bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microglial function, INPP5D/SHIP1 signaling, and NLRP3 inflammasome activation: implications for Alzheimer’s disease
Authors: Terzioglu Gizem , Young-Pearse Tracy L. 
Published: November 2023

AbstractRecent genetic studies on Alzheimer’s disease (AD) have brought microglia under the spotlight, as loci associated with AD risk are enriched in genes expressed in microglia. Several of these genes have been recognized for their central roles in microglial functions. Increasing evidence suggests that SHIP1, the protein encoded by the AD-associated gene INPP5D, is an important regulator of microglial phagocytosis and immune response. A recent study from our group identified SHIP1 as a negative regulator of the NLRP3 inflammasome in human iPSC-derived microglial cells (iMGs). In addition, we found evidence for a connection between SHIP1 activity and inflammasome activation in the AD brain. The NLRP3 inflammasome is a multiprotein complex that induces the secretion of pro-inflammatory cytokines as part of innate immune responses against pathogens and endogenous damage signals. Previously published studies have suggested that the NLRP3 inflammasome is activated in AD and contributes to AD-related pathology. Here, we provide an overview of the current understanding of the microglial NLRP3 inflammasome in the context of AD-related inflammation. We then review the known intracellular functions of SHIP1, including its role in phosphoinositide signaling, interactions with microglial phagocytic receptors such as TREM2 and evidence for its intersection with NLRP3 inflammasome signaling. Through rigorous examination of the intricate connections between microglial signaling pathways across several experimental systems and postmortem analyses, the field will be better equipped to tailor newly emerging therapeutic strategies targeting microglia in neurodegenerative diseases.
Presence of variable extrathoracic airflow limitation in patients with a negative methacholine challenge test
Authors: Elfessi Zane Z. , Zavala Sarah , Rubinstein Israel 
Published: November 2023

Abstract
Purpose
Determine whether variable extrathoracic airflow limitation (VEAL) is observed in patients with negative methacholine challenge tests (MCT).

Methods
Electronic medical records of patients undergoing MCT at Jesse Brown VA Medical Center between January 2017 and December 2019 were reviewed. Only patients with negative MCT were selected. Pertinent demographic, clinical, and pulmonary function tests (PFT) and MCT data were abstracted from each record. Spirometric flow-volume loops recorded during each test were inspected by one co-author to determine the first inhaled methacholine concentration at which FEF50/FIF50 was either > 1 or further increased if baseline FEF50/FIF50 after nebulized saline (vehicle) already exceeded 1. Student’s t-test was used for statistical analysis. P < 0.05 was considered statistically significant.

Results
One hundred and twenty-seven consecutive patients with normal baseline PFT and negative MCT were identified. Thirteen patients (10.2%) had negative MCT and FEF50/FIF50 > 1 after testing. They were predominately obese (BMI, 31.3 ± 6.6), non-smoking (10), White (8) males (9) aged 51.3 ± 14.1 years (mean ± SD) referred for symptoms suggestive of asthma (n = 7) or for chronic cough (n = 6). Five had obstructive sleep apnea, three gastroesophageal reflux disease, and two chronic rhinosinusitis. FEF50/FIF50 increased significantly from 0.72 ± 0.21 after nebulized saline (vehicle) to 1.21 ± 0.13 after inhaled methacholine (p < 0.001). Median inhaled methacholine concentration eliciting these responses was 1.0 mg/mL (range, 0.25–16 mg/mL).

Conclusions
VEAL is observed in a subset of patients with a negative MCT. This phenomenon should be recognized and reported to the referring healthcare providers and its clinical significance addressed as indicated.
Spinal cord ischemia revealed by a Brown-Sequard syndrome and caused by a calcified thoracic disc extrusion with spontaneous regression: a case report and review of the literature
Authors: Petrovic Sonja , Le Forestier Nadine , Pradat Pierre-François , Pascal-Moussellard Hugues , Chougar Lydia 
Published: November 2023

Abstract
Background
Thoracic disc herniation is relatively uncommon, accounting for less than 1% of all spinal herniations. Although most often asymptomatic, they may represent a rare cause of spinal cord ischemia.

