Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions.

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range.

Survival and thermal resistance among four Salmonella serovars inoculated onto flaxseeds.

Thermal resistance among Salmonella serovars has been shown to vary, however, such data are minimal for Salmonella inoculated onto low moisture foods. We evaluated survival and subsequent thermal resistance for 32 strains of Salmonella from four serovars (Agona, Enteritidis, Montevideo, and Tennessee) on flaxseed over 24 weeks. After inoculation, flaxseeds were adjusted to aw = 0.5 and stored at 22 °C. After 24 weeks at 22 °C, strains of serovar Agona had a significantly slower rate of reduction compared to those of Enteritidis and Montevideo (adj. p < 0.05). Inoculated flaxseeds were processed at 71 °C with vacuum steam pasteurization at 4 time points during storage. Average initial D71°C values ranging from 1.0 to 1.5 min were similar across serovars. Over 24 weeks, D71°C varied in a serovar-dependent manner. D71°C at 8, 16, and 24 weeks did not change significantly for Enteritidis and Montevideo but did for Tennessee and Agona. While significant, the differences in D71°C over time were less than 1 min, indicating that storage time prior to heat treatment would have a minimal effect on the processing time required to inactivate Salmonella on flaxseed.

Salmonella enterica in Soils Amended with Heat-Treated Poultry Pellets Survived Longer than Bacteria in Unamended Soils and More Readily Transferred to and Persisted on Spinach.

Untreated biological soil amendments of animal origin (BSAAO) are commonly used as biological fertilizers but can harbor foodborne pathogens like Salmonella enterica, leading to potential transfer from soils to fruits and vegetables intended for human consumption. Heat-treated poultry pellets (HTPP) can provide produce growers with a slow-release fertilizer with a minimized risk of pathogen contamination. Little is known about the impact of HTPP-amended soil on the survival of Salmonella enterica The contributions of RpoS and formation of viable but nonculturable cells to Salmonella survival in soils are also inadequately understood. We quantified the survival of Salmonella enterica subsp. enterica serovar Newport wild-type (WT) and rpoS-deficient (ΔrpoS mutant) strains in HTPP-amended and unamended soil with or without spinach plants over 91 days using culture and quantitative PCR methods with propidium monoazide (PMA-qPCR). Simulated "splash" transfer of S. Newport from soil to spinach was evaluated at 35 and 63 days postinoculation (dpi). The S. Newport WT and ΔrpoS mutant reached the limit of detection, 1.0 log CFU/g (dry weight), in unamended soil after 35 days, whereas 2 to 4 log CFU/g (dry weight) was observed for both WT and ΔrpoS mutant strains at 91 dpi in HTPP-amended soil. S. Newport levels in soils determined by PMA-qPCR and plate count methods were similar (P > 0.05). HTPP-amended soils supported higher levels of S. Newport transfer to and survival on spinach leaves for longer periods of time than did unamended soils (P < 0.05). Salmonella Newport introduced to HTPP-amended soils survived for longer periods and was more likely to transfer to and persist on spinach plants than was S. Newport introduced to unamended soils.IMPORTANCE Heat-treated poultry pellets (HTPP) often are used by fruit and vegetable growers as a slow-release fertilizer. However, contamination of soil on farms may occur through contaminated irrigation water or scat from wild animals. Here, we show that the presence of HTPP in soil led to increased S. Newport survival in soil and to greater likelihood of its transfer to and survival on spinach plants. There were no significant differences in survival durations of WT and ΔrpoS mutant isolates of S. Newport. The statistically similar populations recovered by plate count and estimated by PMA-qPCR for both strains in the amended and unamended soils in this study indicate that all viable populations of S. Newport in soils were culturable.

Genomic and phenotypic diversity of Listeria monocytogenes clonal complexes associated with human listeriosis.

Listeria monocytogenes is a pathogen of significant concern in many ready to eat foods due to its ability to survive and multiply even under significant environmental stresses. Listeriosis in humans is a concern, especially to high-risk populations such as those who are immunocompromised or pregnant, due to the high rates of morbidity and mortality. Whole genome sequencing has become a routine part of assessing L. monocytogenes isolated from patients, and the frequency of different genetic subtypes associated with listeriosis is now being reported. The recent abundance of genome sequences for L. monocytogenes has provided a wealth of information regarding the variation in core and accessory genomic elements. Newly described accessory genomic regions have been linked to greater virulence capabilities as well as greater resistance to environmental stressors such as sanitizers commonly used in food processing facilities. This review will provide a summary of our current understanding of stress response and virulence phenotypes of L. monocytogenes, within the context of the genetic diversity of the pathogen.

Complications of gastrojejunal feeding tubes in children.

BACKGROUND: Long-term gastrojejunal (GJ) feeding is an increasingly popular alternative to gastric fundoplication for children with pathologic reflux, particularly those with neurologic impairment. We sought to evaluate morbidity associated with GJ feeding tubes in a large population of children. MATERIALS AND METHODS: The records of all children who underwent placement of a GJ feeding tube in a large children's hospital between January 2005 and September 2013 were reviewed. Indications for GJ feedings were noted. Events including a requirement for tube replacement and intestinal complications attributable to a GJ tube that required a laparotomy were evaluated. Risk factors for morbidity were assessