bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating pedigree- and SNP-associated components of heritability in a wild population of Soay sheep
Authors: James Caelinn , Pemberton Josephine M. , Navarro Pau , Knott Sara 
Published: February 2024

AbstractEstimates of narrow sense heritability derived from genomic data that contain related individuals may be biased due to the within-family effects such as dominance, epistasis and common environmental factors. However, for many wild populations, removal of related individuals from the data would result in small sample sizes. In 2013, Zaitlen et al. proposed a method to estimate heritability in populations that include close relatives by simultaneously fitting an identity-by-state (IBS) genomic relatedness matrix (GRM) and an identity-by-descent (IBD) GRM. The IBD GRM is identical to the IBS GRM, except relatedness estimates below a specified threshold are set to 0. We applied this method to a sample of 8557 wild Soay sheep from St. Kilda, with genotypic information for 419,281 single nucleotide polymorphisms. We aimed to see how this method would partition heritability into population-level (IBS) and family-associated (IBD) variance for a range of genetic architectures, and so we focused on a mixture of polygenic and monogenic traits. We also implemented a variant of the model in which the IBD GRM was replaced by a GRM constructed from SNPs with low minor allele frequency to examine whether any additive genetic variance is captured by rare alleles. Whilst the inclusion of the IBD GRM did not significantly improve the fit of the model for the monogenic traits, it improved the fit for some of the polygenic traits, suggesting that dominance, epistasis and/or common environment not already captured by the non-genetic random effects fitted in our models may influence these traits.
Association study of the complement component C4 gene and suicide risk in schizophrenia
Authors: Ebrahimi Mahbod , Teymouri Kowsar , Chen Cheng C. , Mohiuddin Ayeshah G. , Pouget Jennie G. , Goncalves Vanessa F. , Tiwari Arun K. , Zai Clement C. , Kennedy James L. 
Published: February 2024

AbstractSchizophrenia is a severe mental illness and a major risk factor for suicide, with approximately 50% of schizophrenia patients attempting and 10% dying from suicide. Although genetic components play a significant role in schizophrenia risk, the underlying genetic risk factors for suicide are poorly understood. The complement component C4 gene, an immune gene involved in the innate immune system and located in the major histocompatibility complex (MHC) region, has been identified to be strongly associated with schizophrenia risk. In addition, recent findings have also suggested that the MHC region has been associated with suicide risk across disorders, making C4 a potential candidate of interest for studying suicidality in schizophrenia patients. Despite growing interest in investigating the association between the C4 gene and schizophrenia, to our knowledge, no work has been done to examine the potential of C4 variants as suicide risk factors in patients with schizophrenia. In this study, we investigated the association between different C4 copy number variants and predicted C4 brain expression with suicidal outcomes (suicide attempts/suicidal ideation). We directly genotyped 434 schizophrenia patients to determine their C4A and C4B copy number variants. We found the C4AS copy number to be marginally and negatively associated with suicide risk, potentially being protective against suicide attempts (OR = 0.49; p = 0.05) and suicidal ideation (OR = 0.65; p = 0.07). Furthermore, sex-stratified analyses revealed that there are no significant differences between males and females. Our preliminary findings encourage additional studies of C4 and potential immune dysregulation in suicide.
Regional variations in relative sea-level changes influenced by nonlinear vertical land motion
Authors: Oelsmann Julius , Marcos Marta , Passaro Marcello , Sanchez Laura , Dettmering Denise , Dangendorf Sönke , Seitz Florian 
Published: February 2024

