bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fast likelihood solution to the genetic clustering problem
Authors: Beugin Marie‐Pauline , Gayet Thibault , Pontier Dominique , Devillard Sébastien , Jombart Thibaut 
Published: January 2018

Abstract

The investigation of genetic clusters in natural populations is an ubiquitous problem in a range of fields relying on the analysis of genetic data, such as molecular ecology, conservation biology and microbiology. Typically, genetic clusters are defined as distinct panmictic populations, or parental groups in the context of hybridisation. Two types of methods have been developed for identifying such clusters: model‐based methods, which are usually computer‐intensive but yield results which can be interpreted in the light of an explicit population genetic model, and geometric approaches, which are less interpretable but remarkably faster.

Here, we introduce snapclust, a fast maximum‐likelihood solution to the genetic clustering problem, which allies the advantages of both model‐based and geometric approaches. Our method relies on maximising the likelihood of a fixed number of panmictic populations, using a combination of geometric approach and fast likelihood optimisation, using the Expectation‐Maximisation (EM) algorithm. It can be used for assigning genotypes to populations and optionally identify various types of hybrids between two parental populations. Several goodness‐of‐fit statistics can also be used to guide the choice of the retained number of clusters.

Using extensive simulations, we show that snapclust performs comparably to current gold standards for genetic clustering as well as hybrid detection, with some advantages for identifying hybrids after several backcrosses, while being orders of magnitude faster than other model‐based methods. We also illustrate how snapclust can be used for identifying the optimal number of clusters, and subsequently assign individuals to various hybrid classes simulated from an empirical microsatellite dataset.

snapclust is implemented in the package adegenet for the free software R, and is therefore easily integrated into existing pipelines for genetic data analysis. It can be applied to any kind of co‐dominant markers, and can easily be extended to more complex models including, for instance, varying ploidy levels. Given its flexibility and computer‐efficiency, it provides a useful complement to the existing toolbox for the study of genetic diversity in natural populations.
Factors Related to Frailty among the Elderly in South Korea: A 3‐year Longitudinal Study
Authors: Park Jin‐Kyoung , Lee Jong‐Eun 
Published: January 2018

PURPOSETo examine factors associated with frailty among the young‐old elderly (YOE) and old–old elderly (OOE).METHODSThis longitudinal study with a 3‐year follow‐up included 486 participants who received home care services.FINDINGSPrecipitous weight loss and depression in the YOE and worsening of complex mobility and depression in the OOE were associated with worsened frailty over the 3‐year period.CONCLUSIONSTo prevent frailty, we suggest weight‐loss prevention programs for the YOE, lower‐limb exercise programs for the OOE, and depression management programs for both groups.Implications for Nursing PracticeThe findings may be used by geriatric nurses in developing programs to prevent frailty in the OOE and YOE, and in administering nursing intervention programs at nursing home centers.
Pecan phenology in Southeastern China
Authors: Han M. , Peng F. , Marshall P. 
Published: January 2018

AbstractPecan (Carya illinoensis) is heterodicogamous, which often leads to unstable yield of its nut crops. Relating pecan orchard management to the phenological stage of the trees is the key to increasing yields; however, describing morphology alone does not lead to an orchard management system that is simple and practical. In this work, we extend the BBCH (Biologische Bundesanstalt, Bundessortenamt und Chemische Industrie) coding method to describe the morphology of the protogynous Mahan pecan cultivar over two consecutive years in southern China. Eight main growth stages, from vegetative bud dormancy to fruit harvest, were described and each phenological period was photographed. Pecan orchard management activities were listed for each stage in pecan BBCH scale to allow orchard managers to better manage their trees. This codification will facilitate breeding, conservation of genetic resources and general orchard management of this commercial crop. As well, recording the dates of various morphological stages over time will allow the influence of global climate change on pecan development to be tracked.
Endothelium‐specific CYP2J2 overexpression attenuates age‐related insulin resistance
Authors: Yang Yan , Dong Ruolan , Chen Zhihui , Hu Danli , Fu Menglu , Tang Ying , Wang Dao Wen , Xu Xizhen , Tu Ling 
Published: January 2018