Case report
We report the case of a healthy 43-year-old North African male who presented with a Brown-Sequard syndrome revealing a spinal cord ischemia caused by a thoracic disc extrusion. The initial MRI revealed a calcified disc extrusion at the level of T5-T6 without significant spinal cord compression or signal abnormality. A pattern consistent with a medullary ischemia only appeared 48 h later. The patient was treated conservatively with Aspirin and Heparin, which were discontinued later because of a negative cardiovascular work-up. The calcified disc extrusion, which was later recognized as the cause of the ischemia, decreased spontaneously over time and the patient recovered within a few months.

Conclusions
Our case highlights the challenge in diagnosing and managing this uncommon condition. We propose a literature review showing the different therapeutic strategies and their corresponding clinical outcomes.
Three systems of molecular markers reveal genetic differences between varieties sabina and balkanensis in the Juniperus sabina L. range
Authors: Jadwiszczak Katarzyna A. , Mazur Małgorzata , Bona Agnieszka , Marcysiak Katarzyna , Boratyński Adam 
Published: November 2023

Abstract
Key message
J. sabina var. balkanensis, that is of hybrid origin, and its maternal progenitor J. sabina var. sabina are genetically distinct with respect to cpDNA, SNP, and SilicoDArT loci. Mostly non-overlapping distributions of the sabina and balkanensis varieties are the result of their different climatic requirements.

Context
Juniperus sabina L. is present in the Eurasian mountains, but its range is severely fragmented. In Europe, two varieties of J. sabina occur: var. sabina and var. balkanensis, the latter being an allotetraploid hybrid between the diploid var. sabina and a tetraploid ancestor of Juniperus thurifera L. The distribution of the two varieties is mostly disjunct.

Aims
Assess the taxonomic affiliation and genetic differentiation of the populations of var. sabina and var. balkanensis in Europe and Asia using cpDNA, SilicoDArT, and SNP markers. Identify climatic niches of both juniper varieties in Europe.

Methods
Altogether, 21,134 SilicoDArT, 8,579 SNP, and four cpDNA loci were used. Seven climatic variables were compared in sites inhabited by var. balkanensis and the two parental species.

Results
The SilicoDArTs and SNPs revealed a pattern of population differentiation that was congruent with the cpDNA analysis. The hybrid var. balkanensis occupies habitats with higher temperatures and intermediate levels of precipitation compared to both parental taxa.

Conclusion
The low genetic variation and significant genetic differentiation among J. sabina populations likely result from the restriction of gene flow imposed by the mountain ranges. The balkanensis variety is able to cope with hot and dry climates probably thanks to the admixture of J. thurifera genes.
The role of intraoperative neurophysiological monitoring in intramedullary spinal cord tumor surgery
Authors: Liu Kai , Ma Chengyuan , Li Dapeng , Li Haisong , Dong Xuechao , Liu Bo , Yu Ying , Fan Yuxiang , Song Hongmei 
Published: November 2023

Abstract Intramedullary tumors are a class of central nervous system tumors with an incidence of 2 to 4%. As they are located very deep and frequently cause postoperative neurological complications, surgical resection is difficult. In recent years, many surgeons have performed electrophysiological monitoring to effectively reduce the occurrence of postoperative neurological complications. Modern electrophysiological monitoring technology has advanced considerably, leading to the development of many monitoring methods, such as SSEPs, MEPs, DCM, and EMG, to monitor intramedullary tumors. However, electrophysiological monitoring in tumor resection is still being studied. In this article, we discussed the different monitoring methods and their role in monitoring intramedullary tumors by reviewing previous studies. Intratumorally tumors need to be monitored for a summary of the condition of the patient. Only by using various monitoring methods flexibly and through clear communication between surgeons and neurophysiological experts can good decisions be made during surgery and positive surgical results be achieved.
Bayesian multilevel modelling of the association between socio-economic status and stunting among under-five-year children in Tanzania
Authors: Musheiguza Edwin , Mbegalo Tukae , Mbukwa Justine N. 
Published: November 2023

Abstract
Background
Stunting is associated with socioeconomic status (SES) which is multidimensional. This study aimed to compare different SES indices in predicting stunting.

