bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical profile ,socio-demographic features, and treatment outcome of native Kashmiri patients with HIV/AIDS : A 12-year study.
Authors: Hassan Amir , Siraj Farhana , A.Koul Parvaiz , Mehfooz Nazia , Qadri Syed Mudasir , Koul Aijaz Nabi , Mantoo Suhail 
Published: October 2023

Abstract
Introduction
Profile of HIV/AIDS differs considerably through different regions of the world depending upon various factors. Jammu and Kashmir in north India is considered the low HIV/AIDS prevalence area. There is very scant data about the HIV/AIDS amongst the native Kashmiri population. In this study we present the clinical and demographic profile and treatment outcomes of native Kashmiri patients seen at Anti-retroviral therapy (ART) center in our hospital over a period of twelve years.
Material & Method
All native Kashmiri HIV positive patients referred to the integrated counseling and testing centre (ICTC/ART) center of our hospital for evaluation and initiation of treatment from January 2007 to December 2019 were enrolled.
Results
Among 346 native Kashmiri patients with mean age of 34 ± SD 11.35 years (ranging from 11–56 years) seen over the study period, there were 226 (65.3%) males and 120 females (34.7%). Majority of our patients belonged to rural areas (n = 276; 79.8%) More than 2/3rd of the patients were in the age-group of 15–49 years (n = 269; 77.7%).Among the studied population majority of male patients had a history of working outside Kashmir valley as labourers and majority of females were house wives. More than half of the patients (55.5%) had studied upto primary level and 30.3% were illiterate. Fever was the commonest presenting symptom followed by diarrhoea and weight loss. Tuberculosis and candidiasis were the predominant opportunistic infections. WHO stage 1 disease was seen in 50.9% (n = 176) of patients. The mean CD4 count was 271 ± 236.75 /µL at presentation. Nearly 74.6% (n = 258) patients were alive after 12years of diagnosis and 25.4% patients (n = 88) had died. Age > 50years, less educated, poor compliance to treatment, TB co-infection and lower base line CD4 counts were associated with increased mortality.
Conclusion
The majority of our patients were form rural areas, had low education level and belonged to the productive age group of 15–49 years which had a negative impact on the economic and overall development of family, community and country. The data presented should help healthcare planners and policymakers for introducing the interventions for implementing preventive strategies and early and effective treatment for affected individuals.
Polyunsaturated Fatty Acids May Not Be Helpful for People with Osteoarthritis: A Two-sample Mendelian Randomization Analysis
Authors: Xu Chunlei , Shi Wei , Xu Qian , Zhang Huafeng , Li Zhijun , Li Hui 
Published: October 2023

Abstract

Background
In recent years, researchers have examined the use of polyunsaturated fatty acids (PUFA) or a low omega-6/3 ratio to protect the knee joint. The current study is based on genome-wide association study (GWAS) analysis and uses the Mendelian randomization (MR) method to evaluate the effect of total PUFA, omega-3, omega-6, and omega-6/3 ratios on osteoarthritis (OA).
Methods
First, we downloaded the latest PUFA and OA GWAS data. The PUFA data were divided into four groups: total PUFA, omega-3, omega-6, and omega-6/3 ratios. The OA data were split into nine groups: hip OA (total, males, and females), knee OA (total, males, and females), and hand OA (total, males, and females). Then, qualified SNPs were selected as instrumental variables. Inverse variance weighting (IVW), weighted median, and the MR‒Egger method were used for MR analysis. Finally, MR‒Egger, MR-Presso, and Cochran's Q statistical methods were used to evaluate the heterogeneity and pleiotropy.
Results
Thirty-six IVW results showed that total PUFA, omega-3, omega-6, and omega-6/3 ratios did not significantly increase or decrease the risk of knee, hip, and hand OA. There was no obvious horizontal polytropy in all the analyses, and there was heterogeneity in some analyses.
Conclusions
Our study does not indicate that total PUFA, mega-3, and low omega-6/3 ratios are helpful for people with OA, nor does it indicate that omega-6 increases the risk of OA. The dietary management of PUFA in OA patients needs to be performed cautiously.
Intersectional gender analysis for inclusive health system in Nepal: taking Tuberculosis as a case example
Authors: Parajuli Ayuska , Kakchapati Sampurna , Arjyal Abriti , Joshi Deepak , Kharel Chandani , Barrio Mariam Otmani del , Baral Sushil C 
Published: October 2023