SummaryAmple evidences demonstrate that cytochrome P450 epoxygenase‐derived epoxyeicosatrienoic acids (EETs) exert diverse biological activities, which include potent vasodilatory, anti‐inflammatory, and cardiovascular protective effects. In this study, we investigated the effects of endothelium‐specific CYP2J2 overexpression on age‐related insulin resistance and metabolic dysfunction. Endothelium‐specific targeting of the human CYP epoxygenase, CYP2J2, transgenic mice (Tie2‐CYP2J2‐Tr mice) was utilized. The effects of endothelium‐specific CYP2J2 overexpression on aging‐associated obesity, inflammation, and peripheral insulin resistance were evaluated by assessing metabolic parameters in young (3 months old) and aged (16 months old) adult male Tie2‐CYP2J2‐Tr mice. Decreased insulin sensitivity and attenuated insulin signaling in aged skeletal muscle, adipose tissue, and liver were observed in aged adult male mice, and moreover, these effects were partly inhibited in 16‐month‐old CYP2J2‐Tr mice. In addition, CYP2J2 overexpression‐mediated insulin sensitization in aged mice was associated with the amelioration of inflammatory state. Notably, the aging‐associated increases in fat mass and adipocyte size were only observed in 16‐month‐old wild‐type mice, and CYP2J2 overexpression markedly prevented the increase in fat mass and adipocyte size in aged Tie2‐CYP2J2‐Tr mice, which was associated with increased energy expenditure and decreased lipogenic genes expression. Furthermore, these antiaging phenotypes of Tie2‐CYP2J2‐Tr mice were also associated with increased muscle blood flow, enhanced active‐phase locomotor activity, and improved mitochondrial dysfunction in skeletal muscle. Collectively, our findings indicated that endothelium‐specific CYP2J2 overexpression alleviated age‐related insulin resistance and metabolic dysfunction, which highlighted CYP epoxygenase‐EET system as a potential target for combating aging‐related metabolic disorders.
Estimating radiotherapy demands in South East Asia countries in 2025 and 2035 using evidence‐based optimal radiotherapy fractions
Authors: Yahya Noorazrul , Roslan Nurhaziqah 
Published: January 2018

AbstractBackground and purposeAs about 50% of cancer patients may require radiotherapy, the demand of radiotherapy as the main treatment to treat cancer is likely to rise due to rising cancer incidence. This study aims to quantify the radiotherapy demand in countries in Southeast Asia (SEA) in 2025 and 2035 using evidence‐based optimal radiotherapy fractions.Materials and methodsSEA country‐specific cancer incidence by tumor site for 2015, 2025 and 2035 was extracted from the GLOBOCAN database. We utilized the optimal radiotherapy utilization rate model by Wong et al. (2016) to calculate the optimal number of fractions for all tumor sites in each SEA country. The available machines (LINAC & Co‐60) were extracted from the IAEA's Directory of Radiotherapy Centres (DIRAC) from which the number of available fractions was calculated.ResultsThe incidence of cancers in SEA countries are expected to be 1.1 mil cases (2025) and 1.4 mil (2035) compared to 0.9 mil (2015). The number of radiotherapy fractions needed in 2025 and 2035 are 11.1 and 14.1 mil, respectively, compared to 7.6 mil in 2015. In 2015, the radiotherapy fulfillment rate (RFR; required fractions/available fractions) varied between countries with Brunei, Singapore and Malaysia are highest (RFR > 1.0 – available fractions > required fractions), whereas Cambodia, Indonesia, Laos, Myanmar, Philippines, Timor‐Leste and Vietnam have RFR < 0.5. RFR is correlated to GDP per capita (ρ = 0.73, P = 0.01). To allow RFR ≥1 in 2025 and 2035, another 866 and 1177 machines are required, respectively. The number are lower if longer running hours are implemented.ConclusionWith the optimal number of radiotherapy fractions, estimation for number of machines required can be obtained which will guide acquisition of machines in SEA countries. RFR is low with access varied based on the economic status.
Immunomodulation characteristics by thermal ablation therapy in cancer patients
Authors: Yang Wuwei , Wang Wei , Liu Bing , Zhu Baorang , Li Jing , Xu Debao , Ni Yanli , Bai Li , Liu Guangxian 
Published: January 2018

