. , Šmíd Michal , Thomas Alec G. R. , Thornton Chris , Watt Robbie , Mangles Stuart P. D. 
Published: July 2024

AbstractLaser-driven compact particle accelerators can provide ultrashort pulses of broadband X-rays, well suited for undertaking X-ray absorption spectroscopy measurements on a femtosecond timescale. Here the Extended X-ray Absorption Fine Structure (EXAFS) features of the K-edge of a copper sample have been observed over a 250 eV window in a single shot using a laser wakefield accelerator, providing information on both the electronic and ionic structure simultaneously. This capability will allow the investigation of ultrafast processes, and in particular, probing high-energy-density matter and physics far-from-equilibrium where the sample refresh rate is slow and shot number is limited. For example, states that replicate the tremendous pressures and temperatures of planetary bodies or the conditions inside nuclear fusion reactions. Using high-power lasers to pump these samples also has the advantage of being inherently synchronised to the laser-driven X-ray probe. A perspective on the additional strengths of a laboratory-based ultrafast X-ray absorption source is presented.
Optimization of floodwater redistribution from Lake Nasser could recharge Egypt’s aquifers and mitigate its excessive floods
Authors: Elhaddad Hesham , Sultan Mohamed , Yan Eugene , Abdelmohsen Karem , Mohammad Abdullah T. , Badawy Ahmed , Karimi Hadi , Saleh Hassan , Emil Mustafa Kemal 
Published: July 2024

AbstractExtreme precipitation periods, possibly related to climate change, over the Nile River source areas caused flooding in Sudan and excess runoff reaching Lake Nasser in Egypt in 1998–2002 and 2019–2022. Excess water from the 1st event (25.5 × 109 m3) was channeled to depressions within the plateau west of the Nile Valley, forming the Tushka Lakes, where it was left to evaporate, a fate that awaits the 53.5 × 109 m3 from the 2nd event while the underlying fossil Nubian Sandstone Aquifer System is being depleted (−0.98 × 109 m3/yr). We simulated release scenarios of excess Lake Nasser waters (53.5 × 109 m3) to proximal lowlands; preference was given to the scenario that recharged the aquifer through infiltration (74.3%) and minimized losses to evaporation (20.1%) and surface runoff (5.6%). Findings serve as an example of adaptations that replace catastrophic consequences of climate change with beneficial and sustainable development opportunities.
Bronchoscopic Lung Volume Reduction: A Review
Authors: Podder Shreya , Khan Marium , Sink Zane , Verga Steven , Kurman Jonathan S. , Malsin Elizabeth 
Published: July 2024

AbstractBronchoscopic lung volume reduction (BLVR) is an established treatment modality for the management of advanced chronic obstructive pulmonary disease complicated by severe emphysema and hyperinflation refractory to other therapies. BLVR aims to reduce hyperinflation and residual volume, thereby improving pulmonary function, symptom control, and quality of life. Multiple distinct devices and technologies, including endobronchial coils, thermal vapor ablation, bio-lung volume reduction, and airway bypass stenting, have been developed to achieve lung volume reduction with varying degrees of accessibility and evidence. The most promising BLVR treatment modality to date has been the placement of one-way endobronchial valves (EBVs), with more than 25,000 cases performed worldwide. Identifying symptomatic patients who would benefit from BLVR is challenging and can be time and resource intensive, and candidacy may be limited by physiologic parameters. Additional new technologies may be able to improve the identification and evaluation of candidates as well as increase the portion of evaluated patients who ultimately qualify for BLVR. In this review, we aim to provide historical context to BLVR, summarize the available evidence regarding its use, discuss potential complications, and provide readers with a clear guide to patient selection and referral for BLVR, with a focus on EBV placement. In addition, we will highlight potential future directions for the field.