bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of two commercially-available Salmonella vaccines on Salmonella in the peripheral lymph nodes of experimentally-infected cattle
Authors: Edrington Thomas S. , Arthur Terrance M. , Loneragan Guy H. , Genovese Kenneth J. , Hanson Devin L. , Anderson Robin C. , Nisbet David J. 
Published: October 2020

Background: Salmonella is a common inhabitant of the ruminant gastrointestinal tract, where it often resides asymptomatically and may be shed into the feces. More recently it was discovered that Salmonella may be contained within the peripheral, non-mesenteric lymph nodes, where it is impervious to in-plant pathogen control interventions and may serve as a source of Salmonella-contamination of ground beef. Over the past 10 years considerable research effort has been expended at understanding how this pathogen gets to these lymph nodes, the duration of infection, and, most importantly, screening and developing potential intervention strategies that may be employed on farm prior to the animal being presented for slaughter. Methods: Utilizing an experimental model of Salmonella inoculation of bovine peripheral lymph nodes (PLNs), two pilot vaccine experiments were conducted to evaluate two Salmonella vaccines: Salmonella Newport Bacterial Extract (Experiment I) and Endovac-Bovi® (Experiment II) on preventing Salmonella acquisition by these nodes. In Experiment I, 4 months following the booster vaccination, 30 steers were inoculated with three Salmonella serotypes intradermally: Newport, Montevideo, and Anatum administered to the right legs, left legs, and to the caudal thorax and abdomen, respectively. Cattle were inoculated every other day over the course of five days (three total inoculation events) and 6 and 12 days following the final Salmonella inoculation, 16 and 14 head in each treatment were euthanized, respectively. In Experiment II, 12 head of Holstein steers were utilized. Seven days following the booster and weekly thereafter for 3 weeks (four total inoculation events), cattle were inoculated as above and euthanized 7 days following final inoculation. Right and left sub-iliac, popliteal and pre-scapular lymph nodes were collected in each experiment, weighed and cultured for Salmonella. Results: In Experiment I, no treatment differences were observed in Salmonella prevalence 6 days post-inoculation (necropsy 1). However, in vaccinated cattle at the second necropsy, a reduction ( p = 0.05) in Salmonella prevalence was observed in the sub-iliac and pre-scapular lymph nodes as well as when all nodes were evaluated collectively ( p = 0.04). In Experiment II, the vaccine reduced ( p = 0.03) Salmonella prevalence in the right popliteal and tended ( p = 0.09) to decrease prevalence in both popliteal lymph nodes. Conclusion: Under these experimental conditions, the data generated provide evidence of a partial vaccine effect on Salmonella within PLNs and indicate that further research may be warranted.
Zanubrutinib (BGB-3111) plus obinutuzumab in patients with chronic lymphocytic leukemia and follicular lymphoma
Authors: Tam Constantine S. , Quach Hang , Nicol Andrew , Badoux Xavier , Rose Hannah , Prince H. Miles , Leahy Michael F. , Eek Richard , Wickham Nicholas , Patil Sushrut S. , Huang Jane , Prathikanti Radha , Cohen Aileen , Elstrom Rebecca , Reed William , Schneider Jingjing , Flinn Ian W. 
Published: October 2020

Abstract
Zanubrutinib (BGB-3111) is a next-generation Bruton tyrosine kinase inhibitor designed to be more selective with fewer off-target effects. We conducted a phase 1 study to assess the safety of its combination with obinutuzumab and evaluate early efficacy in 81 patients with chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL) or relapsed/refractory (R/R) follicular lymphoma (FL). In this phase 1b study, zanubrutinib was tolerable at 160 mg twice daily or 320 mg once daily combined with IV obinutuzumab in patients with CLL/SLL (n = 45) and FL (n = 36). Common adverse events (AEs) included upper respiratory tract infection (51%; n = 23), neutropenia (44%; n = 20), contusion (33%; n = 15), cough, diarrhea, or fatigue (27%; n = 12 each), and pyrexia (22%; n = 10) in CLL/SLL patients and upper respiratory tract infection (39%; n = 14), contusion (28%; n = 10), fatigue (25%; n = 9), and cough (22%; n = 8) in FL patients. Neutropenia was the most common grade 3/4 AE (CLL/SLL, 31% [n = 14]; FL, 14% [n = 5]). Five patients required temporary dose reductions, and 5 discontinued the study drug because of AEs. Overall response rate (ORR) was 100% (n = 20) in treatment-naïve CLL patients and 92% (n = 23) in R/R CLL patients. ORR in 36 R/R FL patients was 72% (n = 26), with 14 complete and 12 partial responses. Median follow-up was 29 months (range, 8-37) for CLL patients and 20 months (range, 2-37) for FL patients. Zanubrutinib and obinutuzumab combination therapy was generally well tolerated. This trial was registered at www.clinicaltrials.gov as #NCT02569476.
Multiple donor-derived leukemias in a recipient of allogeneic hematopoietic cell transplantation for myeloid malignancy
Authors: Aldoss Ibrahim , Song Joo Y. , Curtin Peter T. , Forman Stephen J. 
Published: October 2020

