bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kcat data
Authors: Wang Yutao , Mao Zhitao , Dong Jiacheng , Zhang Peiji , Gao Qiang , Liu Defei , Tian Chaoguang , Ma Hongwu 
Published: February 2024

Abstract
Background:
Genome-scale metabolic models (GEMs) serve as effective tools for understanding cellular phenotypes and predicting engineering targets in the development of industrial strain. Enzyme-constrained genome-scale metabolic models (ecGEMs) have emerged as a valuable advancement, providing more accurate predictions and unveiling new engineering targets compared to models lacking enzyme constraints. In 2022, a stoichiometric GEM, iDL1450, was reconstructed for the industrially significant fungus Myceliophthora thermophila. To enhance the GEM’s performance, an ecGEM was developed for M. thermophila in this study.
Results:
Initially, the model iDL1450 underwent refinement and updates, resulting in a new version named iYW1475. These updates incuded adjustments to biomass components, correction of gene-protein-reaction (GPR) rules, and a consensus on metabolites. Subsequently, the first ecGEM for M. thermophila, designated ecMTM, was constructed using machine learning-based kcat data predicted by TurNuP within the ECMpy framework. Comparing ecMTM to iYW1475, the solution space was reduced and the growth simulation results more closely resembled realistic cellular phenotypes. Metabolic adjustment simulated by ecMTM revealed a trade-off between biomass yield and enzyme usage efficiency at varying glucose uptake rates. Notably, hierarchical utilization of five carbon sources derived from plant biomass hydrolysis was accurately captured and explained by ecMTM. Furthermore, based on enzyme cost considerations, ecMTM successfully predicted reported targets for metabolic engineering modification and introduced some new potential targets for chemicals produced in M. thermophila.
Conclusions:
In this study, the incorporation of enzyme constraint to iYW1475 not only improved prediction accuracy but also broadened the model’s applicability. This research demonstrates the effectiveness of integrating of machine learning-based kcat data in the construction of ecGEMs especially in situations where there is limited measured enzyme kinetic parameters for a specific organism.
Identification of the Genetic Association Between Ferroptosis and immune in Pancreatic Cancer
Authors: Zhang Xu , Liu pan , Fu Qiang , Liu ChuanJiang , Luo QianKun , Yu PengFei , Bian JinDa , Pan ChangJie , Zhang HongWei , Qin Tao 
Published: February 2024

Abstract

The morbidity and mortality rates of pancreatic cancer are increasing annually. Immunotherapy for pancreatic cancer has not yielded good results, and immunosuppression is now thought to be the key factor. Ferroptosis plays an important role in pancreatic cancer. However, the mechanism of ferroptosis in pancreatic cancer immunosuppression remains unclear. To investigate the relationship between Ferroptosis and immunosuppression in pancreatic cancer.We analyzed differentially expressed genes in the center of pancreatic cancer and pancreatic ductal adenocarcinoma (PDAC) tissues using bioinformatics techniques in the Gene Expression Omnibus and found genes associated with Ferroptosis in the FerrDb database. We then performed enrichment and protein–protein interaction (PPI) network analyses to explore DEG-enriched functions and pathways. Additionally, hub gene expression was explored using the STRING database. The TISIDB database was used to analyze correlations among key genes and immune characteristics. Finally, the expression of the key genes was confirmed in vitro. DEGs were first screened from the gene expression profiles of the GSE16515 and TCGA datasets. Simultaneously, the genes associated with ferroptosis intersected. Then, 39 common genes were identified in the three datasets. Functional analysis revealed that common DEGs were mostly related to lipid metabolism and ROS signaling pathways. Among the top 20 hub genes, CA9 was the most significant potential biomarker of PC. CA9 expression strongly correlates with chemokines, chemokine receptors, and immunomodulators. Finally, RT-qPCR was conducted to demonstrate CA9 expression in PC cell lines. Knockdown of CA9 can significantly reduce chemokines expression. We identified 20 hub genes that significantly affects the association between ferroptosis and PC. CA9 maybe a key player in pancreatic cancer immunosuppression and has potential treatment value for PC.
Traditional Home-garden Agro-biodiversity, Agro-ecosystem Services and Management Practices: The Case of Sidama Region in Ethiopia
Authors: Sime Getachew , Tamene Girma , Keneni Yadessa , Senbeta Abate , Mengistu Teramage 
Published: February 2024

