bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caustics and velocity caustics in the diffuse interstellar medium at high Galactic latitudes
Authors: Kalberla P. M. W. 
Published: December 2023

Context. The far-infrared (FIR) distribution at high Galactic latitudes, observed with Planck, is filamentary with coherent structures in polarization. These structures are also closely related to H I filaments with coherent velocity structures. There is a long-standing debate about the physical nature of these structures. They are considered either as velocity caustics, fluctuations engraved by the turbulent velocity field or as cold three-dimensional density structures in the interstellar medium (ISM).
Aims. We discuss different approaches to data analysis and interpretation in order to work out the differences.
Methods. We considered mathematical preliminaries for the derivation of caustics that characterize filamentary structures in the ISM. Using the Hessian operator, we traced individual FIR filamentary structures in H I from channel maps as observed and alternatively from data that are provided by the velocity decomposition algorithm (VDA). VDA is claimed to separate velocity caustics from density effects.
Results. Based on the strict mathematical definition, the so-called velocity caustics are not actually caustics. These VDA data products may contain caustics in the same way as the original H I observations. Caustics derived by a Hessian analysis of both databases are nearly identical with a correlation coefficient of 98%. However, the VDA algorithm leads to a 30% increase in the alignment uncertainties when fitting FIR/H I orientation angles. Thus, the VDA velocity crowding concept fails to explain the alignment of FIR/H I filaments at |b| > 20°. We used H I absorption data to constrain the physical nature of FIR/H I filaments and determine spin temperatures and volume densities of FIR/H I filaments. H I filaments exist as cold neutral medium (CNM) structures; outside the filaments no CNM absorption is detectable.
Conclusions. The CNM in the diffuse ISM is exclusively located in filaments with FIR counterparts. These filaments at high Galactic latitudes exist as cold density structures; velocity crowding effects are negligible.
Availability of web servers significantly boosts citations rates of bioinformatics methods for protein function and disorder prediction
Authors: Song Jiangning , Kurgan Lukasz 
Published: December 2023

Abstract

Motivation
Development of bioinformatics methods is a long, complex and resource-hungry process. Hundreds of these tools were released. While some methods are highly cited and used, many suffer relatively low citation rates. We empirically analyze a large collection of recently released methods in three diverse protein function and disorder prediction areas to identify key factors that contribute to increased citations.

Results
We show that provision of a working web server significantly boosts citation rates. On average, methods with working web servers generate three times as many citations compared to tools that are available as only source code, have no code and no server, or are no longer available. This observation holds consistently across different research areas and publication years. We also find that differences in predictive performance are unlikely to impact citation rates. Overall, our empirical results suggest that a relatively low-cost investment into the provision and long-term support of web servers would substantially increase the impact of bioinformatics tools.
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph
Authors: Liu Ting , Feenstra K Anton , Huang Zhisheng , Heringa Jaap 
Published: December 2023

Abstract

Motivation
Up-to-date pathway knowledge is usually presented in scientific publications for human reading, making it difficult to utilize these resources for semantic integration and computational analysis of biological pathways. We here present an approach to mining knowledge graphs by combining manual curation with automated named entity recognition and automated relation extraction. This approach allows us to study pathway-related questions in detail, which we here show using the ketamine pathway, aiming to help improve understanding of the role of gut microbiota in the antidepressant effects of ketamine.

Results
The thus devised ketamine pathway ‘KetPath’ knowledge graph comprises five parts: (i) manually curated pathway facts from images; (ii) recognized named entities in biomedical texts; (iii) identified relations between named entities; (iv) our previously constructed microbiota and pre-/probiotics knowledge bases; and (v) multiple community-accepted public databases. We first assessed the performance of automated extraction of relations between named entities using the specially designed state-of-the-art tool BioKetBERT. The query results show that we can retrieve drug actions, pathway relations, co-occurring entities, and their relations. These results uncover several biological findings, such as various gut microbes leading to increased expression of BDNF, which may contribute to the sustained antidepressant effects of ketamine. We envision that the methods and findings from this research will aid researchers who wish to integrate and query data and knowledge from multiple biomedical databases and literature simultaneously.

