bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overcoming attenuation bias in regressions using polygenic indices
Authors: van Kippersluis Hans , Biroli Pietro , Dias Pereira Rita , Galama Titus J. , von Hinke Stephanie , Meddens S. Fleur W. , Muslimova Dilnoza , Slob Eric A. W. , de Vlaming Ronald , Rietveld Cornelius A. 
Published: July 2023

AbstractMeasurement error in polygenic indices (PGIs) attenuates the estimation of their effects in regression models. We analyze and compare two approaches addressing this attenuation bias: Obviously Related Instrumental Variables (ORIV) and the PGI Repository Correction (PGI-RC). Through simulations, we show that the PGI-RC performs slightly better than ORIV, unless the prediction sample is very small (N < 1000) or when there is considerable assortative mating. Within families, ORIV is the best choice since the PGI-RC correction factor is generally not available. We verify the empirical validity of the simulations by predicting educational attainment and height in a sample of siblings from the UK Biobank. We show that applying ORIV between families increases the standardized effect of the PGI by 12% (height) and by 22% (educational attainment) compared to a meta-analysis-based PGI, yet estimates remain slightly below the PGI-RC estimates. Furthermore, within-family ORIV regression provides the tightest lower bound for the direct genetic effect, increasing the lower bound for the standardized direct genetic effect on educational attainment from 0.14 to 0.18 (+29%), and for height from 0.54 to 0.61 (+13%) compared to a meta-analysis-based PGI.
A novel perspective for M-polynomials to compute molecular descriptors of borophene nanosheet
Authors: Ismail Rashad , Baby Annmaria , Xavier D. Antony , Varghese Eddith Sarah , Ghani Muhammad Usman , Nair A. Theertha , Karamti Hanen 
Published: July 2023

AbstractNanomaterials feature exceptional, one-of-a-kind qualities that might be used in electronics, medicine, and other industries. Two-dimensional nanomaterials called borophene have a variety of intriguing characteristics, which helped them to leave an indelible impression in the fields of chemistry, material science, nanotechnology, and condensed matter physics. The concept of modelling the structure of a molecule or chemical network to a chemical graph and then quantitatively analysing them with the aid of topological descriptors was a major advance in the fields of mathematics and chemistry, with a wide range of applications. M-polynomial approach is a very versatile and quick method for computing the degree-based descriptors of chemical graphs or networks. The degree-based descriptors of the $$\beta _{12}$$

β
12

-Borophene nanosheet are established in this study utilising the M-polynomial technique. A program code that enables to generate the M-polynomial of any chemical structure was developed in Java platform and the same is displayed. At the conclusion, the numerical and graphical comparison based on the identified analytic expressions is also provided. Additionally, the QSPR analysis was also carried out and the outcoms are presented therein.
Comparative effects of CFTR modulators on phagocytic, metabolic and inflammatory profiles of CF and nonCF macrophages
Authors: Aridgides Daniel S. , Mellinger Diane L. , Gwilt Lorraine L. , Hampton Thomas H. , Mould Dallas L. , Hogan Deborah A. , Ashare Alix 
Published: July 2023

AbstractMacrophage dysfunction has been well-described in Cystic Fibrosis (CF) and may contribute to bacterial persistence in the lung. Whether CF macrophage dysfunction is related directly to Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) in macrophages or an indirect consequence of chronic inflammation and mucostasis is a subject of ongoing debate. CFTR modulators that restore CFTR function in epithelial cells improve global CF monocyte inflammatory responses but their direct effects on macrophages are less well understood. To address this knowledge gap, we measured phagocytosis, metabolism, and cytokine expression in response to a classical CF pathogen, Pseudomonas aeruginosa in monocyte-derived macrophages (MDM) isolated from CF F508del homozygous subjects and nonCF controls. Unexpectedly, we found that CFTR modulators enhanced phagocytosis in both CF and nonCF cohorts. CFTR triple modulators also inhibited MDM mitochondrial function, consistent with MDM activation. In contrast to studies in humans where CFTR modulators decreased serum inflammatory cytokine levels, modulators did not alter cytokine secretion in our system. Our studies therefore suggest modulator induced metabolic effects may promote bacterial clearance in both CF and nonCF monocyte-derived macrophages.
Conductive nerve conduit with piezoelectric properties for enhanced PC12 differentiation
Authors: Javidi Hamideh , Ramazani Saadatabadi Ahmad , Sadrnezhaad S. K. , Najmoddin Najmeh 
Published: July 2023