Methods
This was the secondary data analysis using Tanzania Demographics and Health Surveys (TDHS). The study used 7492, 6668, and 8790 under-five-year children from TDHS 2004/5, 2010, and 2015/16, respectively. The Household Wealth Index (HWI); Water and Sanitation, Assets, Maternal education and Income (WAMI); Wealth Assets, Education, and Occupation (WEO); and the Multidimensional Poverty Index (MPI) indices were compared. The summated scores, principal component analysis (PCA), and random forest (RF) approaches were used to construct indices. The Bayesian and maximum likelihood multilevel generalized linear mixed models (MGLMM) were constructed to determine the association between each SES index and stunting.

Results
The study revealed that 42.3%, 38.4%, and 32.4% of the studied under-five-year children were stunted in 2004/5, 2010, and 2015/16, respectively. Compared to other indicators of SES, the MPI had a better prediction of stunting for the TDHS 2004/5 and 2015/16, while the WAMI had a better prediction in 2010. For each score increase in WAMI, the odds of stunting were 64% [BPOR = 0.36; 95% CCI 0.3, 0.4] lower in 2010, while for each score increase in MPI there was 1 [BPOR = 1.1; 95% CCI 1.1, 1.2] times higher odds of stunting in 2015/16.

Conclusion
The MPI and WAMI under PCA were the best measures of SES that predict stunting. Because MPI was the best predictor of stunting for two surveys (TDHS 2004/5 and 2015/16), studies dealing with stunting should use MPI as a proxy measure of SES. Use of BE-MGLMM in modelling stunting is encouraged. Strengthened availability of items forming MPI is inevitable for child growth potentials. Further studies should investigate the determinants of stunting using Bayesian spatial models to take into account spatial heterogeneity.
Pierre Joris and “The Whole Celan”—a Life's Work
Authors: Frank Christine 
Published: November 2023

Abstract
Pierre Joris is one of the most distinguished translators of the poetry of Paul Celan into English. He is the only person to have translated Celan's complete poetic works and prose over the course of more than fifty years, creating a life's work. His translations, begun in 1967 and published between 1995 and 2020, have had and continue to have a lasting influence on readings and translations of Celan in the United States. This essay outlines the particular challenges that Celan's language poses to the translator; revisits the development of Joris's Celan translations; and provides an example examination using the poem “Todtnauberg,” in which Celan reflects on his encounter with Martin Heidegger. It was Joris's translation of this poem that inspired the poet Charles Bernstein to undertake his own translation experiment.
L’état Naissant: On Celan's Microliths They Are, Little Stones: Posthumous Prose
Authors: Carder Austin 
Published: November 2023

Abstract
Microliths They Are, Little Stones: Posthumous Prose (2020) represents the culmination of Pierre Joris's fifty-year effort of translating the work of Paul Celan into English. The book contains a small library: aphorisms, fiction, dialogues and notes for dramatic works, theoretical prose, interviews, as well as illustrations. This review essay primarily focuses on notes and drafts toward an unfinished essay called “On the Darkness of Poetry.” It is a major statement of Celan's poetics and still stands as an unmet challenge to poets writing today. Its unfinished state should not be considered a liability but read instead as a formal argument (albeit unintended) that “the alleged thought- or language-scheme of the poem is never ‘finished.’”
Worst-Case Iteration Bounds for Log Barrier Methods on Problems with Nonconvex Constraints
Authors: Hinder Oliver , Ye Yinyu 
Published: November 2023

Interior point methods (IPMs) that handle nonconvex constraints such as IPOPT, KNITRO and LOQO have had enormous practical success. We consider IPMs in the setting where the objective and constraints are thrice differentiable, and have Lipschitz first and second derivatives on the feasible region. We provide an IPM that, starting from a strictly feasible point, finds a μ-approximate Fritz John point by solving [Formula: see text] trust-region subproblems. For IPMs that handle nonlinear constraints, this result represents the first iteration bound with a polynomial dependence on [Formula: see text]. We also show how to use our method to find scaled-KKT points starting from an infeasible solution and improve on existing complexity bounds. Funding: This work was supported by Air Force Office of Scientific Research [9550-23-1-0242]. A significant portion of this work was done at Stanford where O. Hinder was supported by the PACCAR, Inc., Stanford Graduate Fellowship and the Dantzig-Lieberman fellowship.
The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples
Authors: Heupink Tim H. , Verboven Lennert , Sharma Abhinav , Rennie Vincent , de Diego Fuertes Miguel , Warren Robin M. , Van Rie Annelies 
Published: November 2023

Background
Whole genome sequencing (WGS) holds great potential for the management and control of tuberculosis. Accurate analysis of samples with low mycobacterial burden, which are characterized by low (<20x) coverage and high (>40%) levels of contamination, is challenging. We created the MAGMA (Maximum Accessible Genome for Mtb Analysis) bioinformatics pipeline for analysis of clinical Mtb samples.