Availability and implementation
Data and query protocols are available in the KetPath repository at https://dx.doi.org/10.5281/zenodo.8398941 and https://github.com/tingcosmos/KetPath.
Vitamin D3 promotes fish oocyte development by directly regulating gonadal steroid hormone synthesis
Authors: Yang Gang , Cheng Ke , Huang Yanqing , Wang Chunfang 
Published: December 2023

Abstract
Vitamin D receptors and vitamin D3-metabolizing enzymes have been found to be highly expressed in the ovaries and spermatophores of fish. However, the role of vitamin D3 on fish gonadal development has rarely been reported. In this study, 2-month-old female zebrafish were fed with different concentrations of vitamin D3 diets (0, 700, 1400, and 11 200 IU/kg) to investigate the effects of vitamin D3 on ovarian development. The diet with 0 IU/kg vitamin D3 resulted in elevated interstitial spaces, follicular atresia, and reproductive toxicity in zebrafish ovaries. Supplementation with 700 and 1400 IU/kg of vitamin D3 significantly increased the oocyte maturation rate; upregulated ovarian gonadal steroid hormone synthesis capacity; and elevated plasma estradiol, testosterone, and ovarian vitellogenin levels. Furthermore, the current study identified a vitamin D response element in the cyp19a1a promoter and demonstrated that 1.25(OH)2D3-vitamin D response directly activated cyp19a1a production through activating the vitamin D response element. In conclusion, this study shows that an appropriate concentration of vitamin D3 can promote zebrafish ovarian development and affect vitellogenin synthesis through the vdr/cyp19a1a/er/vtg gene axis.
Pathological shifts in tryptophan metabolism in human term placenta exposed to LPS or poly I:C
Authors: Abad Cilia , Karahoda Rona , Orbisova Anna , Kastner Petr , Heblik Daniel , Kucera Radim , Portillo Ramon , Staud Frantisek 
Published: December 2023

Abstract
Maternal immune activation during pregnancy is a risk factor for offspring neuropsychiatric disorders. Among the mechanistic pathways by which maternal inflammation can affect fetal brain development and programming, those involving tryptophan (TRP) metabolism have drawn attention because various TRP metabolites have neuroactive properties. This study evaluates the effect of bacterial (lipopolysaccharides/LPS) and viral (polyinosinic:polycytidylic acid/poly I:C) placental infection on TRP metabolism using an ex vivo model. Human placenta explants were exposed to LPS or poly I:C, and the release of TRP metabolites was analyzed together with the expression of related genes and proteins and the functional activity of key enzymes in TRP metabolism. The rate-limiting enzyme in the serotonin pathway, tryptophan hydroxylase, showed reduced expression and functional activity in explants exposed to LPS or poly I:C. Conversely, the rate-limiting enzyme in the kynurenine pathway, indoleamine dioxygenase, exhibited increased activity, gene, and protein expression, suggesting that placental infection mainly promotes TRP metabolism via the kynurenine (KYN) pathway. Furthermore, we observed that treatment with LPS or poly I:C increased activity in the kynurenine monooxygenase branch of the KYN pathway. We conclude that placental infection impairs TRP homeostasis, resulting in decreased production of serotonin and an imbalance in the ratio between quinolinic acid and kynurenic acid. This disrupted homeostasis may eventually expose the fetus to suboptimal/toxic levels of neuroactive molecules and impair fetal brain development.
‘We Taught You How to Teach Us’: An Autoethnography of Decolonising of Social Work Education in a Programme for Bedouin-Arab Social Workers in Israel
Authors: Segev Einav , Allassad Alhuzail Nuzha 
Published: December 2023

Abstract
The need to decolonise social work education has become prominent in curricula developed over the past years. The curriculum in social work schools defines and shapes ways of knowing largely in terms of privileged Western knowledge. It is therefore necessary to change it and adopt pedagogical approaches more suitable for populations from different cultures. This article presents a study on a dedicated training programme for Bedouin-Arab social workers in Israel. Its pedagogies are informed by decolonised and culturally adapted social work education. This qualitative study was conducted in a teacher-researcher reflexive autoethnography approach, based on documentation of thirty-six lessons and reflections by the programme lecturers and on a thematic analysis of their experiences as social work educators. The findings present several pedagogies in terms of ‘bridge’: the pedagogic, the cultural sensitivity, the theory–practice and the safe space bridge. These expand the knowledge base in social work education beyond Western knowledge, demonstrating how knowledge practices unique to different cultures and identities may be adopted and adapted within it. Based on these findings, it is suggested to transform and enrich social work education by decolonising it to include new knowledge from diverse populations.
Expression and clinical diagnostic value of CCHE1 in breast cancer
Authors: Zhao Feng , Zhou Wenjuan , Xin Ran , Miao Xin 
Published: December 2023