AbstractRestoration of nerve tissue remains highly challenging, mainly due to the limited regeneration capacity of the nervous system and the development of fibrosis. This limitation necessitates designing new nerve guidance channel to promote nerve repairing. In this study, we developed a novel core/shell conduit to induce PC12 differentiation. Co-electrospinning method was utilized to produce a fibrous shell containing polycaprolactone/polyvinylidene fluoride PCL/PVDF, gelatin and polyaniline/graphene (PAG) nanocomposite. The core section of the conduit was filled with chitosan–gelatin hydrogel containing PAG and ZnO nanoparticles. Such conduit shows antibacterial activity, electrical conductivity and piezoelectric property. The effect of such engineered conduit on PC12 differentiation was investigated by analyzing differentiation markers Nestin and microtubule-associated protein 2 (MAP2) through immunocytochemistry and PCR-RT techniques. The result revealed that such conduit could significantly induce Nestin and MAP2 gene expression in the PC12 cells and, thus, it is a viable option for effective cell differentiation and nerve regeneration.
Alterations in skeletal muscle morphology and mechanics in juvenile male Sprague Dawley rats exposed to a high-fat high-sucrose diet
Authors: Delgado-Bravo Mauricio , Hart David A. , Reimer Raylene A. , Herzog Walter 
Published: July 2023

AbstractAlthough once a health concern largely considered in adults, the obesity epidemic is now prevalent in pediatric populations. While detrimental effects on skeletal muscle function have been seen in adulthood, the effects of obesity on skeletal muscle function in childhood is not clearly understood. The purpose of this study was to determine if the consumption of a high-fat high-sucrose (HFS) diet, starting in the post-weaning period, leads to changes in skeletal muscle morphology and mechanics after 14 weeks on the HFS diet. Eighteen 3-week-old male CD-Sprague Dawley rats were randomly assigned to a HFS (C-HFS, n = 10) or standard chow diet (C-CHOW, n = 8). Outcome measures included: weekly energy intake, activity levels, oxygen consumption, body mass, body composition, metabolic profile, serum protein levels, and medial gastrocnemius gene expression, morphology, and mechanics. The main findings from this study were that C-HFS rats: (1) had a greater body mass and percent body fat than control rats; (2) showed early signs of metabolic syndrome; (3) demonstrated potential impairment in muscle remodeling; (4) produced lower relative muscle force; and (5) had a shift in the force–length relationship, indicating that the medial gastrocnemius had shorter muscle fiber lengths compared to those of C-CHOW rats. Based on the results of this study, we conclude that exposure to a HFS diet led to increased body mass, body fat percentage, and early signs of metabolic syndrome, resulting in functional deficits in MG of childhood rats.
Evapotranspiration estimation using Surface Energy Balance Model and medium resolution satellite data: An operational approach for continuous monitoring
Authors: Pareeth S. , Karimi P. 
Published: July 2023

AbstractMonitoring spatial and temporal trends of water use is of utmost importance to ensure water and food security in river basins that are challenged by water scarcity and climate change induced abnormal weather patterns. To quantify water consumption by the agriculture sector, continuous monitoring is required over different spatial scales ranging from field (< 1 ha) to basin. The demand driven requirement of covering large areas yet providing spatially distributed information makes the use of in-situ measurement devices unfeasible. Earth observation satellites and remote sensing techniques offer an effective alternative in estimating the consumptive use of water (Actual EvapoTranspiration (ETa) fluxes) by using periodic observations from the visible and infrared spectral region. Optical satellite data, however, is often hindered by noises due to cloud cover, cloud shadow, aerosols and other satellite related issues such as Scan Line Corrector (SLC) failure in Landsat 7 breaking the continuity of temporal observations. These gaps have to be statistically filled in order to compute aggregated seasonal and annual estimates of ETa. In this paper, we introduce an approach to develop a gap-filled multi-year monthly ETa maps at medium spatial resolution of 30 m. The method includes two major steps: (i) estimation of ETa using the python based implementation of surface energy balance model called PySEBAL and (ii) temporal interpolation using Locally Weighted Regression (LWR) model followed by spline based spatial interpolation to fill the gaps over time and space. The approach is applied to a large endorheic Lake Urmia Basin (LUB) basin with a surface area of ~ 52,970 km2 in Iran for the years 2013–2015 using Landsat 7 and 8 satellite data. The results show that the implemented gap filling approach could reconstruct the monthly ETa dynamics over different agriculture land use types, while retaining the high spatial variability. A comparison with a similar dataset from FAO WaPOR reported a very high correlation with R2 of 0.93. The study demonstrates the applicability of this approach to a larger basin which is extendible and reproducible to other geographical areas.
Characterization of cytoskeletal and structural effects of INF2 variants causing glomerulopathy and neuropathy
Authors: Ueda Hiroko , Tran Quynh Thuy Huong , Tran Linh Nguyen Truc , Higasa Koichiro , Ikeda Yoshiki , Kondo Naoyuki , Hashiyada Masaki , Sato Chika , Sato Yoshinori , Ashida Akira , Nishio Saori , Iwata Yasunori , Iida Hiroyuki , Matsuoka Daisuke , Hidaka Yoshihiko , Fukui Kenji , Itami Suzu , Kawashita Norihito , Sugimoto Keisuke , Nozu Kandai , Hattori Motoshi , Tsukaguchi Hiroyasu 
Published: July 2023

