bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genie: The First Open-Source ISO/IEC Encoder for Genomic Data
Authors: Müntefering Fabian , Adhisantoso Yeremia , Chandak Shubham , Ostermann Jörn , Hernaez Mikel , Voges Jan 
Published: May 2023

Abstract

For the last two decades, the amount of genomic data produced by scientific and medical applications has been growing at a rapid pace. To enable software solutions that analyze, process and transmit these data in an efficient and interoperable way, ISO and IEC released the first version of the compression standard MPEG-G in 2019. However, non-proprietary implementations of the standard are not openly available so far, limiting fair scientific assessment of the standard and therefore hindering its broad adoption. In this paper, we present Genie, the first open-source encoder that compresses genomic data according to the MPEG-G standard. We demonstrate that Genie reaches state-of-the-art compression ratios while offering interoperability with any other standard-compliant decoder independent from its manufacturer. Finally, the ISO/IEC ecosystem ensures the long-term sustainability and decodability of the compressed data through the ISO/IEC-supported reference decoder.
Slc20a1 and Slc20a2 Regulate Neuronal Plasticity and Cognition Independently of Their Phosphate Transport Ability
Authors: RAMOS-BROSSIER Mariana , ROMEO-GUITART David , LANTE Fabien , Boitez Valerie , MAILLIET François , SAHA Sohame , RIVAGORDA Manon , SIOPI Eleni , Namazanyy Ivan , Christine Leroy , Moriceau Stéphanie , BECK-CORMIER Sarah , Codogno Patrice , BUISSON Alain , BECK Laurent , Friedlander Gerard , Oury Franck 
Published: May 2023

Abstract
In recent years, primary familial brain calcification (PFBC), a rare neurological disease characterized by a wide spectrum of cognitive disorders, has been associated to mutations in the sodium (Na)-Phosphate (Pi) co-transporter SLC20A2. However, the functional roles of the Na-Pi co-transporters in the brain remain still largely elusive. Here we show that Slc20a1/(PiT-1) and Slc20a2/(PiT-2) are the most abundant Na-Pi co-transporters expressed in the brain and are involved in the control of hippocampal-dependent learning and memory. We reveal that Slc20a1 and Slc20a2 are differentially distributed in the hippocampus and associated with independent gene clusters, suggesting that they influence cognition by different mechanisms. Accordingly, using a combination of molecular, electrophysiological and behavioral analyses, we show that while PiT-2 favors hippocampal neuronal branching and survival, PiT-1 promotes synaptic plasticity. The latter relies on a likely Otoferlin-dependent regulation of synaptic vesicle trafficking, which impacts the GABAergic system. These results provide the first demonstration that Na-Pi co-transporters play key albeit distinct roles in the hippocampus pertaining to the control of neuronal plasticity and cognition. These findings could provide the foundation for the development of novel effective therapies for PFBC and cognitive disorders.
The VLF-induced ionospheric perturbations detected by DEMETER during solar minimum
Authors: Zhang Xuemin , Dong Lei , Nie Lei 
Published: May 2023

Abstract

The VLF-induced ionospheric heating events from the power transmitter NWC are collected at extremely low solar activity years of 2008-2009, and their spatial and temporal distribution features are investigated. The spatial distribution of heating signals exhibits clear north-direction inclination of 2-3°, and covering area within 300 km radius in longitude and latitude. Plasma parameters show the obvious negative correlations between decreasingNeand increasingTe, and positive correlations of the increasing ion density and ion temperature during the VLF heating time. The ions move upwards to cause the perturbations in ULF electric field due toV x B.The VLF heating events easily occur at seasons with low plasma density, which illustrates that low plasma environment plays an important role in VLF-induced ionospheric heating. Typical three enhanced VLF signals are obtained, one at 19.8 kHz, one at the broadened frequency band of 19.8±300 Hz with one order of amplitude decreasing, and one between 19.5 kHz and lower hybrid frequency with at least two orders of amplitude reductions. These quasi electrostatic waves during VLF heating may not be from the VLF whistler conversion, but the lightning-whistler waves are enhanced when they pass through the plasma cavity formed during VLF heating process.
2.5D porous structure design based on mechanical topology optimization and principal stress field
Authors: Mamuti Maimaitijiang , Chao Long , Tian Zongjun 
Published: May 2023