Key Points
A patient with myelodysplastic syndrome was transplanted twice and developed clonally unrelated relapse each time in donor-derived cells. This case supports the concept that a leukemogenic marrow environment may predispose the transplant recipient to malignant transformation.
Distinctive gene and protein characteristics of extremely piezophilic Colwellia
Authors: Peoples Logan M. , Kyaw Than S. , Ugalde Juan A. , Mullane Kelli K. , Chastain Roger A. , Yayanos A. Aristides , Kusube Masataka , Methé Barbara A. , Bartlett Douglas H. 
Published: October 2020

Abstract
Background
The deep ocean is characterized by low temperatures, high hydrostatic pressures, and low concentrations of organic matter. While these conditions likely select for distinct genomic characteristics within prokaryotes, the attributes facilitating adaptation to the deep ocean are relatively unexplored. In this study, we compared the genomes of seven strains within the genus Colwellia, including some of the most piezophilic microbes known, to identify genomic features that enable life in the deep sea.

Results
Significant differences were found to exist between piezophilic and non-piezophilic strains of Colwellia. Piezophilic Colwellia have a more basic and hydrophobic proteome. The piezophilic abyssal and hadal isolates have more genes involved in replication/recombination/repair, cell wall/membrane biogenesis, and cell motility. The characteristics of respiration, pilus generation, and membrane fluidity adjustment vary between the strains, with operons for a nuo dehydrogenase and a tad pilus only present in the piezophiles. In contrast, the piezosensitive members are unique in having the capacity for dissimilatory nitrite and TMAO reduction. A number of genes exist only within deep-sea adapted species, such as those encoding d-alanine-d-alanine ligase for peptidoglycan formation, alanine dehydrogenase for NADH/NAD+ homeostasis, and a SAM methyltransferase for tRNA modification. Many of these piezophile-specific genes are in variable regions of the genome near genomic islands, transposases, and toxin-antitoxin systems.

Conclusions
We identified a number of adaptations that may facilitate deep-sea radiation in members of the genus Colwellia, as well as in other piezophilic bacteria. An enrichment in more basic and hydrophobic amino acids could help piezophiles stabilize and limit water intrusion into proteins as a result of high pressure. Variations in genes associated with the membrane, including those involved in unsaturated fatty acid production and respiration, indicate that membrane-based adaptations are critical for coping with high pressure. The presence of many piezophile-specific genes near genomic islands highlights that adaptation to the deep ocean may be facilitated by horizontal gene transfer through transposases or other mobile elements. Some of these genes are amenable to further study in genetically tractable piezophilic and piezotolerant deep-sea microorganisms.
RNA-Seq and differential gene expression analysis in Temora stylifera copepod females with contrasting non-feeding nauplii survival rates: an environmental transcriptomics study
Authors: Russo Ennio , Lauritano Chiara , d’Ippolito Giuliana , Fontana Angelo , Sarno Diana , von Elert Eric , Ianora Adrianna , Carotenuto Ylenia 
Published: October 2020

