bluuebunny/crossref_metadata_2025_split huggingface dataset:
TALAIA: a 3D visual dictionary for protein structures
Authors: Alemany-Chavarria Mercè , Rodríguez-Guerra Jaime , Maréchal Jean-Didier 
Published: August 2023

Abstract

Motivation
Graphical analysis of the molecular structure of proteins can be very complex. Full-atom representations retain most geometric information but are generally crowded, and key structural patterns can be challenging to identify. Non-full-atom representations could be more instructive on physicochemical aspects but be insufficiently detailed regarding shapes (e.g. entity beans-like models in coarse grain approaches) or simple properties of amino acids (e.g. representation of superficial electrostatic properties). In this work, we present TALAIA a visual dictionary that aims to provide another layer of structural representations.
TALAIA offers a visual grammar that combines simple representations of amino acids while retaining their general geometry and physicochemical properties. It uses unique objects, with differentiated shapes and colors to represent amino acids. It makes easier to spot crucial molecular information, including patches of amino acids or key interactions between side chains. Most conventions used in TALAIA are standard in chemistry and biochemistry, so experimentalists and modelers can rapidly grasp the meaning of any TALAIA depiction.

Results
We propose TALAIA as a tool that renders protein structures and encodes structure and physicochemical aspects as a simple visual grammar. The approach is fast, highly informative, and intuitive, allowing the identification of possible interactions, hydrophobic patches, and other characteristic structural features at first glance. The first implementation of TALAIA can be found at https://github.com/insilichem/talaia.
The Harmonising Outcome Measures for Eczema (HOME) implementation roadmap
Authors: Leshem Yael A , Simpson Eric L , Apfelbacher Christian , Spuls Phyllis I , Thomas Kim S , Schmitt Jochen , Howells Laura , Gerbens Louise A A , Jacobson Michael E , Katoh Norito , Williams Hywel C 
Published: August 2023

Abstract

Background
Core outcome sets (COS) are consensus-driven sets of minimum outcomes that should be measured and reported in all clinical trials. COS aim to reduce heterogeneity in outcome measurement and reporting, and selective outcome reporting. Implementing COS into clinical trials is challenging. Guidance to improve COS uptake in dermatology is lacking.

Objectives
To develop a structured practical guide to COS implementation.

Methods
Members of the Harmonising Outcome Measurement for Eczema (HOME) executive committee developed an expert opinion-based roadmap founded on a combination of a review of the COS implementation literature, the Core Outcome Measures in Effectiveness Trials (COMET) initiative resources, input from HOME members and experience in COS development and clinical trials.

Results
The data review and input from HOME members was synthesized into themes, which guided roadmap development: (a) barriers and facilitators to COS uptake based on stakeholder awareness/engagement and COS features; and (b) key implementation science principles (assessment-driven, data-centred, priority-based and context-sensitive). The HOME implementation roadmap follows three stages. Firstly, the COS uptake scope and goals need to be defined. Secondly, during COS development, preparation for future implementation is supported by establishing the COS as a credible evidence-informed consensus by applying robust COS development methodology, engaging multiple stakeholders, fostering sustained and global engagement, emphasizing COS ease of use and universal applicability, and providing recommendations on COS use. Thirdly, incorporating completed COS into primary (trials) and secondary (reviews) research is an iterative process starting with mapping COS uptake and stakeholders’ attitudes, followed by designing and carrying out targeted implementation projects. Main themes for implementation projects identified at HOME are stakeholder awareness/engagement; universal applicability for different populations; and improving ease-of-use by reducing administrative and study burden. Formal implementation frameworks can be used to identify implementation barriers/facilitators and to design implementation strategies. The effect of these strategies on uptake should be evaluated and implementation plans adjusted accordingly.

