bluuebunny/crossref_metadata_2025_split huggingface dataset:
The prevalence of people who inject drugs among those with HIV late presentation: a meta-analysis
Authors: Farhadian Negin , Karami Matin Behzad , Farnia Vahid , Zamanian Mohammad Hossein , Najafi Farid , Farhadian Maryam 
Published: February 2022

Abstract
Background
One of the most important routes of HIV transmission is through injections of drugs, and this group, due to unawareness of their infection, causes the spread of HIV. The coexistence of other opportunistic infections and diseases with HIV among people who inject drugs (PWID) imposes healthcare costs and is associated with high morbidity/mortality rates. Early detection of HIV among PWID is essential to prevent and control the spread of the disease.

Objectives
This study aimed to determine the prevalence of PWID among those with late presentation (LP).

Methods
Three electronic databases of PubMed, Scopus, and Web of science were searched using appropriate keywords. Besides the prevalence data reported for PWID among LP, the other outcomes of interest were LP defined as having CD4 count < 350 cells/μL or HIV or advanced disease defined with CD4 count < 200 cells/μL or HIV at the time of diagnosis.

Results
Of the 160 studies found, only eight met the inclusion criteria. Among those presented late, 36.5% were PWID (95% CI = 24.88–48.17). Compared with men who have sex with men (MSM), HIV-infected PWID had a higher risk of LP [OR = 1.51; 95% CI = 0.96–2.06].

Conclusion
The results of this study show that HIV is diagnosed late in the majority of PWID when CD4 is less than 350 cells/μL. Targeted interventions/strategies are highly required to reduce LP among HIV-infected PWID.
Cost analysis of negative-pressure wound therapy versus standard treatment of acute conflict-related extremity wounds within a randomized controlled trial
Authors: Älgå Andreas , Löfgren Jenny , Haweizy Rawand , Bashaireh Khaldoon , Wong Sidney , Forsberg Birger C. , von Schreeb Johan , Malmstedt Jonas 
Published: February 2022

Abstract
Background
Clinical outcomes after negative-pressure wound therapy (NPWT) and standard treatment of conflict-related extremity wounds are similar. In resource-limited settings, cost affects the choice of treatment. We aimed to estimate treatment-related costs of NPWT in comparison with standard treatment for conflict-related extremity wounds.

Methods
We derived outcome data from a randomized, controlled superiority trial that enrolled adult (≥ 18 years) patients with acute (≤ 72 h) conflict-related extremity wounds at two civilian hospitals in Jordan and Iraq. Primary endpoint was mean treatment-related healthcare costs (adjusted to 2019 US dollars).

Results
Patients were enrolled from June 9, 2015, to October 24, 2018. A total of 165 patients (155 men [93.9%]; 10 women [6.1%]; and median [IQR] age, 28 [21–34] years) were included in the analysis. The cost per patient treated with NPWT was $142 above that of standard treatment. Overall, results were robust in a sensitivity analysis.

Conclusions
With similar clinical outcomes compared to standard care, our results do not support the use of NPWT in routine treatment of conflict-related extremity wounds at civilian hospitals in resource scarce settings.
Trial registration NCT02444598.
HPV-mediated regulation of SMAD4 modulates the DNA damage response in head and neck cancer
Authors: Citro Simona , Miccolo Claudia , Medda Alessandro , Ghiani Lavinia , Tagliabue Marta , Ansarin Mohssen , Chiocca Susanna 
Published: February 2022

Abstract
Background
Head and Neck cancer (HNC) is a fatal malignancy with poor prognosis. Human Papillomavirus (HPV) infection is becoming the prominent cause of HNC in the western world, and studying the molecular mechanisms underlying its action in cancers is key towards targeted therapy. To replicate, HPV regulates the host DNA damage repair (DDR) pathway. SMAD4 is also involved in the regulation of the DDR machinery and likely plays important role in maintaining cell viability upon genotoxic stress. In this study, we investigated the role of HPV in the upregulation of SMAD4 to control the DDR response and facilitate its lifecycle.