Abstract
In engineering applications, 2.5D mechanical parts are widely used, and can be further optimized using porous structure to meet the requirements of high specific strength and lightweight. In this paper, a topological design methodology driven by principal stress field was proposed to realize the optimal distribution of materials while keeping the macroscopic model unchanged. The shape of pores relies on the Voronoi-Tessellation by offsetting the closed Non-Uniform Rational B-Spline (NURBS) curves. To improve the mechanical properties, information of Principal Stress Line (PSL) curves and stress values calculated from finite element analysis were fully utilized. It is expected that this work can offer some insights for Functionally Graded Porous Materials (FGPMs) design.
Synthesis of nano-silica oxide for heavy metals decontamination from aqueous solutions
Authors: Soliman Mohamed , Salama Eslam , Elsayed Mahmoud , Naeem Soheair , Ossman Mona , Meky Naira 
Published: May 2023

Abstract
In the current study, nano-silica oxide (nano-SiO2) was fabricated via the sol-gel technique. Then, the prepared nano-SiO2 was characterized using X-ray diffractometer (XRD), transmission electron microscopy (TEM) coupled with energy-dispersive X-ray spectroscopy (EDS), Fourier transform infrared (FTIR), thermogravimetric analysis (TGA), and Brunauer-Emmett-Teller. Furthermore, the fabricated nano-SiO2 was applied for the adsorption of lead Pb (II) and chromium Cr (VI) from aqueous solutions. Additionally, the influence of different operating factors such as contact time, nano-SiO2 dose, initial pH, initial metal ions concentration, and the temperature was investigated. The nano-SiO2 dosages of 0.5 and 1 g L-1 were selected as the optimal adsorbent dose for the removal of Pb (II) and Cr (VI), respectively. These doses achieved a removal efficiency of 83.29% and 78.65% for Pb (II) and Cr (VI), after 60 and 90 min, respectively, (at initial pH values of 7, using 10 mg L-1 initial metals concentration, and at room temperature). Lastly, kinetic and equilibrium studies were competently fitted using the pseudo-second-order and Freundlich models, respectively. Adsorption thermodynamic studies designate the spontaneous and thermodynamic of the adsorption processes nature. These results reveal the efficiency of the fabricated nano-SiO2 as an adsorbent for heavy metals removal from aqueous solutions.
Potential Use of Vermicompost Against Tomato Bacterial Canker and Wilt Disease
Authors: Belgüzar Sabriye 
Published: May 2023

Abstract
This study was conducted to investigate the effectiveness of vermicompost (VC) in the control of tomato bacterial canker and wilt disease (Clavibacter michiganensis subsp. michiganensis), which causes significant yield losses in tomato production. In pot experiments, vermicompost was added to pot soil at 10, 20, 30 and 40% doses. In field experiments, vermicompost was applied to soil at a dose of 600 kg/da. In pot experiments, effect of vermicompost on disease severity varied between 53.4-90.8%. In 40% VC treatments, a low rate of lesions was detected in vascular bundles and the disease infection was suppressed by 66.77%. In field experiments, a low rate of disease was also detected in VC-treated plants and disease severity was affected by 66.6%. The infection rate in vascular bundles was suppressed by 69.9%. Present findings revealed that vermicompost significantly suppressed tomato bacterial canker and wilt disease and it could be used as an important component of integrated pests and disease management.
Non-alcoholic fatty liver disease promotes breast cancer progression through upregulated hepatic fibroblast growth factor 21
Authors: Chen Jianping , SUI Yue , LIU Qingqing , XU Cong , GANESAN Kumar , YE Zhen , Li Yan , Wu Jian-Ming , DU Bing , GAO Fei 
Published: May 2023

Abstract
Non-alcoholic fatty liver disease influences breast cancer progression, however, the mechanisms remain unclear. Here, we found promoted breast cancer tumor growth and cell viability in NAFLD models and screened out the possible mediator hepatic fibroblast growth factor 21. Both peritumoral and systemic FGF21 administration facilitated breast cancer tumor growth, whereas FGF21 knockout diminished the tumor-promoting effects of the high-fat diet. Mechanically, exogenous FGF21 treatment enhanced the anti-apoptotic ability of breast cancer cells via STAT3 and Akt/FoXO1 signaling pathways and mitigated doxorubicin-induced cell death. Furthermore, overexpressed FGF21 was observed in tumor tissues from breast cancer patients and associated with poor prognosis. Taken together, our findings support a new role of FGF21 as a mediator upregulated in the NAFLD context that promotes breast cancer development, serving as a promising cancer therapeutic target.
Ufmylation on UFBP1 alleviates non-alcoholic fatty liver disease by modulating hepatic endoplasmic reticulum stress
Authors: Chen Fengling , Mao Ziming , Ma Xiaowen , Jing Yu , Shen Minyan , Ma Xirui , Zhu Jing , Liu Huifang , Zhang Guangya 
Published: May 2023

Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease characterized by lipid accumulation and endoplasmic reticulum (ER) stress, while effective therapies targeting NAFLD characteristics are limited. Ufmylation is a newly found post-translational modification in which the Ubiquitin-fold modifier 1 (UFM1) protein is attached to its substrate via ufmylation modification system components. Ufmylation has been proposed to regulate ER stress via modifying UFM1 binding protein 1 (UFBP1), suggesting a potential role for ufmylation in the pathogenesis of NAFLD. However, the role of ufmylation in NAFLD is unknown. Herein, we aimed to reveal the role of ufmylation on UFBP1 in NAFLD and explore the underlying mechanisms. We observed an up-regulated expression of UFM1-conjugated proteins and ufmylation modification system components in livers with steatosis derived from NAFLD patients and NAFLD models, which was an adaptive response to the hepatic ER stress in NAFLD. In vitro, knocking down UFBP1 promoted lipid accumulation and lipogenesis in hepatocytes treated with free fatty acids (FFA), which could be rescued by re-expressing exogenous wild type UFBP1 (WT UFBP1) but not an UFBP1 mutant deficient in main ufmylation site lys267 (UFBP1 K267R). In vivo, ufmylation on UFBP1 ameliorated obesity, hepatic steatosis, hepatic lipogenesis, dyslipidemia, insulin resistance and liver damage in high fat diet (HFD)-induced NAFLD mice. We also demonstrated that knocking down UFBP1 promoted ER stress while re-expressing or overexpressing UFBP1 relieved ER stress in an ufmylation-dependent manner in NAFLD, which could be the underlying mechanism that led to the relief of abnormal hepatic lipogenesis and insulin resistance. Our data reveal a protective role of ufmylation on UFBP1 against NAFLD and offer a specific target for NAFLD treatment.
Identification of a novel PTH1R variant in a family with primary failure of eruption
Authors: Zha Yunchen , Li Shushu , Yu Yue-lin , Huang Zicheng , Zhang Hai-ying , Kong Weidong 
Published: May 2023

Abstract
Background This work aimed to report a small family of Primary Failure of Eruption(PFE) with a novel PTH1R variant. One of the patients has a rare clinical phenotype of the anterior tooth involved only.Case presentation The proband was a 13-year-old young man with an incomplete eruption of the right upper anterior tooth(11,12,13), resulting in a significant open-bite. His left first molar 26 partially erupted. Family history revealed that the proband's 12-year-old brother and father also had teeth eruption disorders. Genetic testing found a novel PTH1R variant (c.1325-1336del), which has never been reported before. The diagnosis of PFE was based on clinical and radiographic characteristics and the result of genetic testing. Bioinformatic analysis predicted this variant would result in the truncation of the G protein-coupled receptor encoded by the PTH1R, affecting its structure and function.Conclusion A novel PTH1R variant identified through whole-exome sequencing further expands the mutation spectrum of PFE. Patients in this family have different phenotypes, which reflects the characteristics of variable phenotypic expression of PFE.
“I'll meet you at our bench”: Adaptation, Innovation and Resilience among VCSE organisations who supported marginalised and minoritised communities during the COVID-19 pandemic in Northern England – A Qualitative Focus Group Study
Authors: Scott Steph , McGowan Victoria , Wildman Josephine , Bidmead Elaine , Hartley Jane , Mathews Claire , James Becky , Sullivan Claire , Bambra Clare , Sowden Sarah 
Published: May 2023