AbstractAimThermal ablation therapy has recently emerged as a promising noninvasive treatment modality for localized solid malignancies. Except its direct tumor‐cell‐killing effect on local tumor tissues, the immunomodulatory effect has also long been noticed which too has substantial effect on clinical outcome, but it is complicated. Though much has been investigated and rich evidences have been achieved, the fundamental state and profile of immunomodulation by thermal ablation in cancer patients, its exact mechanism, especially the systematic mechanism, and its effect on antitumor immunity remain unclear.MethodsIn this study, we dynamically monitored the immunomodulation by thermal ablation through combined analysis of peripheral lymphocyte populations, functional T cell subtype Th1 (CD3+CD4+IFN‐r+), Th2 (CD3+CD4+IL‐4+), Tc1 (CD3+CD8+IFN‐r+), Tc2 (CD3+CD8+IL‐4+) and mRNA expression of several immune‐active and ‐suppressive molecules including CD25, CD28, cytotoxic T‐lymphocyte‐associated protein 4, programmed cell death protein 1, Foxp3, transforming growth factor beta (TGF‐β) and interleukin (IL‐10) in 16 cancer patients.ResultsThe results show that local cancer thermal ablation modulated the cellular immunity characterized by obviously downregulation of regulatory T cells (Treg) and cytotoxicity T cells followed by CD4, CD8 and suppressor T cells (Ts), but upregulation of natural killer (NK) cells and mRNA expression of TGF‐β and IL‐10, suggesting a slight inhibition of the cellular immunity which may affect antitumor immunity.ConclusionsWe suggest a further immunomodulation therapy after thermal therapy for recovering a Th1‐ and Tc1‐dominant immune response for pursuing a better long‐term antitumor immunity.
Parental education and family income affect birthweight, early longitudinal growth and body mass index development differently
Authors: Bramsved Rebecka , Regber Susann , Novak Daniel , Mehlig Kirsten , Lissner Lauren , Mårild Staffan 
Published: January 2018

AbstractAimThis study investigated the effects of two parental socio‐economic characteristics, education and income, on growth and risk of obesity in children from birth to 8 years of age.MethodsLongitudinal growth data and national register‐based information on socio‐economic characteristics were available for 3,030 Swedish children. The development of body mass index (BMI) and height was compared in groups dichotomised by parental education and income.ResultsLow parental education was associated with a higher BMI from 4 years of age, independent of income, immigrant background, maternal BMI and smoking during pregnancy. Low family income was associated with a lower birthweight, but did not independently predict BMI development. At 8 years of age, children from less educated families had a three times higher risk of obesity, independent of parental income. Children whose parents had fewer years of education but high income had significantly higher height than all other children.ConclusionParental education protected against childhood obesity, even after adjusting for income and other important parental characteristics. Income‐related differences in height, despite similar BMIs, raise questions about body composition and metabolic risk profiles. The dominant role of education underscores the value of health literacy initiatives for the parents of young children.
Long‐term efficacy and safety of ustekinumab in 122 refractory Crohn's disease patients: a multicentre experience
Authors: Wils P. , Bouhnik Y. , Michetti P. , Flourie B. , Brixi H. , Bourrier A. , Allez M. , Duclos B. , Serrero M. , Buisson A. , Amiot A. , Fumery M. , Roblin X. , Peyrin‐Biroulet L. , Filippi J. , Bouguen G. , Abitbol V. , Coffin B. , Simon M. , Laharie D. , Pariente B. ,   Groupe d'Etude Thérapeutique des Affections Inflammatoires du Tube Digestif (GETAID)
Published: January 2018