Conclusions
COS can improve the quality and applicability of research and, so, clinical practice but can only succeed if used and reported consistently. The HOME implementation roadmap is an extension of the original HOME roadmap for COS development and provides a pragmatic framework to develop COS implementation strategies.
MALAT1 regulates network of microRNA-15a/16–VEGFA to promote tumorigenesis and angiogenesis in multiple myeloma
Authors: Yan Han , Gao Su , Xu Aoshuang , Zuo Liping , Zhang Jiasi , Zhao Yuhong , Cheng Qianwen , Yin Xuejiao , Sun Chunyan , Hu Yu 
Published: August 2023

Abstract
MALAT1 is one of the most hopeful members implicated in angiogenesis in a variety of non-malignant diseases. In multiple myeloma (MM), MALAT1 is recognized as the most highly expressed long non-coding RNA. However, the functional roles of MALAT1 in angiogenesis and the responsible mechanisms have not yet been explored. Herein, we discovered a novel regulatory network dependent on MALAT1 in relation to MM tumorigenesis and angiogenesis. We observed that MALAT1 was upregulated in MM and significantly associated with poor overall survival. MALAT1 knockdown suppressed MM cell proliferation and promoted apoptosis, while restricting endothelial cells angiogenesis. Moreover, MALAT1 directly targeted microRNA-15a/16, and microRNA-15a/16 suppression partly reverted the effects of MALAT1 deletion on MM cells in vitro as well as tumor growth and angiogenesis in vivo. In addition, further study indicated that MALAT1 functioned as a competing endogenous RNA for microRNA-15a/16 to regulate vascular endothelial growth factor A (VEGFA) expression. Our results suggest that MALAT1 plays an important role in the regulatory axis of microRNA-15a/16–VEGFA to promote tumorigenicity and angiogenesis in MM. Consequently, MALAT1 could serve as a novel promising biomarker and a potential antiangiogenic target against MM.
Complement terminal pathway inhibition reduces peritoneal injuries in a rat peritonitis model
Authors: Kamegai Naoki , Kim Hangsoo , Suzuki Yasuhiro , Fukui Sosuke , Kojima Hiroshi , Maruyama Shoichi , Morgan B Paul , Zelek Wioleta Milena , Mizuno Masashi 
Published: August 2023

Abstract
Peritonitis and the resulting peritoneal injuries are common problems that prevent long-term peritoneal dialysis (PD) therapy in patients with end-stage kidney diseases. Previously, we have analyzed the relationship between the complement system and progression of peritoneal injuries associated with PD, particularly focusing on the early activation pathways and effects of the anaphylatoxins. We here utilized a novel mAb 2H2 that blocks assembly of the membrane attack complex (MAC) to investigate roles of the complement terminal pathway in PD-associated peritoneal injury. We intraperitoneally injected mAb 2H2 anti-C5b-7 (2.5 or 5 mg/rat) once or twice over the five-day course of the experiment to investigate the effects of inhibiting formation of MAC in a fungal rat peritonitis model caused by repeated intraperitoneal administration of zymosan after methylglyoxal pretreatment (Zy/MGO model). Rats were sacrificed on day 5 and macroscopic changes in both parietal and visceral peritoneum evaluated. Peritoneal thickness, the abundance of fibrinogen and complement C3 and MAC deposition in tissue and accumulation of inflammatory cells were pathologically assessed. The results showed that mAb 2H2, but not isotype control mAb, reduced peritoneal thickness and accumulation of inflammatory cells in a dose and frequency-dependent manner in the Zy/MGO model. These effects were accompanied by decreased C3, MAC, and fibrinogen deposition in peritoneum. In conclusion, in the rat Zy/MGO model, complement terminal pathway activation and MAC formation substantially contributed to development of peritoneal injuries, suggesting that MAC-targeted therapies might be effective in preventing development of peritoneal injuries in humans.
Integrating Intestinal Ultrasound into an Inflammatory Bowel Disease Practice: How to Get Started
Authors: Abraham Bincy P , Reddy Dheeraj , Saleh Adam 
Published: August 2023