AbstractVertical land movements can cause regional relative sea-level changes to differ substantially from climate-driven absolute sea-level changes. Whereas absolute sea level has been accurately monitored by satellite altimetry since 1992, there are limited observations of vertical land motion. Vertical land motion is generally modelled as a linear process, despite some evidence of nonlinear motion associated with tectonic activity, changes in surface loading or groundwater extraction. As a result, the temporal evolution of vertical land motion, and its contribution to projected sea-level rise and its uncertainty, remains unresolved. Here we generate a probabilistic vertical land motion reconstruction from 1995 to 2020 to determine the impact of regional-scale and nonlinear vertical land motion on relative sea-level projections up to 2150. We show that regional variations in projected coastal sea-level changes are equally influenced by vertical land motion and climate-driven processes, with vertical land motion driving relative sea-level changes of up to 50 cm by 2150. Accounting for nonlinear vertical land motion increases the uncertainty in projections by up to 1 m on a regional scale. Our results highlight the uncertainty in future coastal impacts and demonstrate the importance of including nonlinear vertical land motions in sea-level change projections.
Baseline ctDNA gene alterations as a biomarker of survival after panitumumab and chemotherapy in metastatic colorectal cancer
Authors: Shitara Kohei , Muro Kei , Watanabe Jun , Yamazaki Kentaro , Ohori Hisatsugu , Shiozawa Manabu , Takashima Atsuo , Yokota Mitsuru , Makiyama Akitaka , Akazawa Naoya , Ojima Hitoshi , Yuasa Yasuhiro , Miwa Keisuke , Yasui Hirofumi , Oki Eiji , Sato Takeo , Naitoh Takeshi , Komatsu Yoshito , Kato Takeshi , Mori Ikuo , Yamanaka Kazunori , Hihara Masamitsu , Soeda Junpei , Misumi Toshihiro , Yamamoto Kouji , Yamashita Riu , Akagi Kiwamu , Ochiai Atsushi , Uetake Hiroyuki , Tsuchihara Katsuya , Yoshino Takayuki 
Published: February 2024

AbstractCertain genetic alterations and right-sided primary tumor location are associated with resistance to anti-epidermal growth factor (EGFR) treatment in metastatic colorectal cancer (mCRC). The phase 3 PARADIGM trial (n = 802) demonstrated longer overall survival with first-line anti-EGFR (panitumumab) versus antivascular endothelial growth factor (bevacizumab) plus modified FOLFOX6 in patients with RAS wild-type mCRC with left-sided primary tumors. This prespecified exploratory biomarker analysis of PARADIGM (n = 733) evaluated the association between circulating tumor DNA (ctDNA) gene alterations and efficacy outcomes, focusing on a broad panel of gene alterations associated with resistance to EGFR inhibition, including KRAS, NRAS,PTEN and extracellular domain EGFR mutations, HER2 and MET amplifications, and ALK, RET and NTRK1 fusions. Overall survival was prolonged with panitumumab plus modified FOLFOX6 versus bevacizumab plus modified FOLFOX6 in patients with ctDNA that lacked gene alterations in the panel (that is, negative hyperselected; median in the overall population: 40.7 versus 34.4 months; hazard ratio, 0.76; 95% confidence interval, 0.62–0.92) but was similar or inferior with panitumumab in patients with ctDNA that contained any gene alteration in the panel (19.2 versus 22.2 months; hazard ratio, 1.13; 95% confidence interval, 0.83–1.53), regardless of tumor sidedness. Negative hyperselection using ctDNA may guide optimal treatment selection in patients with mCRC. ClinicalTrials.gov registrations: NCT02394834 and NCT02394795.
Protein destabilization underlies pathogenic missense mutations in ARID1B
Authors: Mermet-Meillon Fanny , Mercan Samuele , Bauer-Probst Beatrice , Allard Cyril , Bleu Melusine , Calkins Keith , Knehr Judith , Altorfer Marc , Naumann Ulrike , Sprouffske Kathleen , Barys Louise , Sesterhenn Fabian , Galli Giorgio G. 
Published: February 2024

AbstractARID1B is a SWI/SNF subunit frequently mutated in human Coffin–Siris syndrome (CSS) and it is necessary for proliferation of ARID1A mutant cancers. While most CSS ARID1B aberrations introduce frameshifts or stop codons, the functional consequence of missense mutations found in ARID1B is unclear. We here perform saturated mutagenesis screens on ARID1B and demonstrate that protein destabilization is the main mechanism associated with pathogenic missense mutations in patients with Coffin–Siris Syndrome.
Aqueous humor TGFβ and fibrillin-1 in Tsk mice reveal clues to POAG pathogenesis
Authors: Tan James C. , Ko MinHee K. , Woo Jeong-Im , Lu Kenneth L. , Kelber Jonathan A. 
Published: February 2024

