bluuebunny/crossref_metadata_2025_split huggingface dataset:
HMSS2: An advanced tool for the analysis of sulphur metabolism, including organosulphur compound transformation, in genome and metagenome assemblies
Authors: Tanabe Tomohisa Sebastian , Dahl Christiane 
Published: July 2023

AbstractThe global sulphur cycle has implications for human health, climate change, biogeochemistry and bioremediation. The organosulphur compounds that participate in this cycle not only represent a vast reservoir of sulphur but are also used by prokaryotes as sources of energy and/or carbon. Closely linked to the inorganic sulphur cycle, it involves the interaction of prokaryotes, eukaryotes and chemical processes. However, ecological and evolutionary studies of the conversion of organic sulphur compounds are hampered by the poor conservation of the relevant pathways and their variation even within strains of the same species. In addition, several proteins involved in the conversion of sulphonated compounds are related to proteins involved in sulphur dissimilation or turnover of other compounds. Therefore, the enzymes involved in the metabolism of organic sulphur compounds are usually not correctly annotated in public databases. To address this challenge, we have developed HMSS2, a profiled Hidden Markov Model‐based tool for rapid annotation and synteny analysis of organic and inorganic sulphur cycle proteins in prokaryotic genomes. Compared to its previous version (HMS‐S‐S), HMSS2 includes several new features. HMM‐based annotation is now supported by nonhomology criteria and covers the metabolic pathways of important organosulphur compounds, including dimethylsulphoniopropionate, taurine, isethionate, and sulphoquinovose. In addition, the calculation speed has been increased by a factor of four and the available output formats have been extended to include iTol compatible data sets, and customized sequence FASTA files.
Efficacy of different lures for Phloeosinus aubei and other native and exotic bark and ambrosia beetles
Authors: Fiala Tomáš , Pyszko Petr , Holuša Jaroslav 
Published: July 2023

AbstractPhloeosinus aubei is invasive in Central Europe, spreading northward from the Mediterranean region because of climate change. P. aubei has the potential to become a pest of mature, naturally occurring juniper trees (Juniperus communis) in protected areas, as well as junipers, thujas and cypresses in nurseries and urban environments. In 2020 and 2021, we conducted two experiments to compare various lures for trapping P. aubei. In the first experiment, we compared four lures: α‐pinene; turpentine; a mixture of cade oil, juniper berry oil and ethanol; and a juniper branch (8–10 cm long, 3–5 cm wide) deployed with ethanol. In the second experiment, we compared Hostowit® with a juniper branch (8–10 cm long, 3–5 cm wide) deployed with ethanol. In both experiments, juniper branches deployed with ethanol attracted a greater number of P. aubei beetles compared to the other lures. In total, we captured 1056 individuals belonging to 36 species of Scolytinae. Among the most abundant species, Xyleborinus saxesenii, Xyleborus monographus and Anisandrus dispar were lured by ethanol in combination with other substances or deployed with juniper branches. Xyleborus dryographus showed a positive association with turpentine. Ips typographus was positively associated with α‐pinene, while Orthotomicus laricis, Hylastes attenuatus and Gnathotrichus materiarius were positively associated with Hostowit® lure.
Intronic variants of LGALS13 gene encoding placental protein (PP13) are linked with increased risk of infection‐associated spontaneous preterm birth
Authors: Bhati Tanu , Ray Ankita , Arora Renu , Siraj Fouzia , Parvez Suhel , Rastogi Sangita 
Published: July 2023