Abstract
Intestinal ultrasound (IUS) offers a safe, noninvasive, point-of-care tool for diagnosing and monitoring disease activity in patients with inflammatory bowel disease (IBD). IUS is used widely in Europe and Canada for IBD, but it remains underutilized in the United States. Growing interest in IUS in the United States has prompted many IBD centers to train their faculty in IUS. This, however, raises questions about how to effectively use this new tool in the United States, which does not use a social medicine model like those implemented in Europe and Canada. Here, we provide a practical framework for incorporating IUS in an IBD practice in the United States, including training requirements, equipment, and protocols for implementing IUS in daily practice.
Community efforts to promote vaccine uptake in a rural setting: a qualitative interview study
Authors: Nanyonjo Agnes , Nelson David , Sayers Emma , Lall Priya , Vernon-Wilson Elizabeth , Tetui Moses , Grindrod Kelly , Kane Ros , Gussy Mark , Siriwardena Niro 
Published: August 2023

Abstract
Vaccine hesitancy has been identified as one of the top 10 threats to global health. The causes of low vaccine uptake are many and vary at micro and macro levels. However, rural and remote coastal areas in the UK experience unique vaccine inequalities due to high levels of deprivation and their unique and complex access-related problems. This study aimed to explore community efforts to promote vaccine uptake during the COVID-19 pandemic and understand how the COVID-19 vaccination campaign was experienced by the public. We conducted an exploratory descriptive qualitative study using semi-structured interviews with decision-makers, health professionals and community members in Lincolnshire, a predominantly rural county with a long coastline, a large population of white minority ethnicities, and those living in caravan and temporary housing. Data were analysed using conventional content analysis. Overcoming the various access barriers to vaccination uptake involved working with local media stations, local communities and local community groups, translation of information, bringing vaccines closer to the people through pop-up and mobile clinics and provision of transport and ensuring confidentiality. There is a need to employ inclusive targeted non-conventional care interventions whilst dealing with complex problems as occur in rural and remote coastal regions.
Protecting the Arctic Indigenous Peoples’ Livelihoods in the Face of Climate Change: The Potential of Regional Human Rights Law and the Law of the Sea
Authors: Mardikian Lisa , Galani Sofia 
Published: August 2023

Abstract
Climate change presents existential challenges for the livelihoods of indigenous peoples, which depend on vulnerable ecosystems prone to extreme weather phenomena. Of all indigenous communities, those living in the Arctic have been worst affected. This raises the question to what extent international law can be mobilized to address the endangered livelihoods of Arctic indigenous peoples in light of rapid changes in the Arctic environment. This article examines two dimensions of the protection of livelihoods: an internal one—i.e. legal entitlements over assets, land and income—and an external one—i.e. the living environment in the Arctic. In so doing, the article analyses the right to property under regional human rights law and rules on the protection of marine resources under the law of the sea. Reflecting on relevant jurisprudence, it shows that both legal areas could provide important elements of litigation strategies to address the human rights costs of climate change.
In Quest of Influences of Polish Language Dictionaries on the Oldest Polish Sign Language Dictionary
Authors: Linde-Usiekniewicz Jadwiga , Łozińska Sylwia 
Published: August 2023

Abstract
The paper examines whether the authors of the very first Polish Sign Language dictionary, Słownik mimiczny dla głuchoniemych i osób z nimi styczność mających ‘A gestural dictionary for deaf and dumb and persons who have contact with them’, published in 1879, may have been influenced by any of the spoken Polish monolingual dictionaries available at that time. As there is no historical documentation about the circumstances in which Słownik mimiczny was compiled, the inquiry necessarily relies exclusively on internal evidence: comparison of headword spelling, alphabetical ordering, direction of cross-references and the content of sample entries. The results indicate that such influence, if any, was only minor, and that the lexicographic strategies applied in Słownik mimiczny most likely resulted from the authors’ knowledge of Polish Sign Language and teaching practice.
Pharmacy student contribution to direct patient care during inpatient hospital experiential rotations: a scoping review
Authors: Kennie-Kaulbach Natalie , Cameron Karen , Humphrey Mari , Donovan Cortney , Isenor Jennifer E , Toombs Kent , Fernandes Olavo A 
Published: August 2023

Abstract

Objectives
The aim of this scoping review was to identify and characterise pharmacy students’ contributions to extend pharmacist’s direct patient care during inpatient hospital experiential rotations.

