bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of VirCapSeq-VERT and BacCapSeq In the Diagnosis of Presumed and Definitive Neuroinfectious Diseases
Authors: Boruah Abhilasha P , Kroopnick Adam , Thakkar Riddhi , Wapniarski Annie E , Kim Carla , Dugue Rachelle , Harrigan Eileen , Lipkin W. Ian , Mishra Nischay , Thakur Kiran T 
Published: July 2023

Abstract
Background:
Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity while reducing sequencing costs and complexity of bioinformatic analysis. Here we report the use of virus capture based sequencing for vertebrate viruses (VirCapSeq-VERT) and bacterial capture sequencing (BacCapSeq) in investigating CNS infections.
Design/Methods:
Thirty-four samples were categorized: (1) Patients with definitive CNS infection by routine testing; (2) Patients meeting clinically Brighton Criteria (BC) for meningoencephalitis (3) Patients with presumptive infectious etiology highest on the differential. RNA extracts from cerebrospinal fluid (CSF) were used for VirCapSeq-VERT and DNA extracts were used for BacCapSeq analysis.
Results:
Among 8 samples from known CNS infections in group 1, VirCapSeq and BacCapSeq confirmed 3 expected diagnoses (42.8%), were negative in 2 (25%), yielded an alternative result in 1 (11.1%), and did not detect 2 expected negative pathogens. The confirmed cases identified HHV-6, HSV-2, and VZV while the negative samples included JCV and HSV-2. In groups 2 and 3, 11/26 samples (42%) were positive for at least one pathogen, however 27% of the total samples (7/26) were positive for commensal organisms. No microbial nucleic acids were detected in negative control samples.
Conclusions:
HTS showed limited promise for pathogen identification in presumed CNS infectious diseases in our small sample. Before conducting larger-scale prospective studies to assess clinical value of this novel technique, clinicians should understand benefits and limitations of using this modality.
Spaced Out Data No More: Genomic Harmonization Meets Machine Learning in Murine Livers
Authors: Ilangovan Hari , Kothiyal Prachi , Hoadley Katherine , Elgart Shona , Eley Greg , Eslami Parastou 
Published: July 2023

Abstract

NASA has employed high-throughput molecular assays to identify sub-cellular changes impacting human physiology during spaceflight. Machine learning (ML) methods hold the promise to improve our ability to identify important signals within highly dimensional molecular data. However, the inherent limitation of study subject numbers within a spaceflight mission minimizes the utility of ML approaches. To overcome the sample power limitations, data from multiple spaceflight missions must be aggregated while appropriately addressing intra- and inter-study variabilities. Here we describe an approach to log transform, scale and normalize data from six heterogeneous, mouse liver derived transcriptomics datasets (ntotal=137) which enabled ML-methods to classify spaceflown vs. ground control animals (AUC ≥ 0.87) while mitigating the variability from mission-of-origin. Concordance was found between liver-specific biological processes identified from harmonized ML-based analysis and study-by-study classical omics analysis. This work demonstrates the feasibility of applying ML methods on integrated, heterogeneous datasets of small sample size.
Research on the Spatiotemporal Evolution and Driving Mechanism of Coupling Coordinating Between Green Transition of Urban Land Use and Urban Land Use Efficiency: A Case Study of the Yangtze River Delta Region in China
Authors: Ge Kun , Wang Yin , Ke Shangan , Lu Xinhai 
Published: July 2023