Methods
SMAD4, Rad51 and CHK1 expression was assessed in HPV-positive and HPV-negative HNC using TCGA data, a panel of 14 HNC cell lines and 8 fresh tumour tissue samples from HNC patients. HPV16 expression was modulated by E6/E7 siRNA knock-down or transduction in HPV-positive HNC cell lines and Human Primary keratinocytes respectively. SMAD4 half-life was assessed by cycloheximide treatment in HNC cell lines, together with βTRCP1-dependent SMAD4 ubiquitination. SMAD4 siRNA knock-down was used to determine its role in HPV-mediated regulation of DDR machinery and to assess cisplatin sensitivity in HPV-positive HNC cell lines.

Results
We found that HPV increases SMAD4 expression is both HPV-positive HNC tumours and cell lines, impairing its degradation which is mediated by the E3 ubiquitin ligase βTRCP1. SMAD4 expression highly correlates with the expression of two main players of the DDR pathway, CHK1 and Rad51, which expression is also upregulated by the presence of HPV. In particular, we demonstrate that HPV stabilizes SMAD4 to increase CHK1 and Rad51 expression. In addition, SMAD4-deficient HPV-positive cells have increased sensitivity to cisplatin treatment.

Conclusions
Our results give a clear molecular mechanism at the basis of HPV regulation of the DDR pathway. In particular, we show how HPV stabilizes SMAD4 to promote DDR protein expression, which may be used to facilitate viral replication and HNC onset. Moreover, we found that SMAD4 silencing in HPV-positive HNC cell lines increases sensitivity to cisplatin treatment, suggesting that HPV-positive HNC with low SMAD4 expression may be preferentially susceptible to similar treatments.
Retrospective assessment of barriers and access to genetic services for hereditary cancer syndromes in an integrated health care delivery system
Authors: Muessig Kristin R. , Zepp Jamilyn M. , Keast Erin , Shuster Elizabeth E. , Reyes Ana A. , Arnold Briana , Ingphakorn Chalinya , Gilmore Marian J. , Kauffman Tia L. , Hunter Jessica Ezzell , Knerr Sarah , Feigelson Heather S. , Goddard Katrina A. B. 
Published: February 2022

Abstract
Background
A critical step in access to genetic testing for hereditary cancer syndromes is referral for genetic counseling to assess personal and family risk. Individuals meeting testing guidelines have the greatest need to be evaluated. However, referrals to genetics are underutilized in US patients with hereditary cancer syndromes, especially within traditionally underserved populations, including racial and ethnic minorities, low-income, and non-English speaking patients.

Methods
We studied existing processes for referral to genetic evaluation and testing for hereditary cancer risk to identify areas of potential improvement in delivering these services, especially for traditionally underserved patients.
We conducted a retrospective review of 820 referrals to the Kaiser Permanente Northwest (KPNW) genetics department containing diagnosis codes for hereditary cancer risk. We classified referrals as high- or low-quality based on whether sufficient information was provided to determine if patients met national practice guidelines for testing. Through chart abstraction, we also assessed consistency with practice guidelines, whether the referral resulted in a visit to the genetics department for evaluation, and clinical characteristics of patients receiving genetic testing.

Results
Most referrals (n = 514, 63%) contained sufficient information to assess the appropriateness of referral; of those, 92% met practice guidelines for genetic testing. Half of referred patients (50%) were not offered genetic evaluation; only 31% received genetic testing. We identified several barriers to receiving genetic evaluation and testing, the biggest barrier being completion of a family history form sent to patients following the referral. Those with a referral consistent with testing guidelines, were more likely to receive genetic testing than those without (39% vs. 29%, respectively; p = 0.0058). Traditionally underserved patients were underrepresented in those receiving genetic evaluation and testing relative to the overall adult KPNW population.

Conclusions
Process improvements are needed to increase access to genetic services to diagnose hereditary cancer syndromes prior to development of cancer.
How are progression decisions made following external randomised pilot trials? A qualitative interview study and framework analysis
Authors: Mellor Katie , Dutton Susan J. , Hopewell Sally , Albury Charlotte 
Published: February 2022

Abstract
Background
External randomised pilot trials help researchers decide whether, and how, to do a future definitive randomised trial. The progression criteria are often prespecified to inform the interpretation of pilot trial findings and subsequent progression decision-making. We aimed to explore and understand the perspectives and experiences of key stakeholders when making progression decisions following external pilot trials.

