bluuebunny/crossref_metadata_2025_split huggingface dataset:
Somatic mutations in benign breast disease tissues and association with breast cancer risk
Authors: Winham Stacey J. , Wang Chen , Heinzen Ethan P. , Bhagwate Aditya , Liu Yuanhang , McDonough Samantha J. , Stallings-Mann Melody L. , Frost Marlene H. , Vierkant Robert A. , Denison Lori A. , Carter Jodi M. , Sherman Mark E. , Radisky Derek C. , Degnim Amy C. , Cunningham Julie M. 
Published: July 2021

Abstract
Background
Benign breast disease (BBD) is a risk factor for breast cancer (BC); however, little is known about the genetic alterations present at the time of BBD diagnosis and how these relate to risk of incident BC.

Methods
A subset of a long-term BBD cohort was selected to examine DNA variation across three BBD groups (42 future estrogen receptor-positive (ER+) BC, 36 future estrogen receptor-negative (ER−) BC, and 42 controls cancer-free for at least 16 years post-BBD). DNA extracted from archival formalin fixed, paraffin-embedded (FFPE) tissue blocks was analyzed for presence of DNA alterations using a targeted panel of 93 BC-associated genes. To address artifacts frequently observed in FFPE tissues (e.g., C>T changes), we applied three filtering strategies based on alternative allele frequencies and nucleotide substitution context. Gene-level associations were performed using two types of burden tests and adjusted for clinical and technical covariates.

Results
After filtering, the variant frequency of SNPs in our sample was highly consistent with population allele frequencies reported in 1 KG/ExAC (0.986, p < 1e−16). The top ten genes found to be nominally associated with later cancer status by four of 12 association methods(p < 0.05) were MED12, MSH2, BRIP1, PMS1, GATA3, MUC16, FAM175A, EXT2, MLH1 and TGFB1, although these were not statistically significant in permutation testing. However, all 10 gene-level associations had OR < 1 with lower mutation burden in controls compared to cases, which was marginally statistically significant in permutation testing (p = 0.04). Comparing between the three case groups, BBD ER+ cases were closer to controls in mutation profile, while BBD ER− cases were distinct. Notably, the variant burden was significantly higher in controls than in either ER+ or ER− cases. CD45 expression was associated with mutational burden (p < 0.001).

Conclusions
Somatic mutations were more frequent in benign breast tissue from women who did not develop cancer, opening questions of clonal diversity or immune-mediated restraint on future cancer development. CD45 expression was positively associated with mutational burden, most strongly in controls. Further studies in both normal and premalignant tissues are needed to better understand the role of somatic gene mutations and their contribution to future cancer development.
Variation in brief treatment for substance use disorder: a qualitative investigation of four federally qualified health centers with SBIRT services
Authors: Watson Dennis P. , Staton Monte D. , Dennis Michael L. , Grella Christine E. , Scott Christy K. 
Published: July 2021

Abstract
Background
Brief treatment (BT) can be an effective, short-term, and low-cost treatment option for many people who misuse alcohol and drugs. However, inconsistent implementation is suggested to result in BT that often looks and potentially costs similar to regular outpatient care. Prior research is also rife with inconsistent operationalizations regarding the measurement of BT received by patients. As such, there is a need to more explicitly identify and document variations in BT practice.

Methods
A qualitative investigation of BT in four Federally Qualified Health Centers (FQHC) was undertaken as a sub study of a larger clinical trial. Researchers interviewed 12 staff (administrators and clinicians) involved in BT oversight, referral, or delivery within the four FQHCs. Data were analyzed following an inductive approach guided by the primary research questions.

Results
Findings demonstrate considerable differences in how BT was conceptualized and implemented within the FQHCs. This included a variety of ways in which BT was presented and described to patients that likely impacts how they perceive the BT they receive, including potentially not understanding they received substance use disorder treatment at all.