AbstractBackgroundCopepods are fundamental components of pelagic food webs, but reports on how molecular responses link to reproductive success in natural populations are still scarce. We present a de novo transcriptome assembly and differential expression (DE) analysis inTemora styliferafemales collected in the Gulf of Naples, Mediterranean Sea, where this copepod dominates the zooplankton community. High-Throughput RNA-Sequencing and DE analysis were performed from adult females collected on consecutive weeks (May 23rd and 30th 2017), because opposite naupliar survival rates were observed. We aimed at detecting key genes that may have influenced copepod reproductive potential in natural populations and whose expression was potentially affected by phytoplankton-derived oxylipins, lipoxygenase-derived products strongly impacting copepod naupliar survival.ResultsOn the two sampling dates, temperature, salinity, pH and oxygen remained stable, while variations in phytoplankton cell concentration, oxylipin concentration and oxylipin-per-diatom-cell production were observed.T. styliferanaupliar survival was 25% on May 23rd and 93% on May 30th. De novo assembly generated 268,665 transcripts (isoforms) and 120,749 unique ‘Trinity predicted genes’ (unigenes), of which 50% were functionally annotated. Out of the 331 transcript isoforms differentially expressed between the two sampling dates, 119 sequences were functionally annotated (58 up- and 61 down-regulated). Among predicted genes (unigenes), 144 sequences were differentially expressed and 31 (6 up-regulated and 25 down-regulated) were functionally annotated. Most of the significantly down-regulated unigenes and isoforms wereA5 Putative Odorant Binding Protein(Obp). Other differentially expressed sequences (isoforms and unigenes) related to developmental metabolic processes, protein ubiquitination, response to stress, oxidation-reduction reactions and hydrolase activities. DE analysis was validated through Real Time-quantitative PCR of 9 unigenes and 3 isoforms.ConclusionsDifferential expression of sequences involved in signal detection and transduction, cell differentiation and development offered a functional interpretation to the maternally-mediated low naupliar survival rates observed in samples collected on May 23rd. Down-regulation ofA5 Obpalong with higher quantities of oxylipins-per-litre and oxylipins-per-diatom-cell observed on May 23rd could suggest oxylipin-mediated impairment of naupliar survival in natural populations ofT. stylifera. Our results may help identify biomarker genes explaining variations in copepod reproductive responses at a molecular level.
Recruiting men from across the socioeconomic spectrum via GP registers and community outreach to a weight management feasibility randomised controlled trial
Authors: McDonald Matthew D. , Dombrowski Stephan U. , Skinner Rebecca , Calveley Eileen , Carroll Paula , Elders Andrew , Gray Cindy M. , Grindle Mark , Harris Fiona M. , Jones Claire , Hoddinott Pat ,   on behalf of the Game of Stones team, Avenell Alison , Kee Frank , McKinley Michelle , Tod Martin , van der Pol Marjon 
Published: October 2020

Abstract
Background
Men, particularly those living in disadvantaged areas, are less likely to participate in weight management programmes than women despite similar levels of excess weight. Little is known about how best to recruit men to weight management interventions. This paper describes patient and public involvement in pre-trial decisions relevant to recruitment and aims to report on recruitment to the subsequent men-only weight management feasibility trial, including the: i) acceptability and feasibility of recruitment; and ii) baseline sample characteristics by recruitment strategy.

Methods
Men with BMI ≥30 kg/m2 and/or waist circumference ≥ 40 in. were recruited to the feasibility trial via two strategies; community outreach (venue information stands and word of mouth) and GP letters, targeting disadvantaged areas. Recruitment activities (e.g. letters sent, researcher venue hours) were recorded systematically, and baseline characteristics questionnaire data collated. Qualitative interviews (n = 50) were conducted three months post-recruitment. Analyses and reporting followed a complementary mixed methods approach.

Results
105 men were recruited within four months (community n = 60, GP letter n = 45). Community outreach took 2.3 recruiter hours per participant and GP letters had an opt-in rate of 10.2% (n = 90/879). More men were interested than could be accommodated. Most participants (60%) lived in more disadvantaged areas. Compared to community outreach, men recruited via GP letters were older (mean = 57 vs 48 years); more likely to report an obesity-related co-morbidity (87% vs 44%); and less educated (no formal qualifications, 32% vs 10%, degree educated 11% vs 41%). Recruitment strategies were acceptable, a sensitive approach and trusting relationships with recruiters valued, and the ‘catchy’ study name drew attention.

Conclusions
Targeted community outreach and GP letters were acceptable strategies that successfully recruited participants to a men-only weight management feasibility trial. Both strategies engaged men from disadvantaged areas, a typically underserved population. Using two recruitment strategies produced samples with different health risk profiles, which could add value to research where either primary or secondary prevention is of interest. Further work is required to examine how these strategies could be implemented and sustained in practice.