Methods
Thirty-five remote semi-structured interviews with external randomised pilot trial team members including chief investigators, trial managers, statisticians and patient and public involvement (PPI) representatives. Questions focussed on experiences and perceptions of pilot trial progression decisions and whether and how progression criteria informed this decision. Data were analysed using the framework method approach to thematic analysis. Strategies to ensure trustworthiness and rigour were used.

Results
Interviews were conducted between December 2020 and July 2021. Six descriptive themes were developed to capture the experiences and perspectives of participants. These were (1) divided opinions on the value and development of progression criteria, (2) (avoiding) the potential for personal interest to influence progression criteria and progression decision-making, (3) stakeholder engagement in setting progression criteria and making progression decisions, (4) lessons learned from doing the pilot trial and their impact on progression criteria applicability, (5) other factors that inform the progression decision and (6) progression of external randomised pilot trials—funding considerations and constraints. These themes were underpinned by an overarching interpretative theme ‘a one-size approach to progression does not fit all’ to describe the highly nuanced and complex decision-making process that occurs following external randomised pilot trials. The progression criteria are rarely the only consideration informing the decision to progress to future research; unanticipated events, signals of efficacy and continuity of the research team are other factors that researchers consider.

Conclusions
One size does not fit all when it comes to the progression criteria and pilot trial progression. The progression criteria are only one of many considerations researchers have when deciding whether a pilot trial is feasible. External pilot trial progression is not guaranteed even when a pilot trial is considered feasible (based on the progression criteria and/or other considerations), indicating inefficiency and potential research waste.

Trial registration
Open Science Framework osf.io/5N2KZ
ESD-aid surgery as a new treatment strategy for duodenal adenoma
Authors: Okubo Tomotaka , Ogawa Ryo , Ueno Shuhei , Ito Sunao , Hayakawa Shunsuke , Sagawa Hiroyuki , Tanaka Tatsuya , Takahashi Hiroki , Matsuo Yoichi , Shimura Takaya , Kataoka Hiromi , Takiguchi Shuji 
Published: February 2022

Abstract
Objective
The treatment for nonampullary duodenal adenoma remains to have no consensus and established methods. Although endoscopic treatment is minimally invasive, it was reported to cause delayed perforation in more than 20% of cases. For adenomas in the duodenum, we performed endoscopic submucosal dissection (ESD)-aid surgery, which is a procedure to prophylactically suture the seromuscular structure of the duodenum after ESD. In this procedure, we did not perform Kocher mobilization prior to ESD to facilitate endoscopic resection and full-thickness resection to prevent spread of the tumor and infection to the abdominal cavity. The duodenal wall was reinforced in planes using a suture clip.

Results
Of the 13 cases of duodenal adenoma that underwent ESD-aid surgery at our hospital between April 2018 and December 2020, 1 developed postoperative bleeding, but there was no late perforation. For duodenal adenomas, ESD-aid surgery was considered a safe and minimally invasive treatment.
Effects of different protein sources on nutrient disappearance, rumen fermentation parameters and microbiota in dual-flow continuous culture system
Authors: Mi Hui , Ren Ao , Zhu Jinjia , Ran Tao , Shen Weijun , Zhou Chuanshe , Zhang Bin , Tan Zhiliang 
Published: February 2022

AbstractScarce high-quality protein feed resources has limited the development of animal husbandry. In this study, we used a dual-flow continuous culture system to evaluate effects of difference dietary protein sources including soybean meal (SBM), cottonseed meal (CSM), and rapeseed meal (RSM), on nutrient disappearance, rumen fermentation, and microbiota of XiongDong black goats. Dietary proteins of either CSM, RSM or SBM had no effect on nutrient disappearance (P > 0.05). CSM or RSM significantly reduced (P < 0.01) the pH and enhanced (P < 0.01) the ammonia nitrogen (NH3-N) concentration in fermentation liquid compared to SBM. The short-chain fatty acids (SCFAs) contents were greater (P = 0.05) and acetate was lower (P < 0.01) in SBM than those in RSM and CSM, whereas propionate was greater (P < 0.01) in RSM than that in SBM, consequently reducing the acetate to propionate ratio (A/P) in RSM. Bacteroidetes, Firmicutes, and Proteobacteria were detected as the dominant phyla, and the relative abundances of Spirochaetae (P < 0.01) and Chlorobi (P < 0.05) declined in the CSM and RSM groups as compared to those in the SBM group. At the genus level, Prevotella_1 was the dominant genus; as compared to SBM, its relative abundance was greater (P < 0.01) in CSM and RSM. The abundances of Prevotellaceae_Ga6A1 and Christensenellaceae_R7 were lower (P < 0.05) in CSM, whereas Eubacterium_oxidoreducens_group, and Treponema_2 were lower (P < 0.01) in both CSM and RSM, and other genera were not different (P > 0.10). Although the bacterial community changed with different dietary protein sources, the disappearances of nutrients were not affected, suggesting that CSM and RSM could be used by rumen bacteria, as in case with SBM, and are suitable protein sources for ruminant diets.
Residents’ perspective on duty hours at an Israeli tertiary hospital
Authors: Apt Elad , Regev Tslil , Shapira Jacob , Haberfeld Ori , Duek Ori Samuel , Bar-Yoseph Ronen 
Published: February 2022