Abstract
Background: Nepal is multi-ethnic, multi-lingual, and multi-cultural state with diverse geography, in its early stage of federalization, where Tuberculosis (TB) remains a major public health problem. TB is a disease, which is high among settings with common practice of gender and social inequities. This study aimed to a) explore inclusiveness of gender and other social stratifiers in the key health related national policies and Health Management Information System (HMIS) of National Tuberculosis Programme (NTP) b) to conduct intersectional analysis with available social stratifiers of TB cases enrolled in the NTP.
Methods: Desk review of key policies and HMIS of NTP was conducted. Intersectional analysis was carried out from two secondary sources i.e. annual report data of NTP (2017 - 2021) and 628 recorded TB cases via HMIS 6.5 from two TB centres (2017/18-2018/19). Statistical analysis was carried out to assess association between social stratifers and types of TB, registration category and treatment outcome.
Results: Gender, social inclusion and concept of intersectionality are well incorporated into the different health policies and strategies while lacking in its implementation. NTP has initiated collecting age, sex, ethnicity and location data since 2014/15 through the HMIS. However, only age and sex disaggregated data is routinely reported. Hence, recorded social stratifiers of TB patients have remained static as they were not analyzed and disseminated. Furthermore, some of the key findings from the intersectional analysis conducted by using TB secondary data, gave significant highlights on sex and age wise variation among TB patients. However, ethnicity was not significantly associated with TB treatment outcome.
Conclusion: The study findings illustrated that the biological and the social construct of gender differences are important determinants of TB and treatment outcome. The inadequacy in the availability of social stratifiers in the routine HMIS, limits the NTP’s ability to conduct intersectional analyses, which are essential for unveiling the roles of other social determinants of TB. Such limitation underscores the need for more disaggregated data in routine NTP to better inform policies and plans towards building a more responsive and equitable TB programme and address disparities effectively.
Trial registration: Not Applicable
Pulmonary Artery Pseudoaneurysm; Endovascular treatment of an Ominous Finding
Authors: Fish Adam , Sailer Anne , Pollak Jeffrey , Schlachter Todd 
Published: October 2023

Abstract
The technique and outcomes of pulmonary artery pseudoaneurysm embolization was retrospectively evaluated in 13 patients undergoing pulmonary PSA embolization between January 2014 and September 2023. The etiology of the PSA was iatrogenic (4/13), tumor (3/13), chronic lung (2/13), idiopathic (2/13) and mycotic (2/13). Clinical presentation was massive hemorrhage (6/13), incidental (4/13), and non-massive hemoptysis (3/13). The average PSA size was 13.5mm. Coil embolization of the PSA sac was performed in all but two extenuating cases (11/13). Follow-up of 12 patients over an average 5.3-months showed persistent occlusion in all cases. There were no major adverse events attributed to the embolization. 5/10 patients with procedures performed at least one year before this study were noted to be deceased after an average 7-month time. Pulmonary artery PSAs of various etiologies may be safely and effectively treated by embolizing the PSA sac.
A Comparative Analysis of Quantum Computing Variational Quantum Eigensolver Algorithm and Molecular Dynamics Simulations for Peptide Folding
Authors: Uttarkar Akshay , Niranjan Vidya 
Published: October 2023

Abstract
Quantum computing in biology is one of the most rapidly evolving field of technology. Protein folding is one of the key challenges which requires accurate and efficient algorithms with a quick computational time. Structural conformations of proteins with disordered regions need colossal amount of computational resource to map its least energy conformation state. In this regard, quantum algorithms like Variational quantum eigensolver (VQE) are applied in the current research work to predict the lowest energy value of 50 peptides of 7 amino acids each. VQE is initially used to calculate the energy values over which Variational Quantum Optimization is applied via Conditional Value at Risk (CVaR) over 100 iterations of 500000 shots each to obtain least ground state energy value. This is compared to the molecular dynamics-based simulations of 50 nanoseconds each to calculate the energy values along with the folding pattern. The results suggest efficient folding outcomes from CvaR-VQE compared to MD based simulations. With the ever-expanding quantum hardware and improving algorithms the problem of protein folding can be resolved to obtain in depth insights on the biological process and drug design.
Government Shutdown and SNAP Disbursements: Effects on Household Expenditures
Authors: Marks Mindy , Prina Silvia , Gernhardt Roy 
Published: October 2023