SummaryBackgroundLong‐term outcome of ustekinumab in Crohn's disease (CD) has not been evaluated.AimTo evaluate the long‐term efficacy and safety of ustekinumab and identify the predictive factors of ustekinumab failure‐free persistence in a cohort of anti‐TNF refractory CD patients.MethodsWe performed a retrospective multicentre cohort study including all consecutive CD patients who began subcutaneous ustekinumab and presented a clinical response (defined as a significant improvement of CD‐related clinical symptoms assessed by the patient's physician leading to continued ustekinumab) during the first year of treatment. Primary outcome was treatment failure defined as withdrawal of treatment due to loss of response, intolerance or need for surgery.ResultsEighty‐eight of the 122 (72%) CD patients beginning ustekinumab from March 2011 to December 2014, responded to ustekinumab and were followed up until November 2016. Median time on ustekinumab was 26.6 (13.4‐34.4) months. Forty‐seven patients (54%) continued ustekinumab with a clinical response and 38 (43%) stopped treatment (32 for failure, five for remission and one for pregnancy). Endoscopic response was observed in 82% of patients with endoscopic evaluation and mucosal healing in 39%. Ustekinumab failure‐free persistence rates were 78% at 12 months, 66% at 24 months and 55% at 36 months. No predictive factor of ustekinumab failure‐free persistence was identified. One severe adverse event was observed (anal adenocarcinoma).ConclusionIn this cohort of refractory CD patients receiving long‐term ustekinumab therapy, more than 50% of patients continued ustekinumab treatment with no loss of response, intolerance or surgery and with a good safety profile.
Incarcerated obturator hernia treated using a hybrid laparoscopic and anterior preperitoneal approach: A case report
Authors: Yamazaki Yuta , Otowa Yasunori , Kusano Shunsuke , Nakajima Koichi , Satake Shinsuke , Yamasaki Yoshisada 
Published: January 2018

AbstractObturator hernia (OH) is a rare cause of bowel obstruction. Although several surgical approaches, including the laparoscopic approach, have been reported to date, a standard approach for treating OH has not been established. A 101‐year‐old woman who presented with constipation and vomiting was admitted to our hospital. CT revealed an incarcerated small bowel within the left obturator foramen, and a diagnosis of left‐sided incarcerated OH with small bowel ileus was made. With the patient under general anesthesia, exploratory laparoscopy was performed; we identified an OH with an incarcerated small bowel, which was judged viable after hernia reduction. We repaired the hernia using an anterior preperitoneal approach under laparoscopic assistance and placed a prosthetic mesh over the obturator foramen. The patient recovered with no postoperative complications and was discharged on postoperative day 4. A hybrid laparoscopic and anterior preperitoneal approach is safe and effective for treating an incarcerated OH in an elderly patient.
Colonic ischemia developed after laparoscopic colectomy for rectosigmoid cancer with focal infrarenal aortic stenosis
Authors: Ikeda Atsuyo , Takahashi Hidekazu , Miyoshi Norikatsu , Haraguchi Naotsugu , Hata Taishi , Matsuda Chu , Yamamoto Hirofumi , Mizushima Tsunekazu , Doki Yuichiro , Mori Masaki 
Published: January 2018

AbstractA 69‐year‐old woman with focal infrarenal aortic stenosis was diagnosed with rectosigmoid cancer. Because radical resection for colon cancer required dissection of vessels that supplied blood flow to the legs, revascularization by aortic stent placement was performed before the colectomy. We subsequently performed laparoscopic low anterior resection without any complications. Two and a half years after colectomy, however, the patient developed colonic ischemia due to thrombosis of the dilated marginal artery that served as a collateral artery before stenting. We performed laparoscopic partial colectomy, including the resection of the dilated marginal artery filled with thrombus. An abnormally dilated ex‐collateral artery was thought to have caused vessel occlusion, presumably due to an imbalance in blood flow and vascular diameter.
Evaluation of three hormonal protocols for anovulatory lactating cows under regulations restricting the use of estrogenic compounds
Authors: Yu Guang‐Min , Wu Yue , Wang Xian‐Long , Zhao Shuan , Maeda Teruo , Zeng Shen‐Ming 
Published: January 2018