AbstractProblemSpontaneous preterm birth (sPTB) is a global health issue. Studies suggest infection and infection‐based inflammatory responses are major risk factors for sPTB. Considering the important role of anti‐inflammatory proteins in pregnancy, the study aimed to find the association between anti‐inflammatory LGALS13 gene variants IVS2‐22 A/G (rs2233706) and IVS3+72 T/A (rs2233708) and the risk of sPTB during Chlamydia trachomatis, Mycoplasma hominis and Ureaplasma urealyticum infection in Indian population.Method of studyPlacental samples of 160 sPTB and 160 term women were collected. Pathogens were detected by PCR. The genotyping of LGALS13 gene variants IVS2‐22 A/G (rs2233706) and IVS3+72 T/A (rs2233708) was done by qualitative real‐time PCR using allelic discrimination method (VIC‐ and FAM‐labeled).ResultsThe frequency of AG or GG genotype of LGALS13 IVS2‐22A/G polymorphism (rs2233706) was 75.5% in infected sPTB cases and 14.4% in uninfected sPTB cases and 7.3% in term birth controls (p < .0001), while the frequency of TA or AA genotype of LGALS13 IVS3+72T/A polymorphism (rs2233708) was 83.6% in infected sPTB cases and 18% in uninfected sPTB cases and 12.7% in term birth controls (p < .0001). The genotypic frequencies for both the variants of LGALS13 were statistically significant (p < .0001) in the infected sPTB versus uninfected sPTB and term birth controls.ConclusionsStudy reveals strong association between the presence of immunological gene variants LGALS13 IVS2‐22 A/G (rs2233706) and LGALS13 IVS3+72 T/A (rs2233708) and risk of sPTB during C. trachomatis, M. hominis and U. urealyticum infection.
Design and characteristics of the prophylactic intra‐operative ventricular arrhythmia ablation in high‐risk LVAD candidates (PIVATAL) trial
Authors: Huang David T. , Gosev Igor , Wood Katherine L. , Vidula Hima , Stevenson William , Marchlinski Frank , Supple Gregory , Zalawadiya Sandip K. , Weiss J. Peter , Tung Roderick , Tzou Wendy S. , Moss Joshua D. , Kancharla Krishna , Chaudhry Sunit‐Preet , Patel Parin J. , Khan Arfaat M. , Schuger Claudio , Rozen Guy , Kiernan Michael S. , Couper Gregory S. , Leacche Marzia , Molina Ezequiel J. , Shah Anand D. , Lloyd Michael , Sroubek Jakub , Soltesz Edward , Shivkumar Kalyanam , White Casey , Tankut Sinan , Johnson Brent A. , McNitt Scott , Kutyifa Valentina , Zareba Wojciech , Goldenberg Ilan 
Published: July 2023

AbstractBackgroundThe use of a Left Ventricular Assist Device (LVAD) in patients with advanced heart failure refractory to optimal medical management has progressed steadily over the past two decades. Data have demonstrated reduced LVAD efficacy, worse clinical outcome, and higher mortality for patients who experience significant ventricular tachyarrhythmia (VTA). We hypothesize that a novel prophylactic intra‐operative VTA ablation protocol at the time of LVAD implantation may reduce the recurrent VTA and adverse events postimplant.MethodsWe designed a prospective, multicenter, open‐label, randomized‐controlled clinical trial enrolling 100 patients who are LVAD candidates with a history of VTA in the previous 5 years. Enrolled patients will be randomized in a 1:1 fashion to intra‐operative VTA ablation (n = 50) versus conventional medical management (n = 50) with LVAD implant. Arrhythmia outcomes data will be captured by an implantable cardioverter defibrillator (ICD) to monitor VTA events, with a uniform ICD programming protocol. Patients will be followed prospectively over a mean of 18 months (with a minimum of 9 months) after LVAD implantation to evaluate recurrent VTA, adverse events, and procedural outcomes. Secondary endpoints include right heart function/hemodynamics, healthcare utilization, and quality of life.ConclusionThe primary aim of this first‐ever randomized trial is to assess the efficacy of intra‐operative ablation during LVAD surgery in reducing VTA recurrence and improving clinical outcomes for patients with a history of VTA.
Syn‐ and post‐rift lower crustal flow under the Sunda Shelf, southern Vietnam: A role for climatically modulated erosion
Authors: Clift Peter D. , Wilson Leora J. 
Published: July 2023

AbstractTectonic subsidence on rifted, passive continental margins are largely controlled by patterns of extension and the nature of strain partitioning in the lithosphere. The Sunda Shelf, adjacent to the SW South China Sea, is characterized by deep basins linked to regional Cenozoic extension associated with propagating seafloor spreading caused by slab pull from the south. Analysis of seismic reflection profiles and drilled sections crossing the Nam Con Son and Cuu Long basins highlight Oligocene extension, with most of the thinning concentrated in the ductile mid‐lower crust. Upper crustal extension was modest and ductile flow is inferred to be directed northwestwards, towards the oceanic crust. Basin inversion occurred in the Mid Miocene, associated with the collision of the Dangerous Grounds Block and Borneo. Subsequent accelerated tectonic subsidence exceeded predictions from uniform extension models assumed to relate to extensional collapse after inversion. We correlate this to a period of faster erosion onshore driven by strong monsoon rains in Indochina and Peninsular Thailand at that time. Erosion of the onshore basement, inducing rock uplift and coupled with loading of the basins offshore, drives ductile mid‐lower crustal flow, likely to the northeast under Indochina, and/or to the west where Plio‐Pleistocene subsidence of the shelf is very slow. Significant sediment delivery from the Mekong River into the Cuu Long Basin began in the Late Miocene and migrated seawards as the basin filled. Mass balancing suggests that the basins of this part of the Sunda Shelf are filled through erosion of bedrock sources around the Gulf of Thailand. There is no need for sediment delivery from a major river draining the Tibetan Plateau to account for the deposited volumes.
Health inequalities in the geographic distribution of dental practitioners in Costa Rica: An ecological study
Authors: Barboza‐Solis Cristina , Barahona‐Cubillo Juan , Fantin Romain 
Published: July 2023