Abstract
We test the ability of SNAP eligible households to respond to a temporary change in benefit timing. We exploit the 2018-19 US government shutdown in which all states were federally mandated to pay February SNAP benefits in January. This created a short-term windfall (two payments very close to each other) followed by a longer than normal gap during which no SNAP disbursements were received. Using a triple differences approach, we show that expenditures are lower in February (relative to other months) 2019 (relative to 2018) for SNAP recipients (relative to near-eligible households). We complement this finding by exploiting preexisting state-level differences in disbursement schedules that drove some states to temporarily alter the timing of the 2019 March and April SNAP disbursements. Diff-in-diff estimates show that SNAP eligible households in those states reduced spending. Our findings are inconsistent with the permanent income hypothesis and suggest that the timing of benefits matters for household consumption.
JEL Codes: D12, I3, I38
High-level expression of sucrose isomerase in Bacillus subtilis through expression element optimization and fermentation optimization
Authors: Zhang Kang , Zhao Wenchong , Chen Sheng , Su Lingqia , Wu Jing 
Published: October 2023

Abstract

Sucrose isomerase is an important food enzyme that catalyze the isomerization of sucrose into isomaltulose, a functional sugar widely used in food industrial, while the production level of sucrose isomerase in food safe host strains was much low than industrial requirement. Bacillus subtilis is an excellent host strain for recombinant protein expression, which own the characteristics of powerful secretory capability and generally recognized as safe state. In this study, the expression of sucrose isomerase in B. subtilis was improved through expression element optimization and fermentation optimization. Firstly, the extracellular chaperone PrsA was overexpressed to enhance extracellular folding of sucrose isomerase, which improved the recombinant expression level by 80.02%. Then, the protein synthesize level was optimized through promoter screening, improving the recombinant expression level by 60.40%. On the basis of strain modification, the fermentation conditions including nitrogen source, carbon source, metal ion, pH and temperature were optimized successively in shake-flask. Finally, the 3 L bioreactor cultivation condition was optimized and yielding a sucrose isomerase activity of 862.86 U/mL, the highest level reported to date. This study provides an effective strategy to improve the expression level of food enzymes in B. subtilis.
Placental RNA sequencing implicates IGFBP1 in insulin sensitivity during pregnancy and in gestational diabetes
Authors: Hivert Marie-France , White Frederique , Allard Catherine , James Kaitlyn , Majid Sana , Aguet François , Ardlie Kristin , Edlow Andrea , Florez Jose , Bouchard Luigi , Jacques Pierre-Etienne , Karumanchi S. , Powe Camille 
Published: October 2023

Abstract
Reduced insulin sensitivity (or greater insulin resistance) is a hallmark of normal physiology in late pregnancy and also underlies gestational diabetes mellitus (GDM) pathophysiology. We conducted transcriptomic profiling of 434 human placentas and identified a strong positive association between insulin-like growth factor binding protein 1 gene (IGFBP1) expression in the placenta and insulin sensitivity at ~ 26 weeks’ gestation. Circulating IGFBP1 protein levels rose over the course of pregnancy and declined postpartum, which together with high placental gene expression levels, suggests a placental source. Higher circulating IGFBP1 levels were strongly associated with greater insulin sensitivity (lesser insulin resistance) at ~ 26 weeks’ gestation in the same cohort and two additional pregnancy cohorts. In addition, low circulating IGFBP1 levels in early pregnancy predicted subsequent GDM diagnosis in two cohorts. These results implicate IGFBP1 in the glycemic physiology of pregnancy and suggest a role for placental IGFBP1 deficiency in GDM pathogenesis.
A negative feedback loop underlies the Warburg effect
Authors: Singh Raghvendra , Jaiswal Alok 
Published: October 2023

Abstract
Aerobic glycolysis, or the Warburg effect, is used by cancer cells for proliferation while producing lactate. Although lactate production has wide implications for cancer progression, it is not known how this effect increases cell proliferation and relates to oxidative phosphorylation. Here, we elucidate that a negative feedback loop (NFL) is responsible for the Warburg effect. Further, we show that aerobic glycolysis works as an amplifier of oxidative phosphorylation. On the other hand, quiescence is an important property of cancer stem cells. Based on the NFL, we show that both aerobic glycolysis and oxidative phosphorylation, playing a synergistic role, are required to achieve cell quiescence. Further, our results suggest that the cells in their hypoxic niche are highly proliferative yet close to attaining quiescence by increasing their NADH/NAD + ratio through the severity of hypoxia. The findings of this study can help in a better understanding of the link among metabolism, cell cycle, carcinogenesis, and stemness.
Comparative Assessment of Transmission and Reflection Vis/NIR Spectroscopy for Non-Destructive Evaluation of Multiple Quality Attributes in Tomatoes
Authors: Li Long , Su Qian , Yang Huihui , Fan Bei , Sun Jing , Bai Yajuan , Liu Lei , Wang Qingwei , Wang Yutang , Wang Fengzhong 
Published: October 2023