Conclusions
The findings raise questions regarding the validity of prior research, demonstrating more objective definitions of BT and fidelity checklists are needed to ensure integrity of results. Future work in this area should seek to understand BT as practiced among a larger sample of providers and the direct experiences and perspectives of patients. There is also a need for more consistent implementation, quality assurance guidelines, and standardized stage of change assessments to aid practitioners.
Neutrophil extracellular traps in cancer: not only catching microbes
Authors: Ronchetti Livia , Boubaker Nouha Setti , Barba Maddalena , Vici Patrizia , Gurtner Aymone , Piaggio Giulia 
Published: July 2021

AbstractNeutrophils are the most abundant type of white blood cells circulating throughout the bloodstream and are often considered the frontline defenders in innate immunity. However, neutrophils are increasingly being recognized as having an important role in tumorigenesis and carcinogenesis due to their aberrant activation by molecules released into the tumor microenvironment. One defensive response of neutrophils that is aberrantly triggered during the neoplastic process is called NETosis, where activated neutrophils expel their DNA and intracellular contents in a web-like structure known as a neutrophil extracellular trap (NET). In cancer, NETosis has been linked to increased disease progression, metastasis, and complications such as venous thromboembolism. NET structures released by neutrophils can also serve as a scaffold for clot formation, shining new light on the role of neutrophils and NETosis in coagulation-mediated diseases.Here, we review current available knowledge regarding NET and the related NETosis process in cancer patients, with an emphasis on pre-clinical and clinical data fostering the identification and validation of biomarkers of NET with a predictive/prognostic role in cancer patients treated with immunotherapy agents. NETosis biomarkers, e.g., citH3, may integrate correlates of immunogenicity currently available (e.g., PD-L1 expression, TMB, TILs) and help select the subsets of patients who may most benefit from the use of the therapeutic weapons under discussion.
Transcatheter arterial embolization for severe blunt liver injury in hemodynamically unstable patients: a 15-year retrospective study
Authors: Tamura Satoshi , Maruhashi Takaaki , Kashimi Fumie , Kurihara Yutaro , Masuda Tomonari , Hanajima Tasuku , Kataoka Yuichi , Asari Yasushi 
Published: July 2021

Abstract
Background
Transcatheter arterial embolization (TAE) is the first-line nonsurgical treatment for severe blunt liver injury in patients, whereas operative management (OM) is recommended for hemodynamically unstable patients. This study investigated the comparative efficacy of TAE in hemodynamically unstable patients who responded to initial infusion therapy.

Methods
This retrospective study enrolled patients with severe blunt liver injuries, which were of grades III–V according to the American Association for the Surgery of Trauma Organ Injury Scale (OIS). Patients who responded to initial infusion therapy underwent computed tomography to determine the treatment plan. A shock index > 1, despite undergoing initial infusion therapy, was defined as hemodynamic instability. We compared the clinical outcomes and mortality rates between patients who received OM and those who underwent TAE.

Results
Sixty-two patients were included (eight and 54 who underwent OM and TAE, respectively; mean injury severity score, 26.6). The overall in-hospital mortality rate was 6% (13% OM vs. 6% TAE, p = 0.50), and the hemodynamic instability was 35% (88% OM vs. 28% TAE, p < 0.01). Hemodynamically unstable patients who underwent TAE had 7% in-hospital mortality and 7% clinical failure. Logistic regression analysis showed that the treatment choice was not a predictor of outcome, whereas hemodynamic instability was an independent predictor of intensive care unit stay ≥7 days (odds ratio [OR], 3.80; p = 0.05) and massive blood transfusion (OR, 7.25; p = 0.01); OIS grades IV–V were predictors of complications (OR, 6.61; p < 0.01).