Methods and results
High accuracy variant calling is achieved by using a long seedlength during read mapping to filter out contaminants, variant quality score recalibration with machine learning to identify genuine genomic variants, and joint variant calling for low Mtb coverage genomes. MAGMA automatically generates a standardized and comprehensive output of drug resistance information and resistance classification based on the WHO catalogue of Mtb mutations. MAGMA automatically generates phylogenetic trees with drug resistance annotations and trees that visualize the presence of clusters. Drug resistance and phylogeny outputs from sequencing data of 79 primary liquid cultures were compared between the MAGMA and MTBseq pipelines. The MTBseq pipeline reported only a proportion of the variants in candidate drug resistance genes that were reported by MAGMA. Notable differences were in structural variants, variants in highly conserved rrs and rrl genes, and variants in candidate resistance genes for bedaquiline, clofazmine, and delamanid. Phylogeny results were similar between pipelines but only MAGMA visualized clusters.

Conclusion
The MAGMA pipeline could facilitate the integration of WGS into clinical care as it generates clinically relevant data on drug resistance and phylogeny in an automated, standardized, and reproducible manner.
Diagnostic accuracy of qPCR and microscopy for cutaneous leishmaniasis in rural Ecuador: A Bayesian latent class analysis
Authors: Bezemer Jacob M. , Merckx Joanna , Freire Paspuel Byron P. , Calvopiña Manuel , de Vries Henry J. C. , Schallig Henk D. F. H. , Leeflang Mariska M. G. , Dendukuri Nandini 
Published: November 2023

Background
Clinical and laboratory diagnosis of cutaneous leishmaniasis (CL) is hampered by under-ascertainment of direct microscopy.

Methods
This study compared the diagnostic accuracy of qPCR on DNA extracted from filter paper to the accuracy of direct smear slide microscopy in participants presenting with a cutaneous lesion suspected of leishmaniasis to 16 rural healthcare centers in the Ecuadorian Amazon and Pacific regions, from January 2019 to June 2021. We used Bayesian latent class analysis to estimate test sensitivity, specificity, likelihood ratios (LR), and predictive values (PV) with their 95% credible intervals (95%CrI). The impact of sociodemographic and clinical characteristics on predictive values was assessed as a secondary objective.

Results
Of 320 initially included participants, paired valid test results were available and included in the diagnostic accuracy analysis for 129 from the Amazon and 185 from the Pacific region. We estimated sensitivity of 68% (95%CrI 49% to 82%) and 73% (95%CrI 73% to 83%) for qPCR, and 51% (95%CrI 36% to 66%) and 76% (95%CrI 65% to 86%) for microscopy in the Amazon and Pacific region, respectively. In the Amazon, with an estimated disease prevalence among participants of 73%, negative PV for qPCR was 54% (95%CrI 5% to 77%) and 44% (95%CrI 4% to 65%) for microscopy. In the Pacific, (prevalence 88%) the negative PV was 34% (95%CrI 3% to 58%) and 37% (95%CrI 3% to 63%). The addition of qPCR parallel to microscopy in the Amazon increases the observed prevalence from 38% to 64% (+26 (95%CrI 19 to 34) percentage points).

Conclusion
The accuracy of either qPCR on DNA extracted from filter paper or microscopy for CL diagnosis as a stand-alone test seems to be unsatisfactory and region-dependent. We recommend further studies to confirm the clinically relevant increment found in the diagnostic yield due to the addition of qPCR.
Preschool or/and kindergarten? The long-term benefits of different types of early childhood education on pupils’ skills
Authors: Tang Yalin , Luo Renfu , Shi Yaojiang , Xie Gang , Chen Siwei , Liu Chengfang 
Published: November 2023

Background
Developing countries have witnessed great progress in early childhood education (ECE) enrollment rate over the past three decades. Preschool and kindergarten are the two most common types of ECE in developing countries. Questions remain as to which of the two types of ECE is more effective in promoting child development in developing countries, including both cognitive and non-cognitive skills. The objective of this paper is to examine the long-term benefits of attending preschool or/and kindergarten on pupils’ cognitive and non-cognitive skills in rural China.