Abstract

This study investigated the characteristics of traditional home-garden agro-biodiversity as well as its agro-ecosystem services in diversifying farm household livelihoods and management practices. A total of 373 households were selected from two districts using simple random sampling techniques. Data were collected through questionnaire, key informant interview, direct field observation, free listing and focus group discussion. Results show that households managed different traditional home-garden sizes and diverse plant species delivering wide range of agro-ecosystem services. Most traditional home-gardens were rich in agro-biodiversity and their corresponding agro-ecosystem services. The corporate agro-ecosystem services delivered among others were food and nutritional supplements, income generations, and medicines. Regarding coverage, Ensete ventricosum, Catha edulis and Eucalyptus camaldulensis dominated the majority of home-gardens. The management is essentially a traditional knowledge-based farming system, managed by family members’ knowledge and skill. Soil fertility is managed through adding organic fertilizers sourced from agro-biological resources. The status of the agro-biodiversity varied with the degree of traditional knowledge and management practices. The major challenges were unstable market prices, poor access to market places, and diminishing home-garden sizes. In conclusion, traditional home-garden is a diverse agri-food systems with remarkable contribution to farmer livelihood diversification through delivering multitudes of agro-ecosystem services.
Calculation of machine precision second order derivatives using dual-complex numbers
Authors: Millwater H. , Balcer M. , Millwater N. 
Published: February 2024

Abstract

It is well known that both complex and dual numbers can be employed to obtain machine precision first-order derivatives; however, neither, on their own, can compute machine precision 2nd order derivatives. To address this limitation, it is demonstrated in this paper that combined dual-complex numbers can be used to compute machine precision 1st and 2nd order derivatives. The dual-complex approach is simpler than utilizing multicomplex or hyper-dual numbers as existing dual libraries can be used as is or easily augmented to accept complex numbers, and the complexity of developing, integrating, and deploying multicomplex or hyper-dual libraries is avoided. The efficacy of this approach is demonstrated for both univariant and multivariate functions with examples from the Python, Julia, and Mathematica languages.
An Optimization Approach for Sustainable and Resilient Closed-loop Floating Solar Photovoltaic Supply Chain Network Design
Authors: Nili Maryam , Dehghani Ehsan 
Published: February 2024

Abstract
Growing energy demand and its consequences, such as fossil fuel depletion, greenhouse gas emissions, and global warming, prompted the need for large-scale solar power plants. Floating photovoltaic systems have many advantages over ground-mounted systems, including methods and resources, reducing costs, and improving efficiency. In this regard, this study aims at presenting a scenario-based robust optimization model for developing a sustainable and resilient closed-loop floating solar photovoltaic supply chain network design. The concerned model’s objective function is minimizing the total supply chain costs in addition to maximizing greenhouse gas emissions reduction. In a bid to identify the most suitable dams for establishing the floating photovoltaic system, the hybrid approach by applying the fuzzy best-worst method and the TOPSIS technique is first exploited. Thereinafter, the selected dams are exerted in the presented mathematical model. Eventually, a real case study is implemented on floating photovoltaic systems in Iran to assess the proposed model’s performance, from which important managerial insights are attained.
Genetic Insights into Prepubertal Gynecomastia: A Comprehensive Analysis of a Rare 45,X[2]/ 46,X, + mar[28] Karyotype
Authors: BULUŞ Ayşe Derya , DÜNYA Betül , DİRİCAN Onur , CEYLAN Ahmet Cevdet , YAŞARTEKİN Yüksel , HUSSEINI Abbas Ali 
Published: February 2024

Abstract
Introduction
This case report provides genetic insights into prepubertal gynecomastia through the comprehensive analysis of a rare 45,X[2]/46,X,+mar[28] karyotype. Gynecomastia, characterized by the enlargement of male breast, is typically physiological in pubertal cases but necessitates thorough evaluation in severe instances. Prepubertal gynecomastia is exceptionally rare, and the limited literature results in a deficit of etiological and management data.
Case report
The case involves an eight years and six months old male child with prepubertal bilateral gynecomastia and short stature, presenting a karyotype of 45,X[2]/46,X,+mar[28], with the additional marker chromosome originating from the Y chromosome, revealing Yq microdeletions. The patient's clinical progression, chromosomal analysis, and molecular findings are detailed, emphasizing the importance of karyotyping in prepubertal gynecomastia cases.
Conclusion
In prepubertal gynecomastia cases, karyotyping is crucial to identify potential chromosomal abnormalities contributing to the condition. Particularly, cases with Yq deletion should be closely monitored, especially for short stature.
Radiomics-based prediction of treatment response to TRuC-T cell therapy in patients with mesothelioma: a pilot study
Authors: BEAUMONT Hubert , IANNESSI Antoine , THINNES Alexandre , JACQUES Sebastien , QUINTAS-CARDAMA alfonso 
Published: February 2024