Abstract
Non-destructive evaluation of internal and external quality attributes is imperative for effectively grading and sorting tomatoes. This study compared visible/near-infrared (Vis/NIR) diffuse reflectance and transmission spectroscopy for rapid, non-invasive measurement of key indicators, including color, hardness, total sugar (TS), and total acidity (TA). A sample set of 110 tomatoes across multiple ripeness levels was divided into calibration (n = 82) and prediction (n = 28) subsets. Vis/NIR spectra were obtained using reflectance and transmission systems and pre-processed before multivariate analysis. Partial least squares regression (PLSR) models were developed, relating the spectra to reference measurements using competitive adaptive reweighted sampling (CARS-PLS). For internal parameters of TS and TA, transmission PLS models demonstrated superior performance over reflectance, with prediction R values of 0.9511 and 0.9818. In contrast, for external attributes of color and hardness, reflectance PLS models performed better given consistent bulk fruit maturity, with prediction R values of 0.9595 and 0.9713. This study demonstrates the potential of Vis/NIR diffuse transmission spectroscopy for non-invasive analysis of internal and external tomato quality attributes. The findings provide a basis for developing handheld devices and inline online systems for sorting tomatoes based on comprehensive ripeness assessment.
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Authors: Nelwan Martin 
Published: October 2023

Abstract
Purpose: In this research, I report the relationship between S. ovuncatum, S. sinensium, S. japonicum, S. mekongi, and S. malayensis. In addition, I also report the kinship relationship between five Oncomelania species, with Neotricula aperta, Robertsiella spp, and Tricula spp. Furthermore, I describe the formation of the genus Oncomelania from its precursor forms.
Principal Results: Results of nucleotide BLAST showed S. ovuncatum shared a 99.69% identity similar to S. sinensium, 98.68% with S. mekongi, 97.98% with S. malayensis, and 97.85% with S. japonicum. The tree-view slanted cladogram showed that S. sinensium is a sister to S. ovuncatum. It split into S. japonicum. Schistosoma japonicum splits into S. mekongi and S. malayensis. Results also showed Oncomelania robertsoni shared an 86.12% identity similar to Neotricula aperta, 85.88% with Robertsiella spp., and then 85.28% with Tricula bollingi. The tree-view slanted cladogram showed that Tricula spp. split into N. aperta and Robertsiella spp. This study suggested that Oncomelania rose from its antecedent forms.
Conclusions: Nucleotide BLAST results showed that S. ovuncatum is close to S. sinensium. Schistosoma sinensium split into S. japonicum, S. mekongi, and S. malayensis. Oncomelania robertsoni was close to N. aperta, Robertsiella spp., and then to Tricula spp (Tricula bollingi). Oncomelania species rose from their antecedent forms.
Survival Benefit of Sequential Curative Treatment for TACE Suitable BCLC Stage B HCC Patients
Authors: Ding Yuan-Jie , Chang Te-Sheng , Shen Chien-Heng , Kuo Liang-Mou , Hsu Sheng-Lung , Chen Yi-Hsing , Huang Hui-Ling , Lu Sheng-Nan 
Published: October 2023