AbstractObjectiveThe uneven distribution of dental health services in a territory can cause an imbalance in accessibility, increasing health inequalities. This study aimed to describe the geographical distribution of dental health practitioners according to urbanicity and area‐level socio‐economic status in Costa Rica.MethodsA National Dentist Survey was developed to identify employment status, number of working hours, address and list of the working clinics. Data was completed using information from the national College of Surgeons, including all Costa Rican dentists. The Minimal Geographic Units (MGU) allowed for aggregating the population's individual level socio‐economic position. Local Potential Accessibility (LPA) calculated the density of full‐time hour's equivalents around each MGU using floating sectors. Clinics were geocoded using Geographic Information Systems, creating 2853 clinical points. Distance between each MGU and the nearest accessible clinics considering full‐time working hours equivalents was estimated. MGU were divided into six categories: ‘No accessibility’, ‘Very low accessibility’, ‘Low accessibility’, ‘Good accessibility’ ‘High accessibility’ and ‘Very high accessibility’.ResultsMean national LPA was 6.5 full‐time equivalents per 10 000 inhabitants, 3.4% of the Costa Rican population had no access to dentist; 12.9% had very low accessibility, 22.7% had low accessibility, 35.0% had good accessibility, 16.2% had high accessibility, and 9.8% had very high accessibility. Overall, 39% of the population has a rather low accessibility. LPA was higher in urban districts compared to rural districts and in wealthiest districts compared to most disadvantaged districts. Within districts, after adjustment for district's characteristics, LPA was higher in urban MGU compared to rural MGU and in wealthiest MGU compared to most disadvantaged MGU.ConclusionsThis study found that despite having a high number of dentists, their numbers are small in many areas, increasing inequalities in access to health care. The dentist's free establishment, where they can decide to provide private services within a community, creates zones with very high densities, in particular in the wealthiest urban areas, and others with very low densities, in particular the poorest rural areas. The lack of territorial planning has been one of the reasons that has encouraged an imbalance in the availability of dental human resources. To achieve effective universal health coverage, public institutions should focus their efforts on improving access to dental services in underserved areas.
Paediatric phaeochromocytoma and paraganglioma: A clinical update
Authors: Nazari Matthew A. , Jha Abhishek , Kuo Mickey J. M. , Patel Mayank , Prodanov Tamara , Rosenblum Jared S. , Talvacchio Sara , Derkyi Alberta , Charles Kailah , Pacak Karel 
Published: July 2023

AbstractPaediatric phaeochromocytomas and paragangliomas (PPGLs), though rare tumours, are associated with significant disability and death in the most vulnerable of patients early in their lives. However, unlike cryptogenic and insidious disease states, the clinical presentation of paediatric patients with PPGLs can be rather overt, allowing early diagnosis, granted that salient findings are recognized. Additionally, with prompt and effective intervention, prognosis is favourable if timely intervention is implemented. For this reason, this review focuses on four exemplary paediatric cases, succinctly emphasizing the now state‐of‐the‐art concepts in paediatric PPGL management.
Cuproptosis facilitates immune activation but promotes immune escape, and a machine learning–based cuproptosis‐related signature is identified for predicting prognosis and immunotherapy response of gliomas
Authors: Feng Shi , Zhang Yonggang , Zhu Hua , Jian Zhihong , Zeng Zhi , Ye Yingze , Li Yina , Smerin Daniel , Zhang Xu , Zou Ning , Gu Lijuan , Xiong Xiaoxing 
Published: July 2023