Abstract

Analyzing the spatiotemporal characteristics and driving mechanisms of the coupling coordination between the green transition of urban land use (GTULU) and urban land use efficiency (ULUE) can help explore the future development direction of sustainable land use in cities. In this paper, we construct a theoretical framework for the coupling coordination between GTULU and ULUE. We use several models, including the super-efficiency slack-based model (SBM), the coupling coordination degree model, the non-parametric kernel density estimation method, exploratory spatial data analysis, and the geographically and temporally weighted regression (GTWR) model to examine the real level of GTULU and ULUE in the Yangtze River Delta region (YRDR) from 2003 to 2020. Based on this, we investigate the spatiotemporal evolution characteristics and driving mechanisms of the two coupling coordination processes. The study found that: (1) from 2003 to 2020, the overall trend of the coupling coordination between GTULU and ULUE in the YRDR tended to be coordinated and developed, but still at a primary coordination level, with sufficient room for improvement in the future. (2) The coupling coordination level of each city in the YRDR from 2003 to 2020 showed obvious spatial non-equilibrium and correlation characteristics, initially exhibiting convergent growth and later showing polarization effects; the spatial pattern of high-value areas showed a regularity of prioritizing Shanghai and Zhejiang Province, gradually penetrating into Jiangsu Province and Anhui Province. (3) Economic and social factors positively impacted the coupling coordination degree. Natural factors had a mainly positive impact in the southern and northern regions and a mainly negative impact in the central and eastern regions. The impact of natural factors has undergone a transition from a mainly positive impact to a mainly negative impact. Research conclusions include establishing a regional collaborative development mechanism, utilizing the spatial spillover effect of leading cities; optimizing industrial structure, improving infrastructure, and increasing research investment further to expand the driving effects of economic and social factors; and optimizing the layout of urban and rural construction land, enhancing the connectivity and uniformity of land parcels, and suppressing the negative effects caused by natural factors.
Evaluating the impact of maternal non-communicable disease on adverse pregnancy outcomes and birthweight in Pakistan.
Authors: Wainwright Esther , Sheikh Irfan , Qureshi Rahat , Yousuf Sana , Khan Raheela , Elmes Matthew 
Published: July 2023

Abstract
Background
Non-communicable diseases (NCDs) account for 74% of all global deaths and disproportionately affect lower to middle-income countries (LMICs) like Pakistan. NCDs increase the risk of adverse pregnancy outcomes including preterm birth (PTB), caesarean section (CS) and low birthweight that negatively affect the mother, her offspring and future population health in an intergenerational cycle, resulting from adverse pregnancy outcomes significantly increasing development of NCDs in the adult offspring.
Methods
This study used multinomial logistic regression and generalised linear models to investigate the impact of common NCDs (type 1 and 2 diabetes, hypertension, asthma and thyroid disorders) on adverse pregnancy outcomes and birthweight in Pakistan. Retrospective data from 817 pregnant Pakistani women with pre-existing NCDs were adjusted for confounding factors to calculate odds ratios and means.
Results
Type 2 diabetes increased the risk of preterm birth (aOR 2.05, P = 0.044), elective CS (aOR 3.5, P = 0.036) and labour induction (aOR 3.29, P = 0.056). Elective CS risk was also increased significantly in mothers exhibiting hypertension (aOR 3.22, P = 0.033) or asthma (aOR 3.9, P = 0.011). Interestingly, preterm birth was significantly halved in pregnant mothers with asthma (aOR 0.4, P < 0.047). The only NCD disease to have a significant impact on birthweight was type 1 diabetes, where it was increased with a birthweight of 3253g compared to 2832g (P < 0.001). Operative deliveries were identified to be very high, with elective CS being the most common, increasingly significantly in 3 out of the 5 NCDs investigated. High operative deliveries may result from Pakistan’s privatised health care system and a lack of public awareness on the associated risks.
Conclusions
In conclusion, NCDs increase the risk of some adverse pregnancy outcomes. With the surprising finding that asthma halves PTB, further research to determine potential mechanisms and drug therapies to manage or prevent PTB are justified.
Association between Mitochondrial DNA Levels and Depression: A Systematic Review and Meta-Analysis
Authors: Li Wenhui , Zhu Lingqun , Chen Yi , Zhuo Yudi , Wan Shurun , Guo Rongjuan 
Published: July 2023