Abstract

To clarify the survival benefit of sequential curative treatment post transcatheter arterial chemoembolization (TACE) for Barcelona Clinic Liver Cancer (BCLC) stage B hepatocellular carcinoma (HCC), we retrospectively analyzed HCC patients at a hospital. From July 2017 to July 2020, 787 treatment-naïve HCC patients underwent initial treatment; 77 (9.8%) meeting inclusion criteria were enrolled. Their initial treatments were TACE only (n=68, 88.3%) or TACE with other treatments (n=9, 11.7%). Median survival of the TACE-only group was 30 months. Treatment response was evaluated after 2 or 3 consecutive TACEs for patients (54/68, 79.4%) with available pre-/post-TACE computerized tomography (CT) or magnetic resonance imaging (MRI). Treatment responses was divided into 4 groups: complete (n=14, 26%, group (Gr) 1), incomplete without new tumor growth (n=28, 52.0%, Gr2), incomplete with new growth (n=6, 11%, Gr3), and progression (n=6, 11%, Gr4). Of Gr2, further treatment after TACE were had radiofrequency ablation (n=13, Gr2a), TACE (n=9, Gr2b), other modalities (n=6, Gr2c). Gr2a's median survival was longer than Gr2b's (>60 vs. 20 months, p=0.007). Nine patients in Gr2a (69%, 9/13) achieved a complete response, but none in Gr2b (p=0.001). Conclusively, in TACE-suitable BCLC stage B HCC patients, a partial response without new tumor growth can serve as an indicator of treatment effectiveness following initial TACE treatment. This can facilitate the selection of appropriate candidates to receive RFA, potentially resulting in improved patient survival.
KINtaro – protein kinase-like database
Authors: Baranowski Bartosz , Krysińska Marianna , Gradowski Marcin 
Published: October 2023

Abstract
Objective
The superfamily of protein kinases features a common Protein Kinase-like (PKL) three-dimensional fold. Proteins with PKL structure can also possess enzymatic activities other than protein phosphorylation, such as AMPylation or glutamylation. PKL proteins play a vital role in the world of living organisms, contributing to the survival of pathogenic bacteria inside host cells, as well as being involved in carcinogenesis and neurological diseases in humans. The superfamily of PKL proteins is constantly growing. Therefore, it is crucial to gather new information about PKL families.
Results
To this end, the KINtaro database (http://bioinfo.sggw.edu.pl/kintaro/) has been created as a resource for collecting and sharing such information. KINtaro combines protein sequence information and additional annotations for more than 70 PKL families, including 32 families not associated with PKL superfamily in established protein domain databases. KINtaro is searchable by keywords and by protein sequence and provides family descriptions, sequences, sequence alignments, HMM models, 3D structure models, experimental structures with PKL domain annotations and sequence logos with catalytic residue annotations.
Quality Improvement Project: Patent Ductus Arteriosus (PDA) Score Implementation for Targeted Management of PDA in Preterm Infants
Authors: Noureldein Mona , Rajaraman Nikitha , Yousif Marianne , Madawala Priyankara , Mupanemunda Richard , Gowda Harsha 
Published: October 2023

Abstract
Due to the variation of practice in managing Patent Ductus Arteriosus (PDA) in preterm infants, we have performed a quality improvement project to standardise PDA management using a PDA Score (PDAsc). PDAsc consisted of clinical and echocardiographic parameters that reflected systemic hypoperfusion and pulmonary overcirculation. An echocardiogram was performed at 48–120 hours of life. The model for improvement was followed, and five PDSA cycles were completed. Process measures included the percentage of infants having an echocardiogram at 48–120 hours of life and the rate of PDA treatment. Outcome measures included PDA closure and treatment rates. Implementing PDAsc increased the percentage of early echocardiograms from 58% (36/45) to 79% (30/38). There was a reduction in the PDA treatment rate from 54–44%. The rate of PDA closure stayed the same at 41% (16/39) and 42% (15/36) before and after PDAsc, respectively. In conclusion, PDAsc is an objective tool that facilitates decision-making and standardisation of PDA management. It helps provide early targeted treatment of haemodynamically significant PDA (hsPDA) while avoiding unnecessary treatment of non-hsPDA.
Ultrasound-assisted digestion using choline chloride-oxalic acid deep eutectic solvent for macro and microelements determination in rice by ICP-OES
Authors: Zhao Wenzhi , Xie Xu , He Tian , Zhang Jintao , Liu Jiufen 
Published: October 2023

Abstract
A rapid, straightforward, and environmentally friendly method was developed for the extraction of K, Na, Ca, Mg, Fe, Mn, Cu, Zn and P from rice samples using ultrasound-assisted deep eutectic solvents (DESs). The investigation focused on deep eutectic solvents derived from choline chloride and oxalic acid. The response surface methodology, based on the Box-Behnken design, was employed to determine the optimal conditions of the significant parameters. The determination results of the reference samples revealed a relative error ranging from -8.3% to 3.8%, while the relative standard deviation remained below 5.5%. F-test and t-test results indicated that there was no statistically significant difference observed between the accuracy and precision of the method proposed in this study and the microwave digestion method for determining actual rice samples. The proposed method exhibits advantages over classical microwave-assisted digestion procedures based on concentrated acids, considering critical parameters such as cost, green chemistry, and analyst safety.