bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of merging commercial breeding lines on the genetic diversity of Landrace pigs
Authors: Hulsegge Ina , Calus Mario , Hoving-Bolink Rita , Lopes Marcos , Megens Hendrik-Jan , Oldenbroek Kor 
Published: October 2019

AbstractBackgroundThe pig breeding industry has undergone a large number of mergers in the past decades. Various commercial lines were merged or discontinued, which is expected to reduce the genetic diversity of the pig species. The objective of the current study was to investigate the genetic diversity of different former Dutch Landrace breeding lines and quantify their relationship with the current Dutch Landrace breed that originated from these lines.ResultsPrincipal component analysis clearly divided the former Landrace lines into two main clusters, which are represented by Norwegian/Finnish Landrace lines and Dutch Landrace lines. Structure analysis revealed that each of the lines that are present in the Dutch Gene bank has a unique genetic identity. The current Dutch Landrace breed shows a high level of admixture and is closely related to the six former lines. The Dumeco N-line, which is conserved in the Dutch Gene bank, is poorly represented in the current Dutch Landrace. All seven lines (the six former and the current line) contribute almost equally to the genetic diversity of the Dutch Landrace breed. As expected, the current Dutch Landrace breed comprises only a small proportion of unique genetic diversity that was not present in the other lines. The genetic diversity level, as measured by Eding’s core set method, was equal to 0.89 for the current Dutch Landrace breed, whereas total genetic diversity across the seven lines, measured by the same method, was equal to 0.99.ConclusionsThe current Dutch Landrace breed shows a high level of admixture and is closely related to the six former Dutch Landrace lines. Merging of commercial Landrace lines has reduced the genetic diversity of the Landrace population in the Netherlands, although a large proportion of the original variation is maintained. Thus, our recommendation is to conserve breeding lines in a gene bank before they are merged.
Functional analysis of GhCHS, GhANR and GhLAR in colored fiber formation of Gossypium hirsutum L
Authors: Gao Jianfang , Shen Li , Yuan Jingli , Zheng Hongli , Su Quansheng , Yang Weiguang , Zhang Liqing , Nnaemeka Vitalis Ekene , Sun Jie , Ke Liping , Sun Yuqiang 
Published: October 2019

Abstract

Background
The formation of natural colored fibers mainly results from the accumulation of different anthocyanidins and their derivatives in the fibers of Gossypium hirsutum L. Chalcone synthase (CHS) is the first committed enzyme of flavonoid biosynthesis, and anthocyanidins are transported into fiber cells after biosynthesis mainly by Anthocyanidin reductase (ANR) and Leucoanthocyanidin reductase (LAR) to present diverse colors with distinct stability. The biochemical and molecular mechanism of pigment formation in natural colored cotton fiber is not clear.

Results
The three key genes of GhCHS, GhANR and GhLAR were predominantly expressed in the developing fibers of colored cotton. In the GhCHSi, GhANRi and GhLARi transgenic cottons, the expression levels of GhCHS, GhANR and GhLAR significantly decreased in the developing cotton fiber, negatively correlated with the content of anthocyanidins and the color depth of cotton fiber. In colored cotton Zongxu1 (ZX1) and the GhCHSi, GhANRi and GhLARi transgenic lines of ZX1, HZ and ZH, the anthocyanidin contents of the leaves, cotton kernels, the mixture of fiber and seedcoat were all changed and positively correlated with the fiber color.

Conclusion
The three genes of GhCHS, GhANR and GhLAR were predominantly expressed early in developing colored cotton fibers and identified to be a key genes of cotton fiber color formation. The expression levels of the three genes affected the anthocyanidin contents and fiber color depth. So the three genes played a crucial part in cotton fiber color formation and has important significant to improve natural colored cotton quality and create new colored cotton germplasm resources by genetic engineering.
Comparing complications of urethral stricture across various ages: a retrospective analysis of findings from retrograde urethrogram and voiding cysto-urethrogram over 10 years
Authors: Nnabugwu Ikenna I. , Onuh Augustine C. , Anyimba Solomon K. , Mgbor Samuel O. 
Published: October 2019

Abstract

Objective
To determine the rate and the distribution of the structural defects in the urinary bladder complicating urethral stricture in men, and to compare the complications observed in the younger patients to those observed in the older patients.