AbstractAqueous humor (AH) and blood levels of transforming growth factor β (TGFβ) are elevated in idiopathic primary open angle glaucoma (POAG) representing a disease biomarker of unclear status and function. Tsk mice display a POAG phenotype and harbor a mutation of fibrillin-1, an important regulator of TGFβ bioavailability. AH TGFβ2 was higher in Tsk than wild-type (WT) mice (by 34%; p = 0.002; ELISA); similarly, AH TGFβ2 was higher in human POAG than controls (2.7-fold; p = 0.00005). As in POAG, TGFβ1 was elevated in Tsk serum (p = 0.01). Fibrillin-1 was detected in AH from POAG subjects and Tsk mice where both had similar levels relative to controls (p = 0.45). 350 kDa immunoblot bands representing WT full-length fibrillin-1 were present in human and mouse AH. A 418 kDa band representing mutant full-length fibrillin-1 was present only in Tsk mice. Lower molecular weight fibrillin-1 antibody-reactive bands were present in similar patterns in humans and mice. Certain bands (130 and 32 kDa) were elevated only in human POAG and Tsk mice (p ≤ 0.04 relative to controls) indicating discrete isoforms relevant to disease. In addition to sharing a phenotype, Tsk mice and human POAG subjects had common TGFβ and fibrillin-1 features in AH and also blood that are pertinent to understanding glaucoma pathogenesis.
Maximizing solar radiations of PV panels using artificial gorilla troops reinforced by experimental investigations
Authors: Abdelaal Ashraf K. , Alhamahmy Amira I. A. , Attia Hossam El Deen , El-Fergany Attia A. 
Published: February 2024

AbstractThis article's main objective is to maximize solar radiations (SRs) through the use of the gorilla troop algorithm (GTA) for identifying the optimal tilt angle (OTA) for photovoltaic (PV) panels. This is done in conjunction with an experimental work that consists of three 100 W PV panels tilted at three different tilt angles (TAs). The 28°, 30°, and 50° are the three TAs. The experimental data are collected every day for 181-day and revealed that the TA of 28° is superior to those of 50° and 30°. The GTA calculated the OTA to be 28.445°, which agrees with the experimental results, which show a TA of 28°. The SR of the 28o TA is 59.3% greater than that of the 50° TA and 4.5% higher than that of the 30° TA. Recent methods are used to compare the GTA with the other nine metaheuristics (MHTs)—the genetic algorithm, particle swarm, harmony search, ant colony, cuckoo search, bee colony, fire fly, grey wolf, and coronavirus disease optimizers—in order to figure out the optimal OTA. The OTA is calculated by the majority of the nine MHTs to be 28.445°, which is the same as the GTA and confirms the experimental effort. In only 181-day, the by experimentation it may be documented SR difference between the TAs of 28° and 50° TA is 159.3%. Numerous performance metrics are used to demonstrate the GTA's viability, and it is contrasted with other recent optimizers that are in competition.
Research and design of internal meshing gear pump separating crescent plate
Authors: Guo Shanxin , Yu Guangchi 
Published: February 2024

AbstractThe design of the crescent block is a key factor in the high-pressure operation of the internal meshing gear pump. In order to increase the output pressure of the pump, this article designs a new type of separable crescent plate. Then, taking a certain type of high-pressure internal meshing gear pump as the research object, a nonlinear differential equation for the internal flow field of the gear pump was established, and the pressure distribution law in the transition zone of a cycle was derived. A mathematical model of the device was established based on the equilibrium conditions of the internal and external crescent block forces. Finally, experimental research was conducted on the design parameters of the separation crescent plate. The results showed that under the conditions of displacement of 100.5 ml/r, pressure of 20.5 MPa, and rotational speed of 1800 RPM, the compensation chamber angle range was 31.23°, and the pump's volumetric efficiency could reach 94.6%. There were no abnormal phenomena during the entire operation of the pump, and there was no jamming or jamming of the friction pair.
Transitioning solidification mode via electroplated Ni coatings in martensitic stainless steel resistance spot welds: new insights into fabricating tough microstructure
Authors: Aghajani Hamidreza , Balajaddeh Milad Bahrami , Pouranvari Majid 
Published: February 2024