Abstract

Objective
Breast cancer is a malignant tumor in the epithelial tissue of the breast gland. This study aimed to unveil the expression and clinical diagnostic value of lncRNA cervical cancer high-expressed 1 (CCHE1) in breast cancer.

Methods
CCHE1 expression in breast cancer tissues was evaluated by RT-qPCR. The relationship between the CCHE1 expression and clinicopathological features of breast cancer was analyzed with the chi-square test, and the survival of breast cancer patients was evaluated with the Kaplan–Meier method. The diagnostic value of CCHE1 expression for breast cancer was evaluated by using the receiver operating characteristics (ROC) curve. Breast cancer cell lines (SKBR3, T47D, BT474, and MCF-7) were cultured for detecting CCHE1 expression in the cells. MCF-7 cells were selected for the subsequent experiments, and the small interfering RNA of CCHE1 (si-CCHE1) and CCHE1 overexpression vector (pcDNA-CCHE1) were transfected into MCF-7 cells. The proliferation, migration, and invasive ability were assessed by CCK-8 and Transwell assays. The influence of CCHE1 on the growth of tumors was validated by nude mice xenograft assay.

Results
CCHE1 was up-regulated in breast cancer tissues and breast cancer cells. The high expression level of CCHE1 in cancer tissues of breast cancer patients was correlated with larger tumor size, advanced TNM stage, Ki-67 status, and lymph node metastasis. The area under the ROC curve for CCHE1 in the diagnosis of breast cancer was 0.983 (95% CI: 0.966–1.000), with a sensitivity of 95.00% and a specificity of 91.70%. The 5-year survival rate was higher in patients with low CCHE1 expression than those with high CCHE1 expression. Furthermore, restrained CCHE1 impeded proliferation, invasion, and migration of MCF-7 cells, as well as tumor growth in mice.

Conclusion
Our study highlights that elevated expression of CCHE1 in breast cancer tissues, which is closely related to clinicopathologic features, has some clinical value in the diagnosis of the disease.
Metabolome analysis reveals that cyclic adenosine diphosphate ribose contributes to the regulation of differentiation in mice adipocyte
Authors: Takahashi Haruya , Nishitani Kento , Kawarasaki Satoko , Martin‐Morales Agustin , Nagai Hiroyuki , Kuwata Hidetoshi , Tokura Motohiro , Okaze Haruka , Mohri Shinsuke , Ara Takeshi , Ito Tetsuro , Nomura Wataru , Jheng Huei‐Fen , Kawada Teruo , Inoue Kazuo , Goto Tsuyoshi 
Published: December 2023

AbstractAdipocytes play a key role in energy storage and homeostasis. Although the role of transcription factors in adipocyte differentiation is known, the effect of endogenous metabolites of low molecular weight remains unclear. Here, we analyzed time‐dependent changes in the levels of these metabolites throughout adipocyte differentiation, using metabolome analysis, and demonstrated that there is a positive correlation between cyclic adenosine diphosphate ribose (cADPR) and Pparγ mRNA expression used as a marker of differentiation. We also found that the treatment of C3H10T1/2 adipocytes with cADPR increased the mRNA expression of those marker genes and the accumulation of triglycerides. Furthermore, inhibition of ryanodine receptors (RyR), which are activated by cADPR, caused a significant reduction in mRNA expression levels of the marker genes and triglyceride accumulation in adipocytes. Our findings show that cADPR accelerates adipocytic differentiation via RyR pathway.
MiR‐9 promotes G‐MDSC recruitment and tumor proliferation by targeting SOCS3 in breast cancer
Authors: Gu Xinyue , Wei Fang , Tong Jinzhe , Liu Yichen , Chen Simiao , Zheng Lufeng , Xing Yingying 
Published: December 2023