AbstractFocal segmental glomerulosclerosis (FSGS) is a common glomerular injury leading to end-stage renal disease. Monogenic FSGS is primarily ascribed to decreased podocyte integrity. Variants between residues 184 and 245 of INF2, an actin assembly factor, produce the monogenic FSGS phenotype. Meanwhile, variants between residues 57 and 184 cause a dual-faceted disease involving peripheral neurons and podocytes (Charcot–Marie–Tooth CMT/FSGS). To understand the molecular basis for INF2 disorders, we compared structural and cytoskeletal effects of INF2 variants classified into two subgroups: One (G73D, V108D) causes the CMT/FSGS phenotype, and the other (T161N, N202S) produces monogenic FSGS. Molecular dynamics analysis revealed that all INF2 variants show distinct flexibility compared to the wild-type INF2 and could affect stability of an intramolecular interaction between their N- and C-terminal segments. Immunocytochemistry of cells expressing INF2 variants showed fewer actin stress fibers, and disorganization of cytoplasmic microtubule arrays. Notably, CMT/FSGS variants caused more prominent changes in mitochondrial distribution and fragmentation than FSGS variants and these changes correlated with the severity of cytoskeletal disruption. Our results indicate that CMT/FSGS variants are associated with more severe global cellular defects caused by disrupted cytoskeleton-organelle interactions than are FSGS variants. Further study is needed to clarify tissue-specific pathways and/or cellular functions implicated in FSGS and CMT phenotypes
Characterization of the two tandem repeats for the KPC-2 core structures on a plasmid from hospital-derived Klebsiella pneumoniae
Authors: Ma Liman , Wang Wenji , Qu Ying , Wang Dongguo 
Published: July 2023

AbstractToday, Klebsiella pneumoniae strains are sophisticatedly associated with the transmission of KPC, and ST11 clones carrying KPC-2 are an important target for anti-infective clinical therapy, posing a very high threat to patients. To present the detailed genetic features of two KPC-2 core structures of F94_plasmid pA, the whole genome of K. pneumoniae strain F94 was sequenced by nanopore and illumina platform, and mobile genetic elements associated with antibiotic-resistance genes were analyzed with a series of bioinformatics methods. K. pneumoniae strain F94, identified as a class A carbapenemase-resistant Enterobacteriaceae, was resistant to most tested antibiotics, especially to low-levels of ceftazidime/avibactam (avibactam ≤ 4 mg/L), owing to overexpression of the two KPC-2 in F94_plasmid pA. However, strain F94 was sensitive to high-levels of ceftazidime/avibactam (avibactam ≥ 8 mg/L), which correlated with further inhibition of ceftazidime hydrolysis by the KPC-2 enzyme due to the multiplication of avibactam. Collinearity analysis indicated that multi-drug resistance (MDR) regions of plasmids with the tandam repeats of two or more KPC-2 core structures share highly similar structures. This study characterized the MDR region of the F94_ plasmid pA as homologous to plasmids pKPC2_090050, pKPC2_090374, plasmid unnamed 2, pC2414-2-KPC, pKPC2-020037, pBS1014-KPC2, pKPC-J5501, and pKPC2-020002, which contained the tandem repeats of one, two, or more KPC-2 core structures, providing insight into the evolution of multidrug resistance in K. pneumoniae. An alternative theoretical basis for exploring the tandem repeats of two or more KPC-2 core structures was developed by analyzing and constructing the homologous sequence of F94_ plasmid pA.
Impaired ATF3 signaling involves SNAP25 in SOD1 mutant ALS patients
Authors: Yazar Volkan , Kühlwein Julia K. , Knehr Antje , Grozdanov Veselin , Ekici Arif B. , Ludolph Albert C. , Danzer Karin M. 
Published: July 2023