Trial registration
ClinicalTrials.gov: NCT03040518, 2nd February 2017.
Comparison of prognostic impact of anatomic location of the pancreas on postoperative pancreatic fistula in laparoscopic and open gastrectomy
Authors: Kinoshita Jun , Yamaguchi Takahisa , Saito Hiroto , Moriyama Hideki , Shimada Mari , Terai Shiro , Okamoto Koichi , Nakanuma Shinichi , Makino Isamu , Nakamura Keishi , Tajima Hidehiro , Ninomiya Itasu , Fushida Sachio 
Published: October 2020

Abstract
Background
Postoperative pancreatic fistula (POPF) is a serious complication after gastric cancer surgery. The current study aimed to investigate the significance of the anatomic location of the pancreas as a predictor for POPF in both laparoscopic gastrectomy (LG) and open gastrectomy (OG).

Methods
In total, 233 patients with gastric cancer were assessed retrospectively. We measured the maximum vertical (P-L height; PLH) and horizontal length (P-L depth; PLD) between the upper border of pancreas and the root of left gastric artery on a preoperative CT in the sagittal direction. The maximum length of the vertical line between the surface of the pancreas and the aorta (P-A length), previously reported as prognostic factor of POPF, was also measured. We investigated the correlations between these parameters and the incidence of POPF in LG and OG groups.

Results
Among the patients in this study, 118 underwent OG and 115 underwent LG. In LG, the median PLH and P-A length in patients with POPF were significantly longer compared with those without POPF (p = 0.026, 0.034, respectively), but not in OG. There was no significant difference in the median PLD between the patients with or without POPF in both LG and OG. The multivariate analysis demonstrated that PLH (odds ratio [OR] 4.19, 95% confidence interval [CI] 1.57–11.3, P = 0.004) and P-A length (OR 4.06, 95%CI 1.05–15.7, P = 0.042] were independent factors for predicting POPF in LG. However, intraoperative blood loss (OR 2.55, 95%CI 1.05–6.18, P = 0.038) was extracted as an independent factor in OG. The median amylase level in the drained fluid (D-Amy) were significantly higher in patients with high PLH(≥12.4 mm) or high P-A length (≥45 mm) compared with those with low PLH or low P-A length in LG. However, there were no differences in the D-Amy levels by PLH or P-A length in OG patients.

Conclusions
The anatomic location of the pancreas is a specific and independent predictor of POPF in LG but not in OG. PLH is a simple parameter that can evaluate the anatomic position of the pancreas, and it may be useful for preventing POPF after LG.
Classification of gastrointestinal symptom patterns in young adults
Authors: Vivier Helize , Ross Emily J. , Cassisi Jeffrey E. 
Published: October 2020

AbstractBackgroundThe purpose of this study was to identify common gastrointestinal (GI) symptom groups using the Patient-Reported Outcomes Measurement Information System - GI symptom scales (PROMIS-GI) within a large sample of young adults. An attempt was made to relate the emergent groups to the Rome IV disorders of gut-brain interaction symptom domains. The PROMIS-GI is a freely available, adaptable, normatively referenced symptom measurement system that is applicable to many health assessment situations.MethodsParticipants were 956 introductory psychology students between the ages of 18 and 25 who completed the PROMIS-GI as part of ongoing research monitoring physical and psychological health of students at a major southeastern university. GI symptom groups were determined using a latent class analysis (LCA) approach. These GI symptom groups were then compared on key psychosocial factors including self-reported mood, anxiety, and health related quality of life (HRQoL) using MANOVA.ResultsThree groups were identified based on GI symptom elevations: Normal (n = 649), Mild (n = 257), and Moderate (n = 50). Self-reported anxiety, depression, and bodily pain levels were significantly higher in the Mild and Moderate GI symptom groups, and they indicated significantly lower work functioning, and general health ratings compared to participants in the normal group.ConclusionsApproximately a third of young adults surveyed were experiencing at least one GI symptom of a severity greater than normative levels. Both the Mild and Moderate GI groups demonstrated a similar configuration of symptoms with significantly the higher levels of pain, gas/bloating, and nausea/vomiting compared to the Normal group. The configuration of symptoms did not map discretely onto the Rome IV diagnostic categories for Bowel Disorders, such as IBS with predominant Diarrhea or Functional Constipation as might be expected. Rather, the emergent groups suggest that Bowel Disorders occur on a continuum of severity across multiple symptom areas. Mild to moderate GI symptoms appear to emerge at much earlier ages and are more frequent than previously documented. It is recommended that health service providers evaluate individual patterns of “GI health” when young adults present with anxiety and depression, and conversely, they should assess anxiety and depression when they present with GI complaints.
Non-uptake of viral load testing among people receiving HIV treatment in Gomba district, rural Uganda
Authors: Nakalega Rita , Mukiza Nelson , Kiwanuka George , Makanga-Kakumba Ronald , Menge Robert , Kataike Hajira , Maena Joel , Akello Carolyne , Atuhaire Patience , Matovu-Kiweewa Flavia , Ndikuno-Kuteesa Cynthia , Debem Henry , Mujugira Andrew 
Published: October 2020

Abstract
Background
Viral load (VL) testing is the gold-standard approach for monitoring human immunodeficiency virus (HIV) treatment success and virologic failure, but uptake is suboptimal in resource-limited and rural settings. We conducted a cross-sectional study of risk factors for non-uptake of VL testing in rural Uganda.