Abstract
Background
Disturbances in energy metabolism due to mitochondrial dysfunction have emerged as one of the important cause in the pathogenesis of depression. Many studies have found that mitochondrial DNA(mtDNA) content changes in the peripheral blood or cerebrospinal fluid of patients with depression. Some investigators ask whether it has a clear association between mtDNA and depression. Thus, we conducted a meta-analysis to comprehensively assess the evidence for mtDNA's effect on depression.
Methods
PubMed, Embase, the Cochrane Library, the Web of Science, Wanfang Database, SINOMED, China Science and Technology Journal Databaseand China National Knowledge Infrastructure were searched up to 13 March 2023. RevMan (version 5.4) and Stata (version 16.0) software were used for meta-analysis. Besides, publication bias was assessed with funnel plots, Begg’s test and Egger’s test.
Results
A total of 1372 patients were included in this study, including 686 patients with depression and 686 healthy controls. A meta-analysis including eleven studies showed significantly higher mtDNA level in depression compared with healthy controls [standardised mean difference(SMD) = 0.42, 95% confidence intervals(CI): 0.16, 0.69].
Conclusions
Our study demonstrates significantly higher mtDNA leveles in depression comparison to healthy controls.
Registration number: PROSPERO CRD42023414285.
Performance of monolayer Black Phosphorus DG-JLFET: An ab initio study
Authors: SANDA PANKAJ KUMAR , Dey Anup , Dhar Rudra Sankar 
Published: July 2023

Abstract
Two-dimensional materials are very promising for ultra-short channel future devices. This paper investigates, for the first time, the viability of the junction less transistors based on 2-D materials for future state-of-the-art technology nodes. Specifically, we investigate the performance of a Junction less monolayer black phosphorus (BP) FET (JLFET) with 12nm gate length using ab initio quantum transport simulations. The electrostatic control mechanism of the device and various intrinsic static and dynamic characteristics of the device are studied. The results reveal that BP JLFET performance can fulfill the benchmark requirement of International Roadmap for Devices and Systems (IRDS 2021) for 2028 in terms of HP and HD applications. Therefore, JLFET based on 2D materials can be a promising alternative for nano scale future device applications.
Nomogram to predict pathological axillary lymph node status after neoadjuvant therapy in triple negative or HER2 positive breast cancer
Authors: Chen Shujie , Zhang Qinyu , Ji Min , Yang Li , Wang Jie 
Published: July 2023

Abstract
Purpose: Axillary lymph node (ALN) pathologic complete remission (pCR) rate after neoadjuvant therapy (NAT) is high in triple negative (TN) or human epidermal growth factor receptor 2-positive (HER2+) breast cancer patients. We aimed to identify factors associated with pathological ALN status after NAT in these patients, and establish a nomogram model to avoid unnecessary ALND.
Methods: TN or HER2+ breast cancer patients receiving NAT in the Shanghai Jiao Tong University Breast Cancer Database (SJTU-BCDB) were retrospectively included in training cohort and internal validation cohort. Patients at the International Peace Maternity & Child Health Hospital (IPMCH) of China Welfare Institute were retrospectively collected for external validation. Based on univariate and multivariate logistic regression, a nomogram model was constructed to predict the probability of pathologically node-positive disease after NAT (ypN+) in TN or HER2+ patients.
Results: 1,686 patients were assigned to the training set, and 723 patients in the validation set. Five independent factors including clinical nodal (cN) stage (P < 0.001), molecular subtype (P < 0.001), Ki67 expression (P = 0.003), tumor grade (P < 0.001), and clinical complete response (P < 0.001) together with clinical tumor (cT) stage were selected to construct the nomogram. The nomogram indicated the areas under ROC curve (AUCs) were 0.782, 0.753 and 0.783 in training cohort, internal validation cohort and external validation cohort, respectively.
Conclusion: We developed a nomogram model for predicting the risk of ypN+ in TN or HER2+ breast cancer patients, which may guide the de-escalating ALN surgery after NAT.
Where do people with hypertension or type 2 diabetes seek care when ill? A cross-sectional study on sociodemographic correlates of utilization of healthcare facilities in rural Kenya
Authors: Schwarz MacKenna , Gyawali Bishal , Khamati Sylvia , Nkonge-Ngumba Dorothy Mwari , Ngure Miriam , Dræbel Tania Aase 
Published: July 2023