Abstract
Background
Specialization in medical professions is considered a challenging and intensive period due to the number and sequence of duty hours. Considering the effect of duty hours on residents, both physically and mentally, several models have been created over the years to address this complexity.
The two main model schools aim to decrease the duty hour length and night shift (i.e., night float, NF) frequency. In recent years, duty hours have become a source of disagreement and frustration among the medical community, both residents and attendings. A possible change in the duty hour structure may affect residents in terms of several parameters, such as patient safety, the well-being of the physician and the degree of training of the resident.

Purpose
(1) To investigate medical residents’ perspectives on their duty hours utilizing online questionnaires on their effect on the work environment and (2) to assess residents’ preferences in relation to the suggested shortened shift and NF models.

Methods
Questionnaires were emailed to all residents (main residents and fellows) at an Israeli tertiary medical center between March 2020 and April 2020. Questions were scored from 1 (disagree) to 5 (fully agree).

Results
Two hundred and sixty residents (227 main residents, 43 fellows) participated in the study (40% female). The score for the degree of balance between work and personal life was low (0.9±1.99). The shortened shift model was perceived by the residents as more compatible with a balanced lifestyle than the NF model (3.77 ± 1.20 and 3.14 ± 1.26, respectively, P < 0.0001). Neither model was considered to risk impairing professional training (2.33 ± 1.45 and 2.47 ± 1.25, respectively, P = 0.12). Overall, 74% of the residents were not willing to lower their income if the decision were made to change models, and 56% were not willing to increase the number of shifts.

Conclusions
There is agreement among residents that shortening shift hours to 16 h would have a positive effect on the balance between personal life and work. In the eyes of residents, the change would not impair their training during residency.
“The maize is the cost of the farming, and the cassava is our profit”: smallholders’ perceptions and attitudes to poor crop patches in the eastern region of Ghana
Authors: Wahab Ibrahim , Hall Ola , Jirström Magnus 
Published: February 2022

AbstractBackgroundCrop yields are lowest in sub-Saharan Africa compared to other regions, and this is true even for such an important staple crop as maize. Persistence of patches of low crop vigour side-by-side to patches with healthier maize crops has been shown to significantly contribute to low yields on smallholdings. Farmers' perspectives on the presence of such poor patches are important as far as their on-farm investment attitudes are concerned. We analyse maize yield levels and farmers’ perspectives of their production levels in two farming communities in rural Ghana.ResultsWe find substantial potential for yield improvements; while local attainable yields (average of the yields attained by the top 10% of farmers in each village) were 4.4 t/ha and 3.6 t/ha, average crop cut yields were 2.0 t/ha and 2.4 t/ha for Asitey and Akatawia, respectively. As much as 62% of the maize fields in both study locations were unable to reach the respective average village yield level. From the photo-elicitation interviews, the general attitude of smallholders to the presence of poor patches is that of indifference. We find contradictions in farmers’ perceptions and attitudes towards low yields. While more than half (54%) perceived they were getting adequate yields relative to their expectations, an even greater proportion (88%) of farmers interviewed aver that their plots could yield much more. Similarly, a significant majority (63%) did not attempt to remedy the poor patches even though the same proportion perceive that it is worth it to invest in yield-improving inputs.ConclusionsFarmers in such contexts view investments in fertilizers on their farms as too risky. As alternatives, they would rather invest their already limited resources in non-farm ventures. Farmers opt for yield optimization rather than maximization and this has important implications for diversification off the farm. These findings have important implications for smallholder households’ ability to meet their subsistence needs and for efforts to reduce yield gaps on small farms particularly in resource-poor contexts.
Butyrate in combination with forskolin alleviates necrotic enteritis, increases feed efficiency, and improves carcass composition of broilers
Authors: Yang Qing , Chen Binlong , Robinson Kelsy , Belem Thiago , Lyu Wentao , Deng Zhuo , Ramanathan Ranjith , Zhang Guolong 
Published: February 2022