Methods
We conducted a cross-sectional analysis of uptake of VL testing among randomly selected people with HIV (PWH) receiving anti-retroviral treatment (ART) for at least 6 months at all eight primary health centers in Gomba district, rural Uganda. Socio-demographic and clinical data were extracted from medical records for the period January to December 2017. VL testing was routinely performed 6 months after ART initiation and 12 months thereafter for PWH stable on ART. We used descriptive statistics and multivariable logistic regression to evaluate factors associated with non-uptake of VL testing (the primary outcome).

Results
Of 414 PWH, 60% were female, and the median age was 40 years (interquartile range [IQR] 31–48). Most (62.3%) had been on ART > 2 years, and the median duration of treatment was 34 months (IQR 14–55). Thirty three percent did not receive VL testing: 36% of women and 30% of men. Shorter duration of ART (≤2 years) (adjusted odds ratio [AOR] 2.38; 95% CI:1.37–4.12; p = 0.002), younger age 16–30 years (AOR 2.74; 95% CI:1.44–5.24; p = 0.002) and 31–45 years (AOR 1.92; 95% CI 1.12–3.27; p = 0.017), and receipt of ART at Health Center IV (AOR 2.85; 95% CI: 1.78–4.56; p < 0.001) were significantly associated with non-uptake of VL testing.

Conclusions
One-in-three PWH on ART missed VL testing in rural Uganda. Strategies to improve coverage of VL testing, such as VL focal persons to flag missed tests, patient education and demand creation for VL testing are needed, particularly for recent ART initiates and younger persons on treatment, in order to attain the third Joint United Nations Program on HIV/AIDS (UNAIDS) 95–95-95 target – virologic suppression for 95% of PWH on ART.
The relationship between physical activity and lymphoma: a systematic review and meta analysis
Authors: Davies Gwynivere A. , Strader Christopher , Chibbar Richa , Papatheodorou Stefania , Dmytriw Adam A. 
Published: October 2020

Abstract
Background
The literature suggests an increased risk between anthropometrics including higher body mass index and lymphoma incidence; however, the association with physical activity remains unclear. A systematic review/meta-analysis was therefore performed to examine this association with physical activity (total, recreational or occupational).

Methods
PubMed, Web of Science and Embase were reviewed from inception to October 2019 identifying relevant observational studies. Non-Hodgkin lymphoma (NHL) including subtypes diffuse large B cell lymphoma, follicular lymphoma and chronic lymphocytic leukemia/small lymphocytic lymphoma, and Hodgkin lymphoma (HL) were analyzed. Included studies reported activity, lymphoma cases, effect size and variability measures, and were restricted to human subjects of any age. Data was pooled generating summary relative risk (RR) estimates with 95% confidence intervals (CI) using random-effects models with primary outcome of histologically confirmed incident lymphoma.

Results
One thousand four hundred studies were initially identified with 18 studies (nine cohort, nine case-control) included in final analysis. Comparing highest vs. lowest activity categories was protective for all lymphoma (RR 0.89, 95%CI 0.81–0.98). Sensitivity analysis demonstrated effect persistence within case-control studies (RR 0.82, 95% CI 0.71–0.96), but not cohort studies (RR 0.95, 95%CI 0.84–1.07). Borderline protective effect was seen for NHL (RR 0.92, 95%CI 0.84–1.00), but not HL (RR 0.72, 95%CI 0.50–1.04). Analysis by NHL subtype or gender showed no effect. Dose response analysis demonstrated a protective effect (p = 0.034) with a 1% risk reduction per 3 MET hours/week (RR 0.99, 95%CI 0.98–1.00).

Conclusions
Physical activity may have a protective effect against lymphoma development; further studies are required to generate recommendations regarding health policy.

Trial registration
This study was registered prospectively at PROSPERO: CRD42020156242.