Methods
Retrospectively, case files of patients diagnosed of urethral stricture using retrograde urethrogram (RUG) and voiding cysto-urethrogram (VCUG) from February 2009 to August 2018 were analyzed. Stricture characteristics were outlined. In addition, complicating structural defects in the lower urinary tract proximal to the stricture site were documented. The complicating defects identified in the patients were segregated according to age for any observable associations. Logistic regression analysis was used to define the nature of the association of patient age, stricture site, number and length, with distribution of complicating structural defects. Analyses were done using SPSS® version 20.

Results
Within the 10-year review period, 257 of 421 suspected cases of urethral stricture were confirmed. Patients are between 1 and 104 years of age (mean: 50.1 ± 19.1 years; median: 51.0 years IQR 35.0–65.0). Bulbar (34.2%); short segment (62.6%); partial (73.9%) strictures are prevalent. Forty-seven (18.3%) of 257 patients presented with 1 or more complications. Bladder diverticulum (8.6%) and urethra-cutaneous fistula (6.6%) are prevalent complications. The distribution of complications does not vary with age, or with stricture characteristics.

Conclusion
Presentation with complications is not uncommon. The distribution of these complications does not vary with age or with stricture characteristics.
Muir–Torre syndrome: sebaceous carcinoma concurrent with colon cancer in a kidney transplant recipient; a case report
Authors: Tomonari Masahiro , Shimada Mariko , Nakada Yasuyuki , Yamamoto Izumi , Itoh Munenari , Koike Yusuke , Kobayashi Akimitsu , Miki Jun , Yamada Hiroki , Kimura Takahiro , Saito Shinya , Sugano Kokichi , Sekine Shigeki , Yamamoto Hiroyasu , Asahina Akihiko , Yokoo Takashi 
Published: October 2019

Abstract

Background
Sebaceous carcinoma is a rare but progressive malignant skin cancer, and the incidence is approximately five times higher in post-transplant patients than in people who have not received kidney transplants. Sebaceous carcinoma is sometimes found concurrently with visceral cancers and a genetic abnormality, Muir–Torre syndrome. We report the case of a female kidney transplant recipient with sebaceous carcinoma concurrent with colon cancer 10 years after transplantation.

Case presentation
A 43-year-old woman was admitted due to a rapidly progressive tumor on her head. Histologically, the tumor was diagnosed as sebaceous carcinoma. We diagnosed her with Muir–Torre syndrome based on the following evidence: 1) high prevalence of microsatellite instability in gene locus assay, 2) absence of mismatch repair proteins in the sebaceous carcinoma on immunohistochemical analysis, and 3) a genetic mutation of 1226_1227delAG in the MSH2 exon 7 in the lesion detected by DNA sequencing analysis. Several reports have shown an association between immunosuppressive agents and latent Muir–Torre syndrome progression. Therefore, the progression of colon cancer in this case originated from her genetic mutation for Muir–Torre syndrome and long-term use of immunosuppressive agents.

Conclusion
This case report not only highlights the importance of adequate diagnosis and therapy for Muir–Torre syndrome, but also suggests the further prevention of the development of malignant tumors in kidney transplant recipients. Physicians should be mindful that sebaceous carcinoma in kidney transplant recipients is highly concurrent with Muir–Torre syndrome.
Resection of intrahepatic cholangiocarcinoma in elderly patients – is it reasonable?
Authors: Bartsch Fabian , Baumgart Janine , Tripke Verena , Hoppe-Lotichius Maria , Heinrich Stefan , Lang Hauke 
Published: October 2019

Abstract

Background
Intrahepatic cholangiocarinoma (ICC) has a rising incidence in western countries. Often major or extended resections are necessary for complete tumor removal. Due to demographical trends the number of elderly patients diagnosed with ICC is rising accordingly. Aim of this study is to show whether resection of ICC in elderly patients is reasonable or not.

Methods
Between January 2008 and June 2018 all consecutive patients with ICC were collected. Analyses were focussed on the performed resection, its extent, postoperative morbidity and mortality as well as survival. Statistics were performed with Chi2 test for categorical data and for survival analyses the Kaplan Meier model with log rank test was used.