Abstract
Background
The emergence of antimicrobial resistance has necessitated the development of effective alternatives to antibiotics for livestock and poultry production. This study investigated a possible synergy between butyrate and forskolin (a natural labdane diterpene) in enhancing innate host defense, barrier function, disease resistance, growth performance, and meat quality of broilers.

Methods
The expressions of representative genes involved in host defense (AvBD9 and AvBD10), barrier function (MUC2, CLDN1, and TJP1), and inflammation (IL-1β) were measured in chicken HD11 macrophages in response to butyrate and forskolin in the presence or absence of bacterial lipopolysaccharides (LPS). Intestinal lesions and the Clostridium perfringens titers were also assessed in C. perfringens-challenged chickens fed butyrate and forskolin-containing Coleus forskohlii (CF) extract individually or in combination. Furthermore, growth performance and carcass characteristics were evaluated in broilers supplemented with butyrate and the CF extract for 42 d.

Results
Butyrate and forskolin synergistically induced the expressions of AvBD9, AvBD10, and MUC2 in chicken HD11 cells (P < 0.05) and the synergy was maintained in the presence of LPS. Butyrate and forskolin also suppressed LPS-induced IL-1β gene expression in HD11 cells in a synergistic manner (P < 0.05). The two compounds significantly reduced the intestinal lesions of C. perfringens-challenged chickens when combined (P < 0.05), but not individually. Furthermore, butyrate in combination with forskolin-containing CF extract had no influence on weight gain, but significantly reduced feed intake (P < 0.05) with a strong tendency to improve feed efficiency (P = 0.07) in a 42-d feeding trial. Desirably, the butyrate/forskolin combination significantly decreased abdominal fat deposition (P = 0.01) with no impact on the carcass yield, breast meat color, drip loss, or pH of d-42 broilers.

Conclusions
Butyrate and forskolin has potential to be developed as novel antibiotic alternatives to improve disease resistance, feed efficiency, and carcass composition of broilers.
Dietary branched-chain amino acids modulate the dynamics of calcium absorption and reabsorption in protein-restricted pigs
Authors: Habibi Mohammad , Shili Cedrick N. , Sutton Julia , Goodarzi Parniyan , Pezeshki Adel 
Published: February 2022

Abstract
Background
Very low-protein (VLP) diets negatively impact calcium (Ca) metabolism and absorption. The objective of this study was to investigate the effect of supplemental branched-chain amino acids (BCAA) and limiting amino acids (LAA) on Ca digestibility, absorption and reabsorption in pigs fed with VLP diets. Forty-eight piglets were assigned to six treatments: positive control (PC), negative control (NC), and NC containing LAA 25%, LAA 50%, LAA + BCAA 25% (LB25) and LAA + BCAA 50% (LB50) more than recommendations.

Results
Relative to PC or NC, LB25 and LB50 had higher digestibility of Ca and plasma Ca and phosphorus (P), but lower plasma vitamin D3. LB50 tended to increase vitamin D receptor transcript and protein in the gut, but decreased mRNA or protein abundance of parathyroid hormone 1 receptor (PTH1R), calbindin 1 (CALB1), cytochrome P450 family 27 subfamily B member 1 and occludin in small intestine. LB50 increased the transcript of cytochrome P450 family 24 subfamily A member 1 and PTH1R but decreased the transcript of transient receptor potential cation channel subfamily V member 5, CALB1 and solute carrier family 17 member 4 in kidney.

Conclusion
Overall, BCAA increased Ca digestibility through regulating the transcellular and paracellular Ca absorption in the gut and reabsorption in kidney during protein restriction.