Abstract

T cell receptor fusion constructs (TRuCs), a next generation engineered T cell therapy, hold great promise. To accelerate the clinical development of these therapies, improving patient selection is a crucial pathway forward. We retrospectively analyzed 23 mesothelioma patients (85 target tumors) treated in a phase 1/2 single arm clinical trial (NCT03907852). Five imaging sites were involved, settings of evaluations were Blinded Independent Central Review (BICR) with double reads. Reproducibility of 3416 radiomics and delta-radiomics (Δradiomics) was assessed. Univariate analysis evaluated correlation at target tumor level with 1) tumor diameter response; 2) tumor volume response, according to the Quantitative Imaging Biomarker Alliance and 3) the mean standard uptake value (SUV) response, as defined by positron emission tomography response criteria in solid tumors (PERCIST). A random forest model predicted the response of target pleural tumors. Tumor anatomical distribution was 55.3%, 17.6%, 14.1% and 10.6% in the pleura, lymph nodes, peritoneum and soft tissues, respectively. Radiomics/Dradiomics reproducibility differed across tumors localization. Radiomics were more reproducible than Dradiomics. In the univariate analysis, none of the radiomics/Dradiomics correlated with any response criteria. With an accuracy ranging 0.75–0.9, 3 radiomics/Dradiomics were able to predict response of target pleural tumors. Pivotal studies will require a sample size of 250 to 400 tumors. The prediction of responding target pleural tumors can be achieved using machine learning-based radiomics/Dradiomics analysis. Tumor-specific reproducibility and average values indicated that bridging tumor model to effective patient model would require combining several target tumors models.
Use of a Self-Contained Mechanically Powered Negative Pressure Dressing Reduces Surgical Site Infection After Intestinal Stoma Reversal
Authors: Williams Brian , Wang Johnny , Wlodarczyk Jordan R. , Gupta Abhinav , Cologne Kyle G. , Koller Sarah E. , Hsieh Christine , Duldulao Marjun P. , Shin Joongho 
Published: February 2024

Abstract

Background
The use of closed-incision negative pressure wound therapy (ci-NPWT) has been shown to reduce postoperative wound complications and surgical site infections after stoma closures. However, use of this approach has not been widely adopted due to high cost of the devices. We present a first experience with a self-contained mechanically powered negative pressure dressing (MP-NPD) applied to primarily closed stoma reversal wounds. The study assessed 30-day SSI and wound complication rates using this novel dressing system compared to standard dressings.
Methods
This was a retrospective investigator-initiated study, in which consecutive patients that underwent stoma reversal with primary wound closure dressed with MP-NPD from May 2021-March 2022. 30-day outcomes from the study group were then compared to a control group derived from pooled data extracted from well-designed RCTs comparing patients undergoing primary wound closure versus purse string closure after stoma reversal.
Results
Forty-six patients were identified for the study group and 216 patients in the control group were compared. Patient demographics and surgical variables were similar among the groups. Zero (0%) patients in the study cohort developed superficial SSI within 30 days of their surgery, which was significantly less than the control group (0% vs. 25.9%; p < 0.001). Post-op length of stay (LOS) was shorter in the study group versus control group (4.1 vs. 7.5 days; p < 0.001).
Conclusion
Intestinal stoma reversal wounds closed primarily and dressed with the MP-NPD dressings had significantly reduced stoma site SSI rates, compared to patients undergoing primary closure alone.
Sapovirus – An emerging pathogen in renal transplant recipients?
Authors: Rippl Michaela , Burkhard-Meier Anton , Schönermarck Ulf , Fischereder Michael 
Published: February 2024