Conclusions
TAE in hemodynamically unstable patients who responded to initial infusion therapy to some extent has acceptable in-hospital mortality and clinical failure rates. Hemodynamic instability and OIS, but not treatment choice, affected the clinical outcomes.
Health service experiences and preferences of frail home care clients and their family and friend caregivers during the COVID-19 pandemic
Authors: Weeks Lori E. , Nesto Sue , Hiebert Bradley , Warner Grace , Luciano Wendy , Ledoux Kathleen , Donelle Lorie 
Published: July 2021

Abstract
Objective
The COVID-19 pandemic has brought about a major upheaval in the lives of older adults and their family/friend caregivers, including those utilizing home care services. In this article, we focus on results from a qualitative component added to a pragmatic randomized controlled trial that focuses on the experiences of our study participants during COVID-19. A total of 29 participants responded to the COVID-19 related questions focused on their health services experiences and preferences from March-June 2020 including 10 home care clients and 19 family/friend caregivers in the provinces of Ontario and Nova Scotia, Canada.

Results
Many participants were affected drastically by the elimination or reduction of access to services, highlighting the vulnerability of home care clients and their caregivers during COVID-19. This took an emotional toll on home care clients and increased the need for family/friend caregiver support. While many participants expressed reduced desire to utilize residential long-term care homes, some caregivers found that passive remote monitoring technology was particularly useful within the COVID-19 context. Our results provide important insights into the ways the older adults and their caregivers have been affected during the COVID-19 context and how to better support them in the future.
Combination of mesenchymal stem cells and nicorandil: an emerging therapeutic challenge against COVID-19 infection-induced multiple organ dysfunction
Authors: Safari Anahid , Lionetti Vicenzo , Razeghian-Jahromi Iman 
Published: July 2021

AbstractThe recent COronaVIrus Disease (COVID)-19 pandemic has placed an unprecedented burden on the drug development opportunity to prevent the onset of multi-organ failure.Emerging experimental reports have highlighted the beneficial effects of mesenchymal stem cell (MSC) administration against COVID-19. MSCs and their derived exosomes may attenuate SARS-CoV-2-induced inflammatory response through managing the immune cell function and cytokine expression. Although these are promising results, the exposure of MSCs to chemical compounds with pharmacological activities may further improve their homing, survival, and paracrine machinery.Nicorandil (N-[2-hydroxyethyl]-nicotinamide nitrate), an established adenosine triphosphate-sensitive potassium channel opener, is recently hypothesized to modulate inflammation as well as cell injury and death in COVID-19-affected lungs through inhibiting reactive oxygen species levels and apoptosis. Since it also exerts protective effects against hypoxia-induced MSC apoptosis, we assumed that transplanted MSCs combined to long-term nicorandil administration may survive longer in a severely inflamed microenvironment and have more beneficial effects in the treatment of SARS-CoV-2 infection than MSCs alone.
In situ transplantation of adipose-derived stem cells via photoactivation improves glucose metabolism in obese mice
Authors: Zhu Luochen , Feng Ziqian , Shu Xin , Gao Qian , Wu Jiaqi , Du Zuoqin , Li Rong , Wang Liqun , Chen Ni , Li Yi , Luo Mao , Wu Jianbo 
Published: July 2021

Abstract
Background
Accumulating evidence suggests that enhanced adipose tissue macrophages (ATMs) are associated with metabolic disorders in obesity and type 2 diabetes. However, therapeutic persistence and reduced homing stem cell function following cell delivery remains a critical hurdle for the clinical translation of stem cells in current approaches.

Methods
We demonstrate that the effect of a combined application of photoactivation and adipose-derived stem cells (ASCs) using transplantation into visceral epididymal adipose tissue (EAT) in obesity. Cultured ASCs were derived from subcutaneous white adipose tissue isolated from mice fed a normal diet (ND).

Results
In diet-induced obesity, implantation of light-treated ASCs improved glucose tolerance and ameliorated systemic insulin resistance. Intriguingly, compared with non-light-treated ASCs, light-treated ASCs reduced monocyte infiltration and the levels of ATMs in EAT. Moreover, implantation of light-treated ASCs exerts more anti-inflammatory effects by suppressing M1 polarization and enhancing macrophage M2 polarization in EAT. Mass spectrometry revealed that light-treated human obese ASCs conditioned medium retained a more complete secretome with significant downregulation of pro-inflammatory cytokines and chemokines.