AbstractMyeloid‐derived suppressor cells (MDSCs) are a heterogeneous group of cells that differentiate from myeloid cells, proliferate in cancer and inflammatory reactions, and mainly exert immunosuppressive functions. Nonetheless, the precise mechanisms that dictate both the accumulation and function of MDSCs remain only partially elucidated. In the course of our investigation, we observed a positive correlation between the content of MDSCs especially G‐MDSCs and miR‐9 level in the tumor tissues derived from miR‐9 knockout MMTV‐PyMT mice and 4T1 tumor‐bearing mice with miR‐9 overexpression. Combined with RNA‐seq analysis, we identified SOCS2 and SOCS3 as direct targets of miR‐9. Additionally, our research unveiled the pivotal role of the CCL5/CCR5 axis in orchestrating the chemotactic recruitment of G‐MDSCs within the tumor microenvironment, a process that is enhanced by miR‐9. These findings provide fresh insights into the molecular mechanisms governing the accumulation of MDSCs within the framework of breast cancer development.
Flatfoot Reconstruction for Painful Pediatric Idiopathic Flexible Flatfoot: Prospective Study Demonstrates Improved Alignment, Function, and Patient-reported Outcomes
Authors: DeFrancesco Christopher J. , Conti Matthew S. , Zanini Silvia , Blanco John , Dodwell Emily , Hillstrom Howard J. , Scher David M. 
Published: December 2023

Background:This prospective study was undertaken to report outcomes following reconstructive surgery for patients with painful pediatric idiopathic flexible flatfoot.Methods:Twenty-five patients with pediatric idiopathic flexible flatfoot were evaluated pre- and post flatfoot reconstruction with lateral column lengthening (LCL). All patients had lengthening of the Achilles or gastrocnemius, while 13 patients had medial side soft tissue (MSST) procedures, 7 underwent medial cuneiform plantarflexion osteotomy (MCPO), and 5 had medializing calcaneal osteotomy. Measures of static foot alignment—both radiographic parameters and clinical arch height indices—were compared, as were measures of dynamic foot alignment and loading, including arch height flexibility and pedobarography. Preoperative and postoperative patient-reported outcome (PRO) scores were compared between those treated with or without MSST procedures.Results:The median subject age was 13.8 years (range: 10.3 to 16.5) at the time of surgery. All radiographic parameters improved with surgery (P<0.001). The mean sitting arch height index showed a modest increase after surgery (P=0.023). Arch height flexibility was similar after surgery. The mean center-of-pressure excursion index increased from 14.1% to 24.0% (P<0.001), and the mean first metatarsal head (MH) peak pressure dropped (P<0.001), while the mean fifth MH peak pressure increased (P=0.018). The ratio of peak pressure in the fifth MH to peak pressure in the second MH increased (P=0.010). The ratio of peak pressure in the first MH to peak pressure in the second MH decreased when an MCPO was not used (P<0.002), but it remained stable when an MCPO was included. Mean scores in all PRO domains improved (P<0.001). Patients treated without MSST procedures showed no difference in PROMIS Pain Interference scores compared to those without MSST procedures.Conclusions:Flatfoot reconstruction surgery using an LCL with plantarflexor lengthening results in improved PROs. LCL changes but does not normalize the distribution of MH pressure loading. The addition of an MCPO can prevent a significant reduction in load-sharing by the first MH.
Discovery and characterization of novel inhibitors against ALS-related SOD1(A4V) aggregation through screening of a chemical library using Differerential Scanning Fluorimetry (DSF)
Authors: Giannakou Maria , Vorgias Constantinos , Hatzinikolaou Dimitris G. 
Published: December 2023