Methods
A search of PubMed, Embase and CINAHL databases from 2000 to July 2021 was conducted. Articles were included if they involved pharmacy students during experiential rotations, described student’s contribution to direct patient care in the inpatient hospital setting, and reported outcomes. Included articles were categorised according to clinical pharmacy key performance indicators (cpKPIs) and non-cpKPI care activities. Students’ contributions to reported outcomes were extracted and summarised.

Key findings
Thirty-six of 1182 identified articles were included which were either descriptive or quasi-experimental design. Studies reported student involvement in the delivery of single or multiple cpKPIs: medication reconciliation on admission (n = 13), pharmaceutical care (n = 13), interprofessional care rounds (n = 4), patient education during hospital stay (n = 6), medication reconciliation at discharge (n = 7) and patient education at discharge (n = 10). Eight studies reported student involvement in non-cpKPI activities, including clinical interventions (n = 5), clinical services (n = 2) and postdischarge follow-up (n = 1). Reported outcomes included service measure counts, process and clinical outcome measures.

Summary
This review identified the contributions of pharmacy students in the provision of a range of direct patient care services and associated outcomes during experiential rotations in the inpatient hospital setting. Students delivering care as part of the pharmacy team as ‘care extenders’ has the potential to expose more patients to key pharmacist activities that have been linked to demonstrated positive outcomes.
Prevalence of HIV-1 drug resistance mutations in proviral DNA in the Swiss HIV Cohort Study, a retrospective study from 1995 to 2018
Authors: Jaha Bashkim , Schenkel Corinne D , Jörimann Lisa , Huber Michael , Zaheri Maryam , Neumann Kathrin , Leemann Christine , Calmy Alexandra , Cavassini Matthias , Kouyos Roger D , Günthard Huldrych F , Metzner Karin J ,   Swiss HIV Cohort Study, Anagnostopoulos A , Battegay M , Bernasconi E , Böni J , Braun D L , Bucher H C , Calmy A , Cavassini M , Ciuffi A , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux C A , Günthard H , Haerry D , Hasse B , Hirsch H H , Hoffmann M , Hösli I , Huber M , Kahlert C R , Kaiser L , Keiser O , Klimkait T , Kouyos R D , Kovari H , Kusejko K , Ledergerber B , Martinetti G , Martinez de Tejada B , Marzolini C , Metzner K J , Müller N , Nicca D , Paioni P , Pantaleo G , Perreau M , Rauch A , Rudin C , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Vernazza P , Wandeler G , Weber R , Yerly S 
Published: August 2023

Abstract

Background
Genotypic resistance testing (GRT) is routinely performed upon diagnosis of HIV-1 infection or during virological failure using plasma viral RNA. An alternative source for GRT could be cellular HIV-1 DNA.

Objectives
A substantial number of participants in the Swiss HIV Cohort Study (SHCS) never received GRT. We applied a method that enables access to the near full-length proviral HIV-1 genome without requiring detectable viraemia.

Methods
Nine hundred and sixty-two PBMC specimens were received. Our two-step nested PCR protocol was applied to generate two overlapping long-range amplicons of the HIV-1 genome, sequenced by next-generation sequencing (NGS) and analysed by MinVar, a pipeline to detect drug resistance mutations (DRMs).

Results
Six hundred and eighty-one (70.8%) of the samples were successfully amplified, sequenced and analysed by MinVar. Only partial information of the pol gene was contained in 82/681 (12%), probably due to naturally occurring deletions in the proviral sequence. All common HIV-1 subtypes were successfully sequenced. We detected at least one major DRM at high frequency (≥15%) in 331/599 (55.3%) individuals. Excluding APOBEC-signature (G-to-A mutation) DRMs, 145/599 (24.2%) individuals carried at least one major DRM. RT-inhibitor DRMs were most prevalent. The experienced time on ART was significantly longer in DRM carriers (P = 0.001) independent of inclusion or exclusion of APOBEC-signature DRMs.