Methodology
We pooled data from two large-scale surveys conducted by the authors themselves at 136 rural primary schools in 20 counties from three provinces in northwestern China in 2009. The final study sample consisted of 9,839 pupils who both reported their ECE experience and completed cognitive and non-cognitive tests. We measured pupils’ cognitive skills by standardized math test scores and grade retention, and their non-cognitive skills by both self-reported self-efficacy, mental health, and teacher-reported behaviors. Inverse Probability Weighting (IPW) was used to balance the pre-treatment variables between the treatment (Any ECE, Preschool Only, Kindergarten Only, or Preschool+Kindergarten) and comparison (No ECE) groups.

Results
Results from IPW show that compared with their peers without any ECE experience, pupils with any ECE experience perform better in cognitive skills (0.118 standard deviations (s.d.) increase in the TIMSS, 7.1 percentage point (pp) decrease in the probability of grade retention) but not in non-cognitive skills. By ECE types, attending kindergarten only is associated with a 0.150 s.d. increase in the TIMSS, a 7.0 pp decrease in the probability of grade retention, and a 0.059 s.d. decrease in the index of behavioral problems of pupils. Moreover, attending both preschool and kindergarten predicts a lower probability of grade retention, but attending preschool only has few benefits. Heterogenous analyses suggest that the long-term benefits of ECE are more prominent among the Han pupils from households with higher socio-economic status.

Conclusions
Our findings imply that increasing access to ECE can be an effective instrument to improve pupils’ skills in less-developed rural areas of China, especially their cognitive skills. Among different types of ECE, attending kindergarten contributes more to pupils’ skill development in rural China than other types. We call for strengthened efforts to ensure equal access to quality ECE for preschool-aged children in rural China.
BushenHuoxue formula promotes osteogenic differentiation via affecting Hedgehog signaling pathway in bone marrow stem cells to improve osteoporosis symptoms
Authors: Chen Yuqi , Wei ZhiYong , Shi HongXia , Wen Xin , Wang YiRan , Wei Rong 
Published: November 2023

Background
The BushenHuoxue formula (BSHX) has been previously demonstrated to ameliorate osteoporosis, but the mechanisms underlying this phenomenon are currently unclear. The present study aims at investigating the mechanisms that BSHX induces osteogenesis.

Methods
We established an osteoporosis model in rats by bilateral ovariectomy and then treated the rats with an osteogenic inducer (dexamethasone, β-sodium glycerophosphate and Vitamin C) and BSHX. After that, bone marrow density and histopathological bone examination were evaluated by using HE staining and immunohistochemistry, respectively. We also assessed the differentiation of bone marrow mesenchymal stem cells (BMSCs) into osteoblasts by using immunofluorescence staining. ALP, BMP, and COL1A1 levels were determined by ELISA. We identified genes involved in pathogenesis of osteoporosis through Gene Expression Omnibus (GEO) database and subsequently selected Hedgehog signaling-related genes Shh, Ihh, Gli2, and Runx2 for assessment via qRT-PCR and ELISA, Western blotting. Network pharmacology analysis was performed to identify bioactive metabolites of BSHX.

Results
BSHX treatment in osteoporosis model rats promoted tightening of the morphological structure of the trabecular bone and increased the bone mineral density (BMD). BSHX also increased levels of osteoblast makers ALP, BMP, and COL1A1. Additionally, bioinformatics analysis of the GEO dataset showed that Hedgehog signaling pathway was involved in pathogenesis of osteoporosis, especially related genes Shh, Ihh, Gli2, and Runx2. Remarkably, BHSX upregulated these genes indispensably involved in the osteogenesis-related Hedgehog signaling pathway in both bone tissue and BMSCs. Importantly, we identified that quercetin was the active compounds that involved in the mechanism of BSHX-improved OP via affecting Hedgehog-related genes.

Conclusion
Our results indicate that BSHX promotes osteogenesis by improving BMSC differentiation into osteoblasts via increased expression of Hedgehog signaling-related genes Shh, Ihh, Gli2, and Runx2, and quercetin was the bioactive compound of BSHX.