Abstract
Background The Covid-19 pandemic has exacerbated pre-existing inequalities and increased adversity and challenges for vulnerable and marginalised communities worldwide. In the UK, the Voluntary Community and Social Enterprise (VCSE) sector play a vital role in supporting the health and wellbeing of people who are marginalised or experiencing multiple complex needs. However, only a small number of studies have focused on the impact that Covid-19 had on the VCSE sector.Methods As part of a Health Inequalities Impact Assessment (HIIA), we conducted qualitative focus groups with staff and volunteers from five organisations to examine short, medium and longer-term impacts of COVID-19 upon the VCSE sector in Northern England. Nine online focus groups were conducted between March and July 2021.Findings: Focus group transcripts were analysed using Framework Analysis and yielded three central themes: (1) exacerbation of pre-existing inequalities, adversity and challenges for vulnerable and marginalised populations; (2) the ‘price’ of being flexible, innovative and agile for VCSE staff and volunteers; and (3) the voluntary sector as a ‘lifeline’ - organisational pride and resilience.Conclusions While the voluntary sector ‘adapted at pace’ to provide support during Covid-19 and in its continued aftermath, this resilience has potentially come at the cost of workforce and volunteer wellbeing, compounded by political obstacles and chronic shortage in funding and support. The VCSE sector has a vital role to play in the post-COVID ‘levelling up’ agenda. The expertise, capacity and resilience of VCSE organisations, and their ability to respond to COVID-19, should be celebrated, recognised and supported adequately to maintain its resilience. To not do so threatens the sector’s sustainability and risks jeopardising attempts to involve the sector in addressing the social determinants of health.
Morphological and Dimensional Comparison of Functioning Blebs Following PRESERFLO-Microshunt and XEN-Gel-Stent, a Study Using Anterior Segment OCT
Authors: Hasan Somar , Theilig Theresa , Papadimitriou Menelaos , Meller Daniel 
Published: May 2023

Abstract
Background:
Evaluation of bleb morphology is a vital part of successful filtration glaucoma surgery. The PRESERFLO-MicroShunt (PRESERFLO) and the XEN-Gel-Stent (XEN) are drainage devices which are implanted through different surgical approaches (ab-externo versus ab-interno, respectively). This might result in different bleb morphology. Studying these morphological differences is important in leading post-operative care.
Methods:
Functioning blebs following implantation of PRESERFLO and XEN were retrospectively included and examined using high resolution anterior segment OCT. A qualitative assessment using the Jenaer Bleb Grading System and quantitative assessment by measuring 12 parameters representing bleb dimensions were performed. Results were compared between both groups.
Results:
Included were 80 eyes of 80 patients (41 after PRESERFLO, 39 after XEN). Functioning blebs following PRESERFLO showed higher frequency of hyperreflective tenon changes compared to XEN (31.7% VS 10.3% respectively, p = 0.02) and lower frequency of cavernous changes (17.1%VS 35.9%, p = 0.05) along with higher frequency of visible episcleral lake (92.7% VS 30.8%, p < 0.001). Blebs after PRESERFLO showed larger height (2.13 ± 0.5 VS 1.85 ± 0.6mm, p = 0.03), width (10.31 ± 2.3 VS 9.1 ± 2.3mm, p = 0.02), length (9.13 ± 1.8 VS 8.24 ± 1.9mm, p = 0.04), were located more posterior to limbus (6.21 ± 1.2 VS 5.21 ± 1.8mm, p = 0.005) and showed a thicker bleb wall (1.60 ± 0.5 VS 1.1 ± 0.4mm, p = 0.004).
Conclusions:
Functioning blebs after PRESERFLO and XEN are morphologically different. Main reasons might be the different surgical techniques (ab-externo versus ab-interno) and different dimensions of stents. These morphological differences should be considered when evaluating blebs as this might affect judgement of bleb functionality and thus on the decision when and how to intervene in the post-operative phase.
Fecal carriage and enrichment of multidrug-resistant Enterococci among admitted children in a pediatric intensive care unit
Authors: Shirvani Fariba , Hassanzadeh Romina , Attaran Bahareh , Ghandchi Ghazale , Abdollahi Nafiseh , Gholinjad Zari , Sheikhi Zahra , Behzad Azita , Fallah Fatemeh , Azimi Leila , Safarkhani Azam , Karimi Abdollah , Mahdavi Alireza , Armin Shahnaz , Ghanaie Roxana Mansour , Tabatabaei Sedigheh Rafiei , Fahimzad Seyed Alireza , Alebouyeh Masoud 
Published: May 2023