Abstract
Purpose After including sapovirus to the viral GI-screening routine of our institution's laboratory, we noticed an increasing number of sapovirus diagnosis among kidney transplant recipients. Therefore, we assumed former GI-tract infections with unidentified pathogens could have been caused by sapovirus as well. In order to better understand the characteristics of a sapovirus infection in a high-risk group we initiated this study.Methods 13 renal transplant recipients with GI-tract symptoms and later identified viral/unknown pathogens were included. Four patients suffered from a sapovirus infection. Kidney function, levels of immunosuppressants, CRP-levels and acid-base balance at admission and dismission, as well as onset of symptoms and time of hospitalization were analyzed.Results Even though statistically not significant, creatinine levels at admission tended to be higher in sapovirus patients (p = 0,710, sapovirus: 3,3 mg/dl (1,3; 5,0), non-sapovirus: 2,5 mg/dl (1,1; 4,9)). Also, Tacrolimus levels at admission showed the same trend (sapovirus: 13,6 ng/ml (12,9; 13,6), non-sapovirus: 7 ng/ml (2,6; 22,6), p = 0,279). At dismission creatinine levels improved equally in both groups (sapovirus: 1,7 mg/dl (1,4; 3,2), non-sapovirus: 2 mg/dl (1,0; 3,6), p = 0,825).Conclusion Especially in high-risk patients early symptomatic treatment remains crucial to protect the transplant's function. In our cohort all patients recovered equally well from the sapovirus infection as well as from other viral GI-tract pathogens. Larger cohorts and long-time follow-ups are needed in order to detect the long-term consequences and a potential need for further research regarding specific treatment.Trial registration number: DRKS00033311 date: December 28th 2023
Mineralogical and geochemical facets of the massive deposition of stibnite-metastibnite at a seafloor hydrothermal field (Wakamiko Crater, Kagoshima Bay, Ryukyu Volcanic Arc)
Authors: Dekov Vesselin , Furuma Yukako , Guéguen Bleuenn , Klose Lukas , Yasukawa Kazutaka , Morita Motoaki , Asael Dan , Yamanaka Toshiro , Bindi Luca , Koschinsky Andrea , Pracejus Bernhard , Kato Yasuhiro 
Published: February 2024

Abstract
Stibnite precipitates in the form of massive boulders at two active hydrothermal mounds in the submarine Wakamiko Crater (Ryukyu Volcanic Arc) as opposed to commonly observed accessory stibnite in the seafloor hydrothermal deposits. The stibnite dimorph, metastibnite, found here for the first time on the seafloor, appears to always form whenever stibnite is precipitated under submarine hydrothermal conditions. Our study shows that hydrothermal conditions of low temperatures (&lt;50 °C) and low values of pH (&lt;6) are favorable for the precipitation of stibnite on the seafloor. The stibnite probably does not precipitate at the measured vent fluid temperatures (i.e., 177.6–187.0 °C) along the chimney conduits, but rather at temperatures &lt;50 °C and at slightly reduced to slightly oxic conditions (Eh = –0.5 to +0.5 V) within the chimney walls and hydrothermal mounds. Metastibnite deposition appears to be the result of rapid quenching of hot hydrothermal fluid when mixed with cold seawater and rapid precipitation at the interface between stibnite and vent fluid. The low concentrations (usually below detection limits) of the trace elements (Cd, Co, Cr, Cu, Li, Mn, Mo, Ni, P, Pb, Sr, V, Zn) in the stibnite deposits from Wakamiko Crater are likely a result of the decreased metal-transporting capacity of the precipitating vent fluid due to its low chlorinity. Low-chlorinity venting implies sub-seafloor boiling and phase separation of the hydrothermal fluid. Sluggish hydrothermal fluid/seawater mixing within the walls of the chimneys and mounds favors the reduction of sulfate dissolved in the hydrothermal fluids and results in a heavy S isotope composition of the sulfate in the vent fluids. Sulfate reduction and disproportionation of magmatic SO2, both leading to heavy S isotope composition of sulfate in the vent fluids, seem to be common processes in volcanic arc/back-arc submarine hydrothermal settings.
First widespread occurrence of rare phosphate chladniite in a meteorite, winonaite Graves Nunataks (GRA) 12510: Implications for phosphide–phosphate redox buffered genesis in meteorites
Authors: Anzures Brendan A. , McCubbin Francis M. , Erickson Timmons M. , Jakubek Ryan S. , Fries Marc D. , Le Loan 
Published: February 2024