Results
In total 210 patients underwent surgical exploration with 150 resections (71.4%). Patients were divided in 70-years cut-off groups (> 70 vs < 70 years of age) as well as a young (age 30–50, n = 23), middle-age (50–70, n = 76) and old (> 70, n = 51) group, whose results are presented here. Resectability (p = 0.709), extent of surgery (p = 0.765), morbidity (p = 0.420) and mortality (p = 0.965) was comparable between the different age groups. Neither visceral (p = 0.991) nor vascular (p = 0.614) extension differed significantly, likewise tumor recurrence (p = 0.300) or the localisation of recurrence (p = 0.722). In comparison of patients > or < 70 years of age, recurrence-free survival (RFS) was significantly better for the younger group (p = 0.047). For overall survival (OS) a benefit could be shown, but without reaching significance (p = 0.072). In subgroup analysis the middle-age group had significant better OS (p = 0.020) and RFS (p = 0.038) compared to the old group. Additionally, a better OS (p = 0.076) and RFS (p = 0.179) was shown in comparison with the young group as well, but without reaching significance. The young compared to the old group had analogous OS (p = 0.931) and RFS (p = 0.845).

Conclusion
Resection of ICC in elderly patients is not associated with an increased perioperative risk. Even extended resections can be performed in elderly patients without obvious disadvantages. Middle-age patients have a clear benefit for OS and RFS, while young and old patients have a comparable and worse long-term outcome.
ACR TI-RADS and ATA US scores are helpful for the management of thyroid nodules with indeterminate cytology
Authors: Barbosa Thayse Lozovoy Madsen , Junior Cleo Otaviano Mesa , Graf Hans , Cavalvanti Teresa , Trippia Marcus Adriano , da Silveira Ugino Ricardo Torres , de Oliveira Gabriel Lucca , Granella Victor Hugo , de Carvalho Gisah Amaral 
Published: October 2019

Abstract

Background
Cytologically indeterminate thyroid nodules currently present a challenge for clinical decision-making. The main aim of our study was to determine whether the classifications, American College of Radiology (ACR) TI-RADS and 2015 American Thyroid Association (ATA) guidelines, in association with The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC), could be used to stratify the malignancy risk of indeterminate thyroid nodules and guide their clinical management.

Methods
The institutional review board approved this retrospective study of a cohort of 140 thyroid nodules in 139 patients who were referred to ultrasound-guided fine-needle aspiration cytology (FNAC) from January 2012 to June 2016 with indeterminate cytological results (44 Bethesda III, 52 Bethesda IV and 44 Bethesda V) and in whom pre-FNAC thyroid US images and histological results after surgery were available. Each included nodule was classified by one radiologist blinded to the cytological and histological diagnoses according to the ACR TIRADS scores and the US patterns as recommended in the 2015 ATA guidelines. The risk of malignancy was estimated for Bethesda, TI-RADS scores, ATA US patterns and their combination.

Results
Of the 140 indeterminate thyroid nodules examined, 74 (52.9%) were histologically benign. A different rate of malignancy (p < 0.001) among Bethesda III, IV and V was observed. The rate of malignancy increased according to the US suspicion categories (p < 0.001) in both US classifications (TI-RADS and ATA). Thyroid nodules classified as Bethesda III and the lowest risk US categories (very low, low and intermediate suspicion by ATA and 2, 3 and 4a by TI-RADS) displayed a sensitivity of 95.3% for both classifications and a negative predictive value of 94.3 and 94.1%, respectively. The highest risk US categories (high suspicion by ATA and 4b,4c and 5 by TI-RADS) were significantly associated with cancer (odds ratios [ORs] 14.7 and 9.8, respectively).

Conclusions
Ultrasound classifications, ACR TI-RADS and ATA guidelines, may help guide the management of indeterminate thyroid nodules, suggesting a conservative approach to nodules with low-risk US suspicion and Bethesda III, while molecular testing and surgery should be considered for nodules with high-risk US suspicion and Bethesda IV or V.
Obesity, diabetes and the risk of colorectal adenoma and cancer
Authors: Soltani Ghodratollah , Poursheikhani Arash , Yassi Maryam , Hayatbakhsh Abdorasool , Kerachian Matin , Kerachian Mohammad Amin 
Published: October 2019

Abstract

Background
Colorectal cancer (CRC) is the fourth most commonly diagnosed gastrointestinal (GI) malignancy and the third leading cause of cancer-related death worldwide. In the current case-control study, an association between diagnosis of CRC, obesity and diabetes was investigated.