Conclusions
We successfully applied a reliable and efficient method to analyse near full-length HIV-1 proviral DNA and investigated DRMs in individuals with undetectable or low viraemia. Additionally, our data underscore the need for new computational tools to exclude APOBEC-related hypermutated NGS sequence reads for reporting DRMs.
Effect of dapagliflozin on COVID-19 infection and risk of hospitalization
Authors: Salgado-Barreira Angel , Seijas-Amigo Jose , Rodriguez-Mañero Moises , Piñeiro-Lamas María , Eiras Sonia , Cordero Alberto , Gonzalez-Juanatey Jose Ramon , Figueiras Adolfo 
Published: August 2023

Abstract

Background
Dapagliflozin has been proposed as a potential treatment for coronavirus disease 2019 (COVID-19) by reducing cytokine production and inflammation. However, there are limited data on its effectiveness. We aimed to evaluate the impact of dapagliflozin on COVID-19 severity (including hospitalization risk, ICU admission, in-hospital death and progression to severe COVID-19) and its potential on susceptibility to COVID-19 infection.

Methods
We conducted a population-based case-control study. For aim 1, we assessed COVID-19 severity in cases (positive PCR patients requiring hospitalization) and matched controls (negative PCR patients or positive PCR patients not requiring hospitalization). For aim 2, we compared positive PCR cases (hospitalized and non-hospitalized) with controls. Adjusted odds ratios (aORs) were calculated using a generalized linear mixed model.

Results
We analysed 86 602 subjects: 3060 were hospitalized cases, 26 757 were non-hospitalized cases and 56 785 were controls. Among the hospitalized COVID-19 patients, 228 were admitted to the ICU and 413 died. Dapagliflozin had no effect on the risk of hospitalization (aOR 0.98; 95% CI 0.65–1.48; P = 0.915), ICU admissions (aOR 1.21; 95% CI 0.34–4.25; P = 0.767) or in-hospital death (aOR 1.33; 95% CI 0.53–3.30; P = 0.543). Dapagliflozin reduced the risk of progression to severe COVID-19 by 35%, but this was not statistically significant (aOR 0.65; 95% CI 0.40–1.06; P = 0.086). Dapagliflozin was associated with a 30% increased risk of susceptibility to COVID-19 infection (aOR 1.31; 95% CI 1.05–1.62; P = 0.015).

Conclusions
Use of dapagliflozin prior to SARS-CoV-2 infection was not associated with an increased risk of hospitalization, ICU admission, mortality or progression to severe COVID-19. However, it was associated with an increased risk of susceptibility to COVID-19 infection.
Alkylation of nucleobases by 2-chloro-N,N-diethylethanamine hydrochloride (CDEAH) sensitizes PARP1-deficient tumors
Authors: Wie Minwoo , Khim Keon Woo , Groehler IV Arnold S , Heo Soomin , Woo Junhyeok , Son Kook , Lee Eun A , Ra Jae Sun , Hong Sung You , Schärer Orlando D , Choi Jang Hyun , Myung Kyungjae 
Published: August 2023

Abstract
Targeting BRCA1- and BRCA2-deficient tumors through synthetic lethality using poly(ADP-ribose) polymerase inhibitors (PARPi) has emerged as a successful strategy for cancer therapy. PARPi monotherapy has shown excellent efficacy and safety profiles in clinical practice but is limited by the need for tumor genome mutations in BRCA or other homologous recombination genes as well as the rapid emergence of resistance. In this study, we identified 2-chloro-N,N-diethylethanamine hydrochloride (CDEAH) as a small molecule that selectively kills PARP1- and xeroderma pigmentosum A-deficient cells. CDEAH is a monofunctional alkylating agent that preferentially alkylates guanine nucleobases, forming DNA adducts that can be removed from DNA by either a PARP1-dependent base excision repair or nucleotide excision repair. Treatment of PARP1-deficient cells leads to the formation of strand breaks, an accumulation of cells in S phase and activation of the DNA damage response. Furthermore, CDEAH selectively inhibits PARP1-deficient xenograft tumor growth compared to isogenic PARP1-proficient tumors. Collectively, we report the discovery of an alkylating agent inducing DNA damage that requires PARP1 activity for repair and acts synergistically with PARPi.