Conclusions
These data suggest that the combined application of photoactivation and ASCs using transplantation into dysfunctional adipose tissue contribute to selective suppression of inflammatory responses and protection from insulin resistance in obesity and type 2 diabetes.
BioVerbNet: a large semantic-syntactic classification of verbs in biomedicine
Authors: Majewska Olga , Collins Charlotte , Baker Simon , Björne Jari , Brown Susan Windisch , Korhonen Anna , Palmer Martha 
Published: July 2021

AbstractBackgroundRecent advances in representation learning have enabled large strides in natural language understanding; However, verbal reasoning remains a challenge for state-of-the-art systems. External sources of structured, expert-curated verb-related knowledge have been shown to boost model performance in different Natural Language Processing (NLP) tasks where accurate handling of verb meaning and behaviour is critical. The costliness and time required for manual lexicon construction has been a major obstacle to porting the benefits of such resources to NLP in specialised domains, such as biomedicine. To address this issue, we combine a neural classification method with expert annotation to create BioVerbNet. This new resource comprises 693 verbs assigned to 22 top-level and 117 fine-grained semantic-syntactic verb classes. We make this resource available complete with semantic roles and VerbNet-style syntactic frames.ResultsWe demonstrate the utility of the new resource in boosting model performance in document- and sentence-level classification in biomedicine. We apply an established retrofitting method to harness the verb class membership knowledge from BioVerbNet and transform a pretrained word embedding space by pulling together verbs belonging to the same semantic-syntactic class. The BioVerbNet knowledge-aware embeddings surpass the non-specialised baseline by a significant margin on both tasks.ConclusionThis work introduces the first large, annotated semantic-syntactic classification of biomedical verbs, providing a detailed account of the annotation process, the key differences in verb behaviour between the general and biomedical domain, and the design choices made to accurately capture the meaning and properties of verbs used in biomedical texts. The demonstrated benefits of leveraging BioVerbNet in text classification suggest the resource could help systems better tackle challenging NLP tasks in biomedicine.
Single-crown restorations supported by short implants (6 mm) compared with standard-length implants (13 mm) in conjunction with maxillary sinus floor augmentation: a randomized, controlled clinical trial
Authors: Nielsen Helle Baungaard , Schou Søren , Bruun Niels Henrik , Starch-Jensen Thomas 
Published: July 2021

Abstract
Background
The purpose of the present study was to test the H0-hypothesis of no difference in the clinical and radiographical treatment outcome of single-crown restorations supported by short implants compared with standard length implants in conjunction with maxillary sinus floor augmentation (MSFA) after 1 year of functional implant loading. Forty patients with partial edentulism in the posterior part of the maxilla were randomly allocated to treatment involving single-crown restorations supported by short implants or standard length implants in conjunction with MSFA. Clinical and radiographical evaluation were used to assess survival of suprastructures and implants, peri-implant marginal bone loss (PIMBL), biological, and mechanical complications.

Results
Both treatment modalities were characterized by 100% survival of suprastructures and implants after 1 year. Mean PIMBL was 0.60 mm with short implants compared with 0.51 mm with standard length implants after 1 year of functional loading. There were no statistically significant differences in survival of suprastructure and implants, PIMBL, and mechanical complications between the two treatment modalities. However, a higher incidence of biological complications was associated with standard length implants in conjunction with MSFA.

Conclusion
Within the limitations of the present study, it can be concluded that single-crown restorations supported by short implants seems to be comparable with standard length implants in conjunction with MSFA. However, long-term studies are needed before final conclusions can be provided about the two treatment modalities.