AbstractEpigenetic remodeling is emerging as a critical process for several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Genetics alone fails to explain the etiology of ALS, the investigation of the epigenome might therefore provide novel insights into the molecular mechanisms of the disease. In this study, we interrogated the epigenetic landscape in peripheral blood mononuclear cells (PBMCs) of familial ALS (fALS) patients with either chromosome 9 open reading frame 72 (C9orf72) or superoxide dismutase 1 (SOD1) mutation and aimed to identify key epigenetic footprints of the disease. To this end, we used an integrative approach that combines chromatin immunoprecipitation targeting H3K27me3 (ChIP-Seq) with the matching gene expression data to gain new insights into the likely impact of blood-specific chromatin remodeling on ALS-related molecular mechanisms. We demonstrated that one of the hub molecules that modulates changes in PBMC transcriptome in SOD1-mutant ALS patients is ATF3, which has been previously reported in an SOD1G93A mouse model. We also identified potential suppression of SNAP25, with impaired ATF3 signaling in SOD1-mutant ALS blood. Together, our study shed light on the mechanistic underpinnings of SOD1 mutations in ALS.
A comparative study of severe thunderstorm among statistical and ANN methodologies
Authors: Bhattacharya Sonia , Bhattacharyya Himadri Chakraborty 
Published: July 2023

AbstractSevere Thunderstorms are the extreme weather convective features. It causes local calamities in various ways. Proper prediction with lead time is an important factor to prevent such calamities from saving people. Here, both probabilistic and machine learning techniques are applied to weather data to obtain proper predictions. Traditional methodologies are already available for such prediction purposes. However, Naïve Bayes and RBFN (Radial Basis Function Network) methodology have been introduced here with some specific weather parameters that has not done before remarkably. A comparative study was performed on weather data including Naïve Bayes, Multilayer Perceptron (MLP), K-nearest neighbor (KNN) and Radial Basis Function Network (RBFN). All these data have been procured from Kolkata located in north-east India. The result obtained by applying the Radial Basis Function Network is better among the three methods, yielding a correct prediction of 95% for severe “squall-storms” and 94% for “no storm”. The predictions have a sufficient lead time of 10- 12 h.
Benefits of pancreatic parenchymal endoscopic ultrasonography in predicting microscopic precancerous lesions of pancreatic cancer
Authors: Yamakawa Kohei , Inomata Noriko , Masuda Atsuhiro , Takenaka Mamoru , Toyama Hirochika , Sofue Keitaro , Sakai Arata , Kobayashi Takashi , Tanaka Takeshi , Tsujimae Masahiro , Ashina Shigeto , Gonda Masanori , Abe Shohei , Masuda Shigeto , Uemura Hisahiro , Kohashi Shinya , Nagao Kae , Harada Yoshiyuki , Miki Mika , Irie Yosuke , Juri Noriko , Shiomi Hideyuki , Kanzawa Maki , Itoh Tomoo , Fukumoto Takumi , Kodama Yuzo 
Published: July 2023