AbstractAimsCell death, except for cuproptosis, in gliomas has been extensively studied, providing novel targets for immunotherapy by reshaping the tumor immune microenvironment through multiple mechanisms. This study aimed to explore the effect of cuproptosis on the immune microenvironment and its predictive power in prognosis and immunotherapy response.MethodsEight glioma cohorts were included in this study. We employed the unsupervised clustering algorithm to identify novel cuproptosis clusters and described their immune microenvironmental characteristics, mutation landscape, and altered signaling pathways. We verified the correlation among FDX1, SLC31A1, and macrophage infiltration in 56 glioma tissues. Next, based on multicenter cohorts and 10 machine learning algorithms, we constructed an artificial intelligence–driven cuproptosis‐related signature named CuproScore.ResultsOur findings suggested that glioma patients with high levels of cuproptosis had a worse prognosis owing to immunosuppression caused by unique immune escape mechanisms. Meanwhile, we experimentally validated the positive association between cuproptosis and macrophages and its tumor‐promoting mechanism in vitro. Furthermore, our CuproScore exhibited powerful and robust prognostic predictive ability. It was also capable of predicting response to immunotherapy and chemotherapy drug sensitivity.ConclusionsCuproptosis facilitates immune activation but promotes immune escape. The CuproScore could predict prognosis and immunotherapy response in gliomas.
Photography in dermatology ‐ a scoping review: Practices, skin of color, patient preferences, and medical‐legal considerations
Authors: Kashetsky Nadia , Mar Kristie , Liu Chaocheng , Rivers Jason K , Mukovozov Ilya 
Published: July 2023

SummaryClinical photography is essential in dermatology. However, a comprehensive literature review of photography in dermatology is lacking. This scoping review aims to summarize the literature regarding photography practices in dermatology, photography of skin of color, patient preferences, and medical‐legal considerations. A search was conducted utilizing Embase, MEDLINE, PubMed, and Evidence Based Medicine databases in accordance with the PRISMA extension for Scoping Reviews. In total, 33 studies were summarized. Clinical photography is commonly used in biopsy site marking, assessment, diagnosis, disease monitoring, evaluation of treatment response, medical education, research, seeking advice from colleagues, and teledermatology. Although dermatologic photography remains devoid of skin of color representation, photographic considerations for darker skin are available. Most patients support medical photography, with a preference for clinical photographs to be taken by their own physicians, and for use of clinic/hospital‐owned cameras over personal devices. Pertinent medical‐legal issues include concerns around privacy, personal device use, and documentation of consent. Photography in dermatology is continuously evolving with broader applications. Improved practices and innovations will benefit individuals of various skin tones. Management of consent and privacy must be upheld to sustain the increasing ease of image capture and sharing.
Association between the use of lipid‐lowering drugs and the risk of inflammatory bowel disease
Authors: Liu Xuxu , Lv Zhenyi , Xie Zhihong , Wang Qiang , Yao Wenchao , Yu Jingjing , Jing Qingxu , Meng Xianzhi , Ma Biao , Xue Dongbo , Hao Chenjun 
Published: July 2023

AbstractBackgroundObservational studies have suggested an association between lipid‐lowering drugs and inflammatory bowel disease (IBD) risk. This study aimed to assess the causal influence of lipid‐lowering agents on IBD risk using Mendelian randomization analysis.MethodIn a population of 173,082 individuals of European ancestry, 55 single‐nucleotide polymorphisms were identified as instrumental variables for 6 lipid‐lowering drug targets (HMGCR, NPC1LC, PCSK9, LDLR, CETP and APOB). Summary statistics for the genome‐wide association study of IBD, ulcerative colitis (UC) and Crohn's disease (CD) were obtained from the FinnGen consortium, Program in Complex Trait Genomics and UK Biobank. Inverse‐variance weighted was employed as the primary MR method, and odds ratios (ORs) with 95% confidence intervals were reported as the results. Sensitivity analyses using conventional MR methods were conducted to assess result robustness.ResultsGene‐proxied inhibition of Niemann‐Pick C1‐like 1 (NPC1L1) was associated with an increased IBD risk (OR [95% CI]: 2.31 [1.38, 3.85]; p = .001), particularly in UC (OR [95% CI]: 2.40 [1.21, 4.74], p = .012), but not in CD. This finding was replicated in the validation cohort. Additionally, gene‐proxied inhibition of low‐density lipoprotein receptor was associated with reduced IBD (OR [95% CI]: .72 [.60, .87], p < .001) and UC risk (OR [95% CI]: .74 [.59, .92], p = .006), although this result was not replicated in the validation cohort. Other drug targets did not show significant associations with IBD, UC or CD risk.ConclusionInhibition of the lipid‐lowering drug‐target NPC1L1 leads to an increased IBD risk, mainly in the UC population.
An overlooked mimic? Autoimmune myelofibrosis—A scoping review of the literature
Authors: Amel Riazat‐Kesh Yosef Joseph Rene , Maraveyas Alexander , Martin Lily , Tremblay Douglas 
Published: July 2023