Abstract

Background
Hypertension and type 2 diabetes are among the most common non-communicable diseases that contribute to a large number of adult morbidity and mortality in Kenya. The impact of these conditions may pose the greatest challenge in rural areas with limited access to care. The objective of the study was to assess utilization of healthcare facilities (Primary, Secondary and Tertiary levels) and associated sociodemographic factors among people with hypertension or type 2 diabetes and/or at risk of having these conditions in rural Kenya.
Methods
This study used data from the 2019 Baseline Assessment of the Prevention and Control of Non-Communicable Disease Project in Imenti South, Meru County conducted by the Kenya Red Cross Society. A community-based study using a cross-sectional design was conducted among four hundred and thirty-five participants in Imenti South Sub Country, Meru County in Kenya in November 2019. Chi-square test and logistic regression analyses were conducted to explore sociodemographic factors associated with utilization of healthcare facilities. Unadjusted and adjusted Odds Ratios with a 95% Confidence Interval (CI) were reported.
Results
The mean age of the participants was 49.1 years (standard deviation [SD] = 17.6 years). Of the 435 participants, 51.30% (n = 223), 36.30% (n = 158), and 42.50% (n = 185) utilized primary, secondary and tertiary healthcare facilities respectively. Factors significantly associated with the utilization of a primary healthcare facility were participants living in Mitunguu region (adjusted OR 2.74, 95% CI 1.65–4.60), and College or University education (adjusted OR 0.15, 95% CI 0.04–0.60). Factors significantly associated with the utilization of a tertiary healthcare facility included age group > 40 years (adjusted OR 2.41, 95% CI 1.45-4.00), living in Igoji region (adjusted OR 2.19, 95% CI 1.22–3.11), and Mitunguu region (adjusted OR 0.26, 95% CI 0.15–0.48), College or University education (adjusted OR 8.53, 95% CI 1.97–36.87) and average monthly income (adjusted OR 2.29, 95% CI 1.28–4.08).
Conclusions
The utilization of the primary healthcare facility was associated with ward and educational level, and the utilization of the tertiary healthcare facility was associated with age, ward, educational level, and average monthly income among rural Kenyans who had hypertension or type 2 diabetes and/or were at risk of having these conditions. These results provide insights regarding the sociodemographic factors associated with the utilization of healthcare facilities in rural Kenya that could contribute to evidence-based health policymaking. Additionally, the results highlight the relevance of taking sociodemographic factors into account when designing interventions for people with non-communicable diseases living in rural Kenya.
Characteristics and Risk Factors of Axillary Lymph Node Metastasis of Microinvasive Breast Cancer
Authors: Lee Soo-Young , Lee Sae Byul , Yoo Tae-Kyung , Kim Jisun , Chung Il Yong , Ko Beom Seok , Kim Hee Jeong , Lee Jong Won , Son Byung Ho 
Published: July 2023

Abstract

Purpose
We aimed to select patients who would benefit most from sentinel lymph node biopsy (SLNB) by investigating the characteristics and risk factors of axillary lymph node metastasis (ALNM) of microinvasive breast cancer (MIBC).
Methods
This retrospective study included 1,688 patients with MIBC who underwent breast surgery with axillary staging at the Asan Medical Center from 1995 to 2020.
Results
Most patients underwent SLNB alone (83.5%). Seventy (4.1%) patients were node-positive, and the majority had positive lymph nodes < 10 mm, with micrometastasis occurring most frequently (n = 37, 55%). Node-positive patients were more likely to have undergone total mastectomy and axillary lymph node dissection (ALND) compared to node-negative patients (p < 0.001). In the multivariate analysis, independent predictors of ALNM included young age (OR = 0.960; 95% CI: 0.927–0.995; p = 0.023), ALND (OR = 5.285; 95% CI: 2.576–10.842; p < 0.001), more number of harvested lymph nodes (OR = 1.194; 95% CI: 1.119–1.274; p < 0.001), lymphovascular invasion (OR = 8.058; 95% CI: 2.750–23.354; p < 0.001), multiple foci of microinvasion (OR = 2.953; 95% CI: 1.444–6.041; p = 0.003), and hormone receptor positivity (OR = 2.628; 95% CI: 1.293–5.342; p = 0.008).
Conclusion
A low ALNM rate of 4.1% suggested that routine SLNB for patients with MIBC is unnecessary; however, it can be valuable for selecting patients with specific risk factors. Alongside ongoing trials omitting SLNB in early breast cancer, further sub-analyses focusing on this rare population with MIBC are necessary.
Voxelated Opto-Physically Unclonable Functions via Irreplicable Wrinkles
Authors: Na Jun-Hee , Kim Kitae , Choi Moon-Young , Saeed Mohsin , Kim Se-Um , Kim Youngmin 
Published: July 2023