AbstractPancreatic cancer primarily arises from microscopic precancerous lesions, such as pancreatic intraepithelial neoplasia (PanIN) and acinar-to-ductal metaplasia (ADM). However, no established method exists for predicting pancreatic precancerous conditions. Endoscopic ultrasonography (EUS) can detect changes in pancreatic parenchymal histology, including fibrosis. This study aimed to elucidate the relationship between pancreatic parenchymal EUS findings and microscopic precancerous lesions. We retrospectively analyzed 114 patients with pancreatobiliary tumors resected between 2010 and 2020 and evaluated the association between pancreatic parenchymal EUS findings and the number of PanIN, ADM, and pancreatic duct gland (PDG). Of the 114 patients, 33 (29.0%), 55 (48.2%), and 26 (22.8%) had normal EUS findings, hyperechoic foci/stranding without lobularity, and hyperechoic foci/stranding with lobularity, respectively. Multivariate analyses revealed that abnormal EUS findings were significantly associated with the frequency of PanIN (hyperechoic foci/stranding without lobularity: OR [95% CI] = 2.7 [1.0–7.3], with lobularity: 6.5 [1.9–22.5], Ptrend = 0.01) and ADM (hyperechoic foci/stranding without lobularity: 3.1 [1.1–8.2], with lobularity: 9.7 [2.6–36.3], Ptrend = 0.003) but not with PDG (hyperechoic foci/stranding without lobularity: 2.2 [0.8–5.8], with lobularity: 3.2 [1.0–10.2], Ptrend = 0.12). We observed a trend toward a significantly higher number of precancerous lesions in the following order: normal findings, hyperechoic foci/stranding without lobularity, and hyperechoic foci/stranding with lobularity. Pancreatic parenchymal EUS findings were associated with the increased frequency of PanIN and ADM. Lobularity may help predict the increased number of precancerous lesions.
Surgically treated cervical cancer in a high-risk group in the era of the 2018 FIGO staging schema: a nationwide study
Authors: Shigeta Shogo , Shimada Muneaki , Tsuji Keita , Watanabe Zen , Tanase Yasuhito , Matsuo Koji , Nakanishi Toru , Saito Toshiaki , Aoki Daisuke , Mikami Mikio 
Published: July 2023

AbstractThe 2018 International Federation of Gynecology and Obstetrics (FIGO) revision to the staging criteria for uterine cervical cancer adopted pathological staging for patients who underwent surgery. We investigated the correlation between clinicopathological factors and prognosis in patients with high-risk factors in accordance with the FIGO 2018 staging criteria by analyzing a real-world database of 6,192 patients who underwent radical hysterectomy at 116 institutions belonging to the Japan Gynecologic Oncology Group. A total of 1,392 patients were categorized into the high-risk group. Non-squamous cell carcinoma histology, regional lymph node metastasis, pT2 classification, and ovarian metastasis were identified as independent risk factors for mortality. Based on pathological findings, 313, 1003, and 76 patients were re-classified into FIGO 2018 stages IIB, IIIC1p, and IIIC2p, respectively. Patients with stage IIIC2p disease showed worse prognoses than those with stage IIB or IIIC1p disease. In patients with stage IIIC1p disease, overall survival was significantly better if their tumors were localized in the uterine cervix, except for single lymph node metastasis, with a 5-year overall survival rate of 91.8%. This study clarified the heterogeneity of the high-risk group and provided insights into the feasibility of upfront radical hysterectomy for a limited number of patients harboring high-risk factors.
Extent and predictors of presenteeism among healthcare professionals working in Swiss hospitals, nursing homes and home care organizations
Authors: Peter Karin Anne , Gerlach Maisa , Kilcher Gablu , Bürgin Reto , Hahn Sabine , Golz Christoph 
Published: July 2023

AbstractPresenteeism can have negative impacts on employees’ health and organizational productivity. It occurs more often among occupations with high attendance demands, such as healthcare professionals. Information is lacking regarding the extent to which presenteeism differs between disciplines and settings in the health sector and what the reasons are for presenteeism as well as influencing factors. This study used cross-sectional data on 15,185 healthcare professionals (nursing staff, midwives, physicians, medical-technical and medical-therapeutic professionals) from various settings (acute care, rehabilitation or psychiatric hospitals, nursing homes and home care organizations). Presenteeism was measured by examining how many days participants had gone to work despite feeling sick during the past 12 months. Kruskal–Wallis was used to test for significant differences between healthcare professions/settings and regression analysis to identify significant predictors of presenteeism. Nursing assistants with a formal education reported the most days of presenteeism in the past 12 months (mean = 4.3, SD = 12.0). Healthcare professionals working in nursing homes reported the most days of presenteeism in the past 12 months (mean = 4.2, SD = 8.7). The majority of healthcare professionals had been present at work while being ill due to a sense of duty (83.7%), followed by consideration for colleagues and/or managers (76.5%). In particular, the psychiatric hospitals (β = 0.139; p < 0.001), nursing homes (β = 0.168; p < 0.001) and home care organizations (β = 0.092; p < 0.001), as well as the language regions of Swiss French (β = − 0.304; p < 0.001) and Italian (β = − 0.154; p < 0.001), were significantly associated with presenteeism. Presenteeism differs between disciplines and settings in the health sector. The reasons for presenteeism and its influencing factors in the health sector are mostly consistent with those in other sectors. Cultural differences should be afforded greater relevance in future presenteeism research.