AbstractBackground: The present study aimed to investigate intestinal carrier’s status ofEnterococcusspp. in children and revealing role of hospitalization on alteration of their resistance phenotype and clonal diversity during the admission and discharge periods.Methods: Two separate rectal swab samples were collected from hospitalized patients in pediatric intensive care unit at the admission and discharge time. Culture was done and confirmed colonies ofEnterococcuswere analyzed for antimicrobial susceptibility and carriage of vanA/B/C/Dgene subtypes. Random Amplified Polymorphic DNA (RAPD)-PCR was used for phylogenetic study to check homology of pairs of the isolates.Results: The results showed colonization of Enterococci in 31% of the cases at the admission, 28.7% at the discharge, and 40.1% at both time points. Resistance to vancomycin, ampicillin and rifampicin was higher inE. faecium, but resistance to ciprofloxacin was higher inE. faecalis. The frequency of MDR was higher inE. faecalisthanE. faeciumisolates. No significant difference in colonization with VRE, MDR-Enterococci and resistance to antibiotics were detected at the time of admission and discharge; however, there was a significant relationship between the longer hospitalization stay and VREcolonization. While homology of the isolates was low among different patients, identical and similar RAPD-PCR pattern was detected in 9% and 21% of pairs of the isolates in each patient, respectively.Conclusions: High rate of intestinal colonization with VRE, HLGR, and MDR-Enterococci before admission and their enrichment during hospitalization in PICU shows the importance of antibiotic stewardship programs to control their transmission and spread.
The relationship between Mood Disorder, Personality Disorder and Suicidality in Adolescence: Does personality disorder play a significant role in predicting suicidal behavior?
Authors: Williams Riccardo , Chiesa Marco , Moselli Marta , Frattini Camilla , Casini Maria Pia , Fonagy Peter 
Published: May 2023

Abstract
Introduction:
Current research points to the importance of diagnosing personality pathology emerging patterns in adolescence for understanding suicidal risk. Studies have mainly focused on the role of BPD and only marginally investigated the interaction of personality disorder (PD) as overall diagnosis and individual PDs and major depression (MDD). In this paper, the independent and cumulative effects of MDD and DSM-IV PDs on suicidal risk are investigated in a longitudinal study.
Methods:
A sample of 118 adolescents (mean age = 15.48 ± 1.14) referred for assessment and treatment on account of suicidal ideation or behavior were administered the CSSRS, SCID II, Kiddie-SADS; after six months the CSSRS was applied again to all patients. In order to test the significance of the associations and predictions between categorical and dimensional PD, BPD, NPD, Major Depression, suicide attempts, number of suicide attempts and potential lethality of suicide attempt, non-parametric bivariate correlations, logistic regression models and mixed-effects Poisson regression were performed PD.
Results:
BPD was confirmed to be a significant risk factor for suicide. Personality disorders assessed at a categorical and dimensional level and Unipolar depression exert an influence on suicidal behaviors and their lethality both as independent and cumulative risk factors.
Limitations: While we incorporated dimensional thinking into our approach to assessing psychopathology, our study still relied on traditional defined. Future studies should include AMPD-defined personality pathology in adolescence to truly represent dimensional thinking.
Conclusion:
These results point to the importance of early identification of emerging patterns of personality disorders in adolescence.
Uncommon histology of adnexal masses: A Case Series
Authors: . Shalini , Jha Sangam , Jafeesha B 
Published: May 2023

Abstract
Introduction:
Adnexal masses can arise from uterus, ovary, fallopian tubes or surrounding tissues. They often pose diagnostic and management dilemmas. This diagnostic dilemma exists because their location, clinical presentation and difficult differentiation on imaging. However accurate preoperative diagnosis is desirable to avoid unnecessary extensive radical surgeries.
Case report:
We report cases of adnexal masses with varied histology in reproductive age women. Age group ranged from 20-70 years. All 4 women presented with pain abdomen with progressively increasing abdominal lump. In all the cases CECT abdomen and pelvis revealed malignant ovarian tumor, case1 underwent staging laparotomy with right salpingo-ophorectomy with multiple peritoneal biopsies, however histology returned as ovarian lipoleiomyoma with chondroid differentiation. Case 2 underwent abdominal hysterectomy with bilateral salpingo-ophorectomy, histology reported as chronic salpingitis. Case 3 had staging laparotomy with removal of uterus, bilateral tubes and ovaries, omentectomy and retroperitoneal lymphnode dissection, histology revealed leiomyoma with cystic degeneration. Case 4 was postmenopausal lady with pre-operative diagnosis of bilateral ovarian mass, she also received radical surgery, histology reported as benign mucinous cystadenoma with calcified cyst wall.
Conclusion:
This case series highlight the varied nature of adnexal mass, importance of correct interpretation of imaging and corelation of clinicoradiological findings in reaching to accurate diagnosis thereby managing the cases with less extensive surgery.