Methods
Demographic characteristics, colonoscopy reports, history of drug, smoking, and medical history were collected from patients referred to a colonoscopy unit. The location, size and number of the polyps were recorded during the colonoscopy. Statistically, t-test was conducted for mean comparison for the groups. Pearson’s chi-squared test (χ2) was applied to categorize variables. Five classification methods based on the important clinicopathological characteristics such as age, BMI, diabetes, family history of colon cancer was performed to predict the results of colonoscopy.

Results
Overall, 693 patients participated in this study. In the present study, 115 and 515 patients were evaluated for adenoma/adenocarcinoma and normal colonoscopy, respectively. The mean age of patients positive for adenoma or adenocarcinoma were significantly higher than the negative groups (p value < 0.001). Incidence of overweight and/or obesity (BMI > 25 kg/m2) were significantly higher in adenoma positive patients as compared to controls (49.9 and 0.9% respectively, p value = 0.04). The results also demonstrated a significant association between suffering from diabetes and having colon adenoma (OR = 1.831, 95%CI = 1.058–3.169, p value = 0.023). The experimental results of 5 classification methods on higher risk factors between colon adenoma and normal colonoscopy data were more than 82% and less than 0.42 for the percentage of classification accuracy and root mean squared error, respectively.

Conclusions
In the current study, the occurrence of obesity measured based on BMI and diabetes in the adenoma positive patient group was significantly higher than the control group although there was no notable association between obesity, diabetes and adenocarcinoma.
A pilot study of the in vitro antimicrobial activity and in vivo residual activity of chlorhexidine and acetic acid/boric acid impregnated cleansing wipes
Authors: Rafferty Rebecca , Robinson Victoria H. , Harris Jennifer , Argyle Sally A. , Nuttall Tim J. 
Published: October 2019

AbstractBackgroundTopical antimicrobials are recommended for first line treatment of surface and superficial infections in dogs. This is especially important given the increasing prevalence of antimicrobial resistant infections. Antimicrobial wipes have become popular, but there are a lack of controlled studies assessing their in vitro antimicrobial and in vivo residual activity. We aimed to assess the antimicrobial efficacy of two commercial antimicrobial wipes against frequently isolated pathogens.Ten clinical and one reference isolate each of meticillin-susceptibleStaphylococcus pseudintermedius(MSSP), meticillin-resistantS. pseudintermedius(MRSP),Escherichia coli(EC), extended spectrum beta-lactamase (ESBL) producingE. coli(ESBL-EC),Pseudomonas aeruginosa(PA) andMalassezia pachydermatis(MP) were tested using a modified Kirby-Bauer technique. Each isolate was tested against 6 mm discs of chlorhexidine (CHX) and acetic acid/boric acid (AABA) wipes, and positive and negative controls either overnight (bacteria) or for 3 days (Malassezia).Healthy dogs were treated with the wipes and distilled water on a randomised flank (n = 5 each). Hair samples (1 cm; 0.1 g) taken at days 0, 1 and 3 were inoculated with an isolate of each organism. Zones of inhibition (ZI) were measured.ResultsAll isolates produced confluent growth with AABA and control wipes, except for the cleansing wipes and MP (median ZI 12 mm; 95% CI 8.2–15.8). The median (95% CI) CHX wipe ZIs (mm) were: MP 48.0 (47.0–49.0), MSSP 15.6 (14.2–17.0), MRSP 14.0 (13.6–14.4), EC 13.6 (12.0–15.2) and ESBL-EC 10.0 (9.4–10.6). PA showed confluent growth. The differences between the bacterial isolates was significant (Kruskal-Wallisp < 0.0001; post-tests MSSP = MRSP = EC > EBSL-EC > PA). Confluent growth was visible with all the hair samples.ConclusionCHX but not AABA showed in vitro efficacy against MSSP, MRSP, EC and MP. ESBL-EC were less susceptible and there was no activity against PA. There was no residual activity on hair. Additional studies are required to determine efficacy of these products in clinically affected patients.
Haemostatic, fibrinolytic and inflammatory profiles in West Highland white terriers with canine idiopathic pulmonary fibrosis and controls
Authors: Roels Elodie , Bauer Natali , Lecut Christelle , Moritz Andreas , Gothot André , Clercx Cécile 
Published: October 2019