AbstractWhen European Union regulations restricted the use of estrogenic compounds in food‐producing animals, refined hormonal protocols were no longer applicable for anovulatory cows. However, Ovsynch and its adaptations are routinely and uniformly applied to all cows regardless of ovarian function. To evaluate their efficacy on anovulatory cows, 143, 147 and 144 anovulatory cows received Ovsynch, Presynch and G6G protocols, respectively. In comparison, 150 cyclic cows were bred without using a synchronized protocol. Results showed that cows in the Presynch group had luteolysis responding to the last prostaglandin F2α (PGF2α) injection greater than the Ovsynch group. The serous progesterone levels at the first gonadotropin‐releasing hormone of Ovsych and the last PGF2α injection was greater in the G6G group than the other two hormonal treatment groups. Concentrations of Ca2+ and total protein in cervical mucus in all three hormone‐treated groups before artificial insemination (AI) were significantly different from the controls. The G6G group obtained a greater pregnancy rate compared with Ovsynch and Presynch, but significantly less than the controls. For open cows in the Ovsynch group, estrus rate within 24 days after the first AI was significantly less than the controls. In conclusion, the G6G treatment resulted to better reproductive performance in anovulatory cows.
The effect of transport on the quality of rabbit meat
Authors: Składanowska‐Baryza Joanna , Ludwiczak Agnieszka , Pruszyńska‐Oszmałek Ewa , Kołodziejski Paweł , Bykowska Marta , Stanisz Marek 
Published: January 2018

AbstractThe analyzed material included 40 hybrid rabbits slaughtered at the age of 90 days. The control group was transported directly after weaning, while the transport group was transported directly prior to slaughter. The experiment was designed to assess the transport stress, carcass and meat quality implications, taking into account the muscle type and sex. The transported animals were characterized by a higher level of blood cortisol, glucose and triglycerides (P < 0.0001), and a lower level of insulin (P < 0.0001) compared to the control group. In the presented study the time post‐mortem affected the pH decline in both rabbit groups (P < 0.0001). The lightness, redness and yellowness of rabbit meat were affected by the transport (P < 0.0001, P = 0.001 and P < 0.0001). The percentage of free water and its share in the total water was higher for the non‐transported rabbits compared to the transported ones (P < 0.0001). Moreover, the meat from the control group was characterized by greater plasticity compared to the transport group (P = 0.003). The chemical composition of rabbit meat was not changed by the effect of transport (P = 0.643–0.979). To conclude, the quality traits of meat from the transported hybrid rabbits clearly indicated the development of dark firm and dry‐like lower quality of meat.
Effects of different rearing systems on growth performance, carcass traits, meat quality and serum biochemical parameters of Chaohu ducks
Authors: Zhang Cheng , Ah Kan Razafindrabe Richard‐Hermann , Chen Kaikai , Zhao Xiaohui , Yang Lei , Wang Li , Chen Xingyong , Jin Sihua , Geng Zhaoyu 
Published: January 2018

AbstractThis study was conducted using a total of 360 22‐day‐old Chaohu ducks to evaluate the effect of rearing system on growth performance, carcass traits, meat quality and serum parameters of male and female Chaohu ducks. The birds were divided and raised in separate pens according to sex and rearing system, with three replicate pens of 30 male or 30 female ducks per pen for each rearing system. The rearing systems consisted of a floor rearing system (FRS) and a net rearing system (NRS). Results showed that ducks raised in NRS had better growth performance, whereas, ducks raised in FRS exhibited better carcass traits and meat color, and lower intramuscular fat. For the serum parameters, NRS significantly decreased high‐density lipoprotein cholesterol content, and enhanced total protein and triacylglycerol contents. Male ducks had lower abdominal fat percentage, and higher growth performance and shear force, but there were no other significant differences between sexes. No rearing system × sex interaction was observed in the present study, revealing that rearing system had the same effect on both sexes. In conclusion, NRS was beneficial to the growth performance of Chaohu ducks, whereas this system had some negative effects on carcass traits, meat quality and serum profiles.