AbstractBackground and ObjectivesAutoimmune myelofibrosis (AIMF) is a rare cause of bone marrow fibrosis (BMF) occurring in the presence or absence of a defined autoimmune disease (secondary or primary AIMF, sAIMF/pAIMF, respectively). Unlike primary myelofibrosis (PMF), AIMF responds well to immunosuppressive therapy with a benign clinical course. Diagnostic criteria for AIMF in opposition to PMF have been lacking, though recent work has helped better characterise molecular and pathological features of AIMF, improving diagnostic precision.MethodsUsing a modern clinical and pathophysiological understanding of AIMF, we apply scoping review methodology and rigorous case‐criteria to retrospectively analyse the case literature. We examine its patient‐population, describing patient‐associated factors, presentation, bone marrow pathology, genetics, treatment and outcomes.ResultsFifty‐five studies were identified, describing 139 AIMF patients. Patients were mostly young females (~4:1 ratio female:male, median age 40.8 years) and typically presented with cytopenias. Splenomegaly was rare. sAIMF was more common than pAIMF (~3:1 ratio), and most cases responded well to immunosuppressive therapy.ConclusionsOur results strengthen the emerging picture of AIMF's patient population, natural history and response to treatment. Further work should continue to use reproducible diagnostic criteria, and explore AIMF's pathophysiology, response to different therapies, and sequelae over larger timescales, as well as differences between pAIMF, sAIMF and PMF.
Determinants and effects of trade credit financing: Evidence from the maritime shipping industry
Authors: Mantzari Elisavet , Merika Anna , Sigalas Christos 
Published: July 2023

AbstractThis paper investigates the factors and effects of trade credit, as an alternative source of capital, by employing a generalized method of moments instrumenting for endogeneity based on a panel data set of public maritime shipping companies and compatible companies in other industries. Our study shows that the magnitude of trade credit is affected by profitability, financial leverage, company size, cost of capital, financial distress, institutional ownership, corporate power, corporate liquidity, asset intensity, and corporate growth. It also suggests that trade credit affects financial performance, equity value, and risk. These empirical findings yield important implications for principal financial officers, as discussed herein.
Mimicking fat grafting of fibrotic scars using 3D‐organotypic skin cultures
Authors: Raktoe Rajiv , Kwee Anastasia K. A. L. , Rietveld Marion , Marsidi Nick , Genders Roel , Quint Koen , van Doorn Remco , van Zuijlen Paul , Ghalbzouri Abdoelwaheb E. L. 
Published: July 2023

AbstractWound healing of deep burn injuries is often accompanied by severe scarring, such as hypertrophic scar (HTS) formation. In severe burn wounds, where the subcutis is also damaged, the scars adhere to structures underneath, resulting in stiffness of the scar and impaired motion. Over the recent years, a promising solution has emerged: autologous fat grafting, also known as lipofilling. Previous clinical reports have shown that the anti‐fibrotic effect has been attributed to the presence of adipose‐derived stromal cells (ADSC). In the proposed study, we aim to investigate the effect of fat grafting in 3D organotypic skin cultures mimicking an HTS‐like environment. To this end, organotypic skin cultures were embedded with normal skin fibroblasts (NF) or HTS‐derived fibroblasts with or without incorporation of human adipose subcutaneous tissue (ADT) and one part was thermally wounded to examine their effect on epithelialization. The developed skin cultures were analysed on morphology and protein level. Analysis revealed that ADT‐containing organotypic skin cultures comprise an improved epidermal homeostasis, and a fully formed basement membrane, similar to native human skin (NHS). Furthermore, the addition of ADT significantly reduced myofibroblast presence, which indicates its anti‐fibrotic effect. Finally, re‐epithelialization measurements showed that ADT reduced re‐epithelialization in skin cultures embedded with NFs, whereas HTS‐fibroblast‐embedded skin cultures showed complete wound closure. In conclusion, we succeeded in developing a 3D organotypic HTS‐skin model incorporated with subcutaneous tissue that allows further investigation on the molecular mechanism of fat grafting.