Abstract
The increasing prevalence of the Internet of Things (IoT) and the integration of digital technology into our daily lives have heightened security risks, necessitating more robust security measures. Physical unclonable functions (PUFs) have emerged as a promising solution, and PUFs offer a highly secure method to generate unpredictable and unique random digital values by leveraging inherent physical characteristics. However, traditional PUF implementations often involve complex hardware and circuitry, which can increase system costs and complexity. We propose an innovative approach utilizing a random wrinkles PUF (rw-PUF) based on a unique optical anisotropy and facile procedure. The rw-PUF consists of liquid crystal molecules with random orientations, resulting in a two-dimensional retardation map corresponding to a complex birefringence pattern. Moreover, our proposed technique allows for customization based on specific requirements using a spatial light modulator, enabling fast fabrication. One notable advantage of the rw-PUF is its ability to store multiple data sets within a single PUF without needing physical alterations. Additionally, we introduce the concept of "polyhedron authentication", which utilizes three-dimensional information storage in a voxelated rw-PUF. This approach demonstrates the feasibility of implementing high-level security technology by leveraging the unique properties of the rw-PUF.
Publicly Funded Health Insurance &amp; the Extent of Out-of-pocket Expenditure among the Elderly in India
Authors: Bose Montu 
Published: July 2023

Abstract
The paper attempts to study the effectiveness of publicly funded health insurance (PFHI) schemes in increasing the utilization of hospitalization care service and to reduce the extent of out-of-pocket expenditure (OOPE) among the elderly in India. Using nationally representative data for 2014 and 2017-18 and applying log-linear model, binary logistic regression and propensity score matching techniques the study demonstrates that utilization has increased among the elderly and corresponding OOPE has also decreased. Additionally, elderly with PFHI facilities is paying significantly lower OOPE during hospitalization compared to those elderly who are not covered in the schemes. Analysis also indicates that cost of providing the service is substantially lower in the public facilities compared to the private hospitals. Therefore, strengthening public facilities are suggested to improve in access to healthcare services and to achieve the Universal Health Coverage (UHC) goals of the country.
Deubiquitylating enzyme OTUB1 facilitates neuronal survival after intracerebral hemorrhage via inhibiting NF-κB-triggered apoptotic cascades
Authors: Shen Jiabing , Xue Xiaoli , Yuan Huimin , Song Yan , Wang Jinglei , Cui Ronghui , Ke Kaifu 
Published: July 2023

Abstract
The deubiquitylase OTU domain-containing ubiquitin aldehyde-binding protein 1 (OTUB1) has been implicated in the pathogenesis of various human diseases. However, the molecular mechanism by which OTUB1 participates in the pathogenesis of intracerebral hemorrhage (ICH) remains elusive. In the present study, we established an autologous whole blood fusion-induced ICH model in C57BL/6J mice. We showed that the upregulation of OTUB1 contributes to the attenuation of Nuclear factor kappa B (NF-κB) signaling and its downstream apoptotic signaling after ICH. OTUB1 directly associates with NF-κB precursors p105 and p100 after ICH, leading to attenuated polyubiquitylation of p105 and p100. Moreover, we revealed that NF-κB signaling was modestly activated both in ICH tissues and hemin-exposed HT-22 neuronal cells, accompanied with the activation of NF-κB downstream pro-apoptotic signaling. Notably, overexpression of OTUB1 strongly inhibited hemin-induced NF-κB activation, whereas interference of OTUB1 led to the opposite effect. Finally, we revealed that lentiviral transduction of OTUB1 markedly ameliorated hemin-induced apoptotic signaling and HT-22 neuronal death. Collectively, these findings suggest that the upregulation of OTUB1 serves as a neuroprotective mechanism in antagonizing neuroinflammation-induced NF-κB signaling and neuronal death, shed new light on manipulating intracellular deubiquitylating pathways as novel interventive approaches against ICH-induced secondary neuronal damage and death.