Trial registration
Clinicaltrials.Gov ID: NCT04518020. Date of registration: August 14, 2020, retrospectively registered.
Incidence and determinants of perinatal mortality among women with obstructed labour in eastern Uganda: a prospective cohort study
Authors: Musaba Milton W. , Ndeezi Grace , Barageine Justus K. , Weeks Andrew D. , Wandabwa Julius N. , Mukunya David , Waako Paul , Odongkara Beatrice , Arach Agnes , Tulya-muhika Mugabe Kenneth , Kasede Napyo Agnes , Nankabirwa Victoria , Tumwine James K. 
Published: July 2021

Abstract
Background
In Uganda, the incidence and determinants of perinatal death in obstructed labour are not well documented. We determined the incidence and determinants of perinatal mortality among women with obstructed labour in Eastern Uganda.

Methods
Between July 2018 and September 2019, 584 with obstructed labour were recruited and followed up to the 7th day postnatal. Information on maternal characteristics, obstetric factors and laboratory parameters was collected. Each patient received the standard perioperative care. We used a generalized linear model for the Poisson family, with a log link and robust variance estimation to determine the association between the exposure variables and perinatal death.

Results
Of the 623 women diagnosed with obstructed labour, 584 met the eligibility criteria. There were 24 fresh still births (FSB) and 32 early neonatal deaths (ENND) giving an FSB rate of 43.8 (95% CI 28.3–64.4) deaths per 1000 total births; early neonatal death rate of 58.4 (95% CI 40.3–81.4) deaths per 1000 and an overall perinatal mortality rate of 102.2 (95% CI 79.4–130.6) deaths in the first 7 days of life. A mother being referred in active labour adjusted risk ratio of 2.84 (95% CI: 1.35–5.96) and having high blood lactate levels at recruitment adjusted risk ratio 2.71 (95% CI: 1.26–4.24) were the determinants of perinatal deaths.

Conclusions
The incidence of perinatal death was four times the regional and national average. Babies to women referred in active labour and those with high maternal blood lactate were more likely to die.
Immune-mediated inflammatory diseases and nutrition: results from an online survey on patients’ practices and perceptions
Authors: Pham Thao , Sokol Harry , Halioua Bruno , Pourcel Graziella , Brun Manuel , Pain Emilie , Testa Damien 
Published: July 2021

Abstract
Background
The central role of microbiota and the contribution of diet in immune-mediated inflammatory diseases (IMID) are increasingly examined. However, patients’ perspectives on nutrition and its impact on their disease has not received a lot of attention. We aimed to directly collect information from patients with IMID about their dietary behaviors and their perceptions of the influence of nutrition on their disease.

Methods
Adult patients with rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis, Crohn’s disease, ulcerative colitis or psoriasis registered in an online patient community were invited to participate in the study and complete an online self-administered questionnaire. We assessed patients’ dietary knowledge and choices by collecting information on the diet regimens they were following or recommended and their perceptions of the diet and its consequences on their disease.

Results
Fifty patients per target disease were included with a mean age of 48.1 years (95%CI 46.7–49.6). Other sociodemographic and clinical characteristics varied across the diseases. Since diagnosis, 44% of the patients changed their eating habits, mainly patients with inflammatory bowel disease with 69% of these making the change on their own initiative. Patients who did not change their diet habits reported not having received nutritional advice from their healthcare professionals (HCP) in 69% of the cases. The perceived impact of nutrition on their symptoms was mixed (overall 74% of the patients reported positive consequences and 60% negative ones) and varied across the diseases. Patients with psoriasis only experienced positive consequences from changing their diet, such as reduction of stress and improved mental health, while patients with Crohn’s disease reported more negative effects such as increased fatigue and disturbed sleep. Patients with rheumatic diseases and ulcerative colitis reported weight loss and better physical fitness, but also increased fatigue.

Conclusions
Even if differences exist across diseases, the importance of nutrition and its potential positive role in symptom management is acknowledged by the majority of the patients. However, there is a need and a demand from patients to receive more dietary advice. Developing therapeutic education tools on nutrition for people with IMID and involving patients’ organizations would provide useful information and encourage communication between HCP and patients.