Abstract

Background
Canine idiopathic pulmonary fibrosis (CIPF) is a progressive interstitial lung disease mainly affecting old West Highland white terriers (WHWTs). The aetiology of CIPF is currently unknown and pathogenesis poorly understood. A genetic basis is strongly suspected based on the breed predisposition. CIPF shares clinical and pathological features with human IPF. In human IPF, coagulation disorders favouring a local and systemic pro-thrombotic state have been demonstrated in association with disease severity and outcome. The aim of this study was to compare the systemic haemostatic, fibrinolytic and inflammatory profiles of WHWTs affected with CIPF with breed-matched controls (CTRLs). Additionally, data collected in both groups were interpreted with regard to the reference intervals (when available) to assess possible pro-thrombotic features of the WHWT breed that may be related to CIPF predisposition. A total of 14 WHWTs affected with CIPF and 20 CTRLs were included.

Results
WHWTs affected with CIPF had prolonged activated partial thromboplastine time in comparison with CTRLs (12.2 ± 0.9 s vs. 11.5 ± 0.7 s, P = 0.028), whereas results obtained in both groups were all within reference ranges. There was no significant difference between groups for the other factors assessed including plasmatic concentrations of fibrinogen, D-dimers concentration, antithrombin III activity, protein S and protein C activities, anti-factor Xa activity, activated protein C ratio, serum C-reactive protein concentration, and rotational thromboelastometry indices. Platelet count and plasmatic fibrinogen concentration were found to be above the upper limit of the reference range in almost half of the WHWTs included, independently of the disease status.

Conclusions
Results of this study provide no clear evidence of an altered systemic haemostatic, fibrinolytic or inflammatory state in WHWTs affected with CIPF compared with CTRLs. The higher platelet counts and fibrinogen concentrations found in the WHWT breed may serve as predisposing factors for CIPF or simply reflect biological variation in this breed.
Gene expression profiling in blood from cerebral malaria patients and mild malaria patients living in Senegal
Authors: Thiam Alassane , Sanka Michel , Ndiaye Diallo Rokhaya , Torres Magali , Mbengue Babacar , Nunez Nicolas Fernandez , Thiam Fatou , Diop Gora , Victorero Geneviève , Nguyen Catherine , Dieye Alioune , Rihet Pascal 
Published: October 2019

Abstract

Background
Plasmodium falciparum malaria remains a major health problem in Africa. The mechanisms of pathogenesis are not fully understood. Transcriptomic studies may provide new insights into molecular pathways involved in the severe form of the disease.

Methods
Blood transcriptional levels were assessed in patients with cerebral malaria, non-cerebral malaria, or mild malaria by using microarray technology to look for gene expression profiles associated with clinical status. Multi-way ANOVA was used to extract differentially expressed genes. Network and pathways analyses were used to detect enrichment for biological pathways.

Results
We identified a set of 443 genes that were differentially expressed in the three patient groups after applying a false discovery rate of 10%. Since the cerebral patients displayed a particular transcriptional pattern, we focused our analysis on the differences between cerebral malaria patients and mild malaria patients. We further found 842 differentially expressed genes after applying a false discovery rate of 10%. Unsupervised hierarchical clustering of cerebral malaria-informative genes led to clustering of the cerebral malaria patients. The support vector machine method allowed us to correctly classify five out of six cerebral malaria patients and six of six mild malaria patients. Furthermore, the products of the differentially expressed genes were mapped onto a human protein-protein network. This led to the identification of the proteins with the highest number of interactions, including GSK3B, RELA, and APP. The enrichment analysis of the gene functional annotation indicates that genes involved in immune signalling pathways play a role in the occurrence of cerebral malaria. These include BCR-, TCR-, TLR-, cytokine-, FcεRI-, and FCGR- signalling pathways and natural killer cell cytotoxicity pathways, which are involved in the activation of immune cells. In addition, our results revealed an enrichment of genes involved in Alzheimer’s disease.

Conclusions
In the present study, we examine a set of genes whose expression differed in cerebral malaria patients and mild malaria patients. Moreover, our results provide new insights into the potential effect of the dysregulation of gene expression in immune pathways. Host genetic variation may partly explain such alteration of gene expression. Further studies are required to investigate this in African populations.