AbstractThe present study addresses the enhancement of fracture toughness of martensitic stainless steel (MSS) spot welds by utilizing through electroplating of Ni on MSS sheets. The equilibrium and non-equilibrium solidification modelling showed that by Ni coating with 50 μm thick on 1.5 mm thick MSSs, the solidification mode changes from δ-ferrite to γ-austenite, leading to a weld nugget (WN) dominated by austenite grains. Moreover, electron backscatter diffraction (EBSD) and electron probe microanalysis (EPMA) showed that the other phases (martensite, δ-ferrite) appeared in band areas of WN owing to incomplete mixing of MSS and the Ni-coating. The tough microstructure in the Ni-coated MSS spot welds provided superior mechanical properties compared to non-coated welds, both in cross-tension (CT) and tensile-shear (TS) tests. Notably, the TS and CT strengths of the Ni-coated MSS spot welds showed a remarkable increase of 57% and 127%, respectively, in comparison to the conventional bare MSS spot welds. Furthermore, in terms of failure energy, the Ni-coated MSS spot welds demonstrated a substantial enhancement of 296% in TS and 520% in CT, when compared to their non-coated counterparts. This research study showcased the effectiveness of Ni electroplating as an industrial method for improving the spot weldability of MSSs.
Detection and isolation of wormhole nodes in wireless ad hoc networks based on post-wormhole actions
Authors: Bhatti David Samuel , Saleem Shahzad , Imran Azhar , Kim Hyeon Jeong , Kim Ki-Il , Lee Kyu-Chul 
Published: February 2024

AbstractThe wormhole attack is one of the most treacherous attacks projected at the routing layer that can bypass cryptographic measures and derail the entire communication network. It is too difficult to prevent a priori; all the possible countermeasures are either too expensive or ineffective. Indeed, literature solutions either require expensive hardware (typically UWB or secure GPS transceivers) or pose specific constraints to the adversarial behavior (doing or not doing a suspicious action). The proposed solution belongs to the second category because the adversary is assumed to have done one or more known suspicious actions. In this solution, we adopt a heuristic approach to detect wormholes in ad hoc networks based on the detection of their illicit behaviors. Wormhole and post wormhole attacks are often confused in literature; that’s why we clearly state that our methodology does not provide a defence against wormholes, but rather against the actions that an adversary does after the wormhole, such as packet dropping, tampering with TTL, replaying and looping, etc. In terms of contributions, the proposed solution addresses the knock-out capability of attackers that is less targeted by the researcher’s community. In addition, it neither requires any additional hardware nor a change in it; instead, it is compatible with the existing network stack. The idea is simulated in ns2.30, and the average detection rate of the proposed solution is found to be 98-99%. The theoretical time to detect a wormhole node lies between 0.07-0.71 seconds. But, from the simulation, the average detection and isolation time is 0.67 seconds. In term of packet loss, the proposed solution has a relatively overhead of$$\approx$$≈22%. It works well in static and mobile scenarios, but the frame losses are higher in mobile scenarios as compared to static ones. The computational complexity of the solution isO(n). Simulation results advocate that the solution is effective in terms of memory, processing, bandwidth, and energy cost. The solution is validated using statistical parameters such as Accuracy, Precision, F1-Score and Matthews correlation coefficient ($$M_{cc}$$Mcc).
Functional coupling between auditory memory and verbal transformations
Authors: Kondo Hirohito M. , Hasegawa Ryuju , Ezaki Takahiro , Sakata Honami , Ho Hao Tam 
Published: February 2024

AbstractThe ability to parse sound mixtures into coherent auditory objects is fundamental to cognitive functions, such as speech comprehension and language acquisition. Yet, we still lack a clear understanding of how auditory objects are formed. To address this question, we studied a speech-specific case of perceptual multistability, called verbal transformations (VTs), in which a variety of verbal forms is induced by continuous repetition of a physically unchanging word. Here, we investigated the degree to which auditory memory through sensory adaptation influences VTs. Specifically, we hypothesized that when memory persistence is longer, participants are able to retain the current verbal form longer, resulting in sensory adaptation, which in turn, affects auditory perception. Participants performed VT and auditory memory tasks on different days. In the VT task, Japanese participants continuously reported their perception while listening to a Japanese word (2- or 3-mora in length) played repeatedly for 5 min. In the auditory memory task, a different sequence of three morae, e.g., /ka/, /hi/, and /su/, was presented to each ear simultaneously. After some period (0–4 s), participants were visually cued to recall one of the sequences, i.e., in the left or right ear. We found that delayed recall accuracy was negatively correlated with the number of VTs, particularly under 2-mora conditions. This suggests that memory persistence is important for formation and selection of perceptual objects.
A dynamic visualization clinical tool constructed and validated based on the SEER database for screening the optimal surgical candidates for bone metastasis in primary kidney cancer
Authors: Jiang Liming , Tong Yuexin , Wang Jun , Jiang Jiajia , Gong Yan , Zhu Dejin , Zheng Linyang , Zhao Dongxu 
Published: February 2024