ABSTRACTCu/Zn Superoxide Dismutase 1 (SOD1) is a 32-kDa cytosolic dimeric metalloenzyme that neutralizes superoxide anions into harmless oxygen and hydrogen peroxide. Mutations in SOD1 are associated with ALS, a disease causing motor neuron atrophy and subsequent mortality. These mutations exert their harmful effects through a gain of function mechanism, rather than loss of function. Despite extensive research, the specific mechanism causing selective motor neuron death still remains unclear. A defining feature of ALS pathogenesis is protein misfolding and aggregation, evidenced by ubiquitinated protein inclusions containing SOD1 in motor neurons. This work aims to identify compounds countering SOD1(A4V) misfolding and aggregation, potentially aiding ALS treatment. The approach employed is drug repurposing andin vitroscreening of a 1280 pharmacologically active compounds library, LOPAC®. Using Differential Scanning Fluorimetry Technique (DSF), compounds were tested for their impact on SOD1(A4V) thermal stability. Screening revealed one compound raising protein-ligand Tmby 7°C, eight inducing a higher second Tm, suggesting stabilzation effect, and five reducing Tmup to 18°C, suggesting possible interactions or non-specific binding.
Genetic modification strategies for electroporation and CRISPR-Cas-based technologies in the non-competent Gram-negative bacteriumAcinetobactersp. Tol 5
Authors: Ishikawa Masahito , Hori Katsutoshi 
Published: December 2023

AbstractEnvironmental isolates are promising candidates for new chassis of synthetic biology because of their inherent conversion capabilities and resilience to environmental stresses; however, many remain genetically intractable and unamenable to established genetic tools tailored for model bacteria.Acinetobactersp. Tol 5 possesses intriguing properties for use in synthetic biology applications. However, genetic manipulation via electroporation is hindered by its low transformation efficiency. This study demonstrated the genetic refinement of the Tol 5 strain, achieving efficient transformation via electroporation. We deleted two genes encoding restriction enzymes. The resulting mutant strain not only exhibited marked efficiency of electrotransformation but also proved receptive to bothin vitroandin vivoDNA assembly technologies, thereby facilitating the construction of recombinant DNA. In addition, we successfully adapted a CRISPR-Cas9-based base-editing platform developed for otherAcinetobacterspecies. Our genetic modification strategy allows for the domestication of non-model bacteria, streamlining their utilization in synthetic biology applications.
MiniRead: a simple and inexpensive do-it-yourself device for multiple analyses of micro-organism growth kinetics
Authors: Falque Matthieu , Bourgais Aurélie , Dumas Fabrice , de Carvalho Mickaël , Diblasi Célian 
Published: December 2023

ABSTRACTFitness in micro-organisms can be proxied by growth parameters on different media and/or temperatures. This is achieved done by measuring optical density at 600 nm using a spectrophotometer, which measures the effect of absorbance and side scattering due to turbidity of cells suspensions. However, when growth kinetics must be monitored in many 96-well plates at the same time, buying several 96-channels spectrophotometers is often beyond budgets. The MiniRead device presented here is a simple and inexpensive do-it-yourself 96-well temperature-controlled turbidimeter designed to measure the interception of white lightviaabsorption or side scattering through liquid culture medium. Turbidity is automatically recorded in each well at regular time intervals for up to several days or weeks. Output tabulated text files are recorded into a micro-SD memory card to be easily transferred to a computer. We propose also an R package which allows (1) to compute the non-linear calibration curves required to convert raw readings into cell concentration values, and (2) to analyze growth kinetics output files to automatically estimate growth parameters such as lag time, maximum growth rate, or cell concentration at the plateau.The MiniRead project is freely available under GPL license fromhttps://forgemia.inra.fr/gqe-base/MiniRead. The project includes (1): user manual (Supplementary Material 1), firmware, list of electronic components and printed circuit board manufacturing files for the MiniRead device, and (2) a release containing the MiniRead R package for calibration and data analysis (Supplementary Material 2) with its tutorial (Supplementary Material 3). Detailed device building instructions are available athttps://moulon.inrae.fr/materiel_labo/miniread/.
An improved workflow for the quantification of orthohantavirus infection using automated imaging and flow cytometry
Authors: Menke Laura , Sieben Christian 
Published: December 2023

AbstractDetermination of the infectious titer is a central requirement when working with pathogenic viruses. The plaque or focus assay is commonly used but a labor- and time-consuming approach to determine the infectious titer of orthohantavirus samples. We have developed an optimized virus quantification approach that relies on the fluorescence-based detection of the orthohantavirus nucleocapsid protein (N) in infected cells with high sensitivity. We present the use of flow cytometry but highlight fluorescence microscopy in combination with automated data analysis as an attractive alternative to increase the information retrieved from an infection experiment. Additionally, we offer an open-source software equipped with a user-friendly graphical interface, eliminating the necessity for advanced programming skills.