Abstract
The first widespread occurrence of rare Na-, Ca-, and Mg, Mn, Fe-bearing phosphate chladniite was observed in meteorite Graves Nunataks (GRA) 12510, which is a primitive achondrite that sits within the winonaite class. Numerous 1–500 µm chladniite grains were found, often on the margins between silicate clasts and the kamacite portions of the large metal veins that permeated through the sample. The largest chladniite grains are associated with merrillite, kamacite, taenite, troilite, albite, forsterite, diopside, and enstatite, with a few tiny chladniite grains and an apatite grain enclosed within merrillite. GRA 12510s average chladniite composition is Na2.7Ca1.25(Mg10.02Mn0.69Fe0.20)Σ10.91(PO4)9. Electron backscattered diffraction (EBSD) patterns indicate varying degrees of nucleation and growth of chladniite grains. Additionally, the first pure Raman spectrum of chladniite is described here, revealing primary ν1 bands at 954, 974, and especially 984 cm–1. The co-occurrence and close association of merrillite, apatite, chladniite, and P-bearing metallic phases within GRA 12510 suggests that the fO2 of IW-2 to IW-4 is an intrinsic property of the precursor chondritic material, and the phosphate-phosphide reaction may have buffered the final winonaite and IAB iron meteorite phase assemblages. Altogether, chladniite appears to form alongside other phosphates, with their chemistries reflecting the diverse environment of their formation. Meteoritic chladniite likely formed through subsolidus oxidation of schreibersite, scavenging Na from albite, Ca from diopside, Mg from enstatite/forsterite, Fe from kamacite/taenite, and Mn from alabandite/chromite when available. A P0-P5+ redox-buffered environment also has implications for thermometry and fast cooling rates, although more experiments are needed to extrapolate powder reaction rates to those of larger crystals. Furthermore, phosphide-phosphate buffered experiments may aid in investigating equilibrium chemistry at fO2 values between IW-2 and IW-4, which have been challenging to explore experimentally due to the limited availability of solid metal-metal oxide buffers between IW (Fe-FeO) and IW-5 (Cr-Cr2O3) at temperatures and pressures relevant to planetary interiors. Future investigations of phosphide-phosphate redox-buffered genesis at fO2 values between IW-2 and IW-4 have important implications for primitive meteorite constituents (e.g., CAI values), partially differentiated planetesimals and planets, including Mercury and core formation on Earth.
Analyses of drinking water quality during a protracted cholera epidemic in Malawi – a cross-sectional study of key physicochemical and microbiological parameters
Authors: Sokemawu Freeman Alex Yao , Ganizani Aaron , Mwale Annie Chauma , Manda Innocent Kauta , Chitete James , Phiri Gift , Stambuli Bashil , Chimulambe Elias , Koslengar Mougabe , Kimambo Neema Rusibamayila , Bita Alisa , Apolot Rebecca Racheal , Mponda Hamid , Mungwira Randy George , Chapotera Gertrude , Yur Chol Thabo , Yatich Nelly Jepkonga , Totah Terence , Mantchombe Freddie , Chamla Dick Damas , Olu Olushayo Oluseun 
Published: February 2024

Abstract

Anecdotal evidence and available literature indicated that contaminated water played a major role in spreading the prolonged cholera epidemic in Malawi from 2022 to 2023. This study assessed drinking water quality in 17 cholera-affected Malawi districts from February to April 2023. Six hundred and thirty-three records were analysed. The median counts/100 ml for thermotolerant coliform was 98 (interquartile range (IQR): 4–100) and that for Escherichia coli was 0 (IQR: 0–9). The drinking water in all (except one) districts was contaminated by thermotolerant coliform, while six districts had their drinking water sources contaminated by E. coli. The percentage of contaminated drinking water sources was significantly higher in shallow unprotected wells (80.0% for E. coli and 95.0% for thermotolerant coliform) and in households (55.8% for E. coli and 86.0% for thermotolerant coliform). Logistic regression showed that household water has three times more risk of being contaminated by E. coli and two and a half times more risk of being contaminated by thermotolerant coliform compared to other water sources. This study demonstrated widespread contamination of drinking water sources during a cholera epidemic in Malawi, which may be the plausible reason for the protracted nature of the epidemic.