AbstractThe implementation of primary tumor resection (PTR) in the treatment of kidney cancer patients (KC) with bone metastases (BM) has been controversial. This study aims to construct the first tool that can accurately predict the likelihood of PTR benefit in KC patients with BM (KCBM) and select the optimal surgical candidates. This study acquired data on all patients diagnosed with KCBM during 2010–2015 from the Surveillance, Epidemiology, and End Results (SEER) database. Propensity score matching (PSM) was utilized to achieve balanced matching of PTR and non-PTR groups to eliminate selection bias and confounding factors. The median overall survival (OS) of the non-PTR group was used as the threshold to categorize the PTR group into PTR-beneficial and PTR-Nonbeneficial subgroups. Kaplan–Meier (K–M) survival analysis was used for comparison of survival differences and median OS between groups. Risk factors associated with PTR-beneficial were identified using univariate and multivariate logistic regression analyses. Receiver operating characteristic (ROC), area under the curve (AUC), calibration curves, and decision curve analysis (DCA) were used to validate the predictive performance and clinical utility of the nomogram. Ultimately, 1963 KCBM patients meeting screening criteria were recruited. Of these, 962 patients received PTR and the remaining 1061 patients did not receive PTR. After 1:1 PSM, there were 308 patients in both PTR and non-PTR groups. The K–M survival analysis results showed noteworthy survival disparities between PTR and non-PTR groups, both before and after PSM (p < 0.001). In the logistic regression results of the PTR group, histological type, T/N stage and lung metastasis were shown to be independent risk factors associated with PTR-beneficial. The web-based nomogram allows clinicians to enter risk variables directly and quickly obtain PTR beneficial probabilities. The validation results showed the excellent predictive performance and clinical utility of the nomograms for accurate screening of optimal surgical candidates for KCBM. This study constructed an easy-to-use nomogram based on conventional clinicopathologic variables to accurately select the optimal surgical candidates for KCBM patients.
Post-extubation dysphagia in pediatric trauma patients: a single-center case-series study
Authors: Yogo Naoki , Abe Takeru , Kano Kyoko , Muto Yuichiro , Kiyonaga Sachi , Hirai Katsuki 
Published: February 2024

AbstractWe aimed to investigate whether ventilator support time influences the occurrence of dysphagia in pediatric trauma patients. This case-series study was conducted in a single pediatric emergency and critical care center from April 2012 to March 2022. Trauma patients aged < 16 years who underwent tracheal intubation were divided into two groups based on the occurrence of dysphagia within 72 h after extubation, and their data were analyzed. Tracheal intubation was performed in 75 pediatric trauma patients, and 53 of them were included in the analysis. A total of 22 patients had post-extubation dysphagia and head trauma. The dysphagia group tended to have more severe head injuries (Abbreviated Injury Scale (AIS) 4 [4–5] vs. 4 [0–4]; p < 0.05), a longer ventilator support time (7 days [4–11] vs. 1 day [1–2.5]; p < 0.05), and a longer length of hospital stay (27 days [18.0–40.3] vs. 11 days [10.0–21.0]; p < 0.05). Severe head trauma and a long duration of tracheal intubation may be risk factors for dysphagia in pediatric trauma patients. Therefore, early recognition of these risk factors could assist in treatment planning for speech-language pathologist intervention and nutritional routes of administration.
Avialan-like brain morphology in Sinovenator (Troodontidae, Theropoda)
Authors: Yu Congyu , Watanabe Akinobu , Qin Zichuan , Logan King J. , Witmer Lawrence M. , Ma Qingyu , Xu Xing 
Published: February 2024

AbstractMany modifications to the skull and brain anatomy occurred along the lineage encompassing non-avialan theropod dinosaurs and modern birds. Anatomical changes to the endocranium include an enlarged endocranial cavity, relatively larger optic lobes that imply elevated visual acuity, and proportionately smaller olfactory bulbs that suggest reduced olfactory capacity. Here, we use micro-computed tomographic (μCT) imaging to reconstruct the endocranium and its neuroanatomical features from an exceptionally well-preserved skull of Sinovenator changii (Troodontidae, Theropoda). While its overall morphology resembles the typical endocranium of other troodontids, Sinovenator also exhibits unique endocranial features that are similar to other paravian taxa and non-maniraptoran theropods. Landmark-based geometric morphometric analysis on endocranial shape of non-avialan and avialan dinosaurs points to the overall brain morphology of Sinovenator most closely resembling that of Archaeopteryx, thus indicating acquisition of avialan-grade brain morphology in troodontids and wide existence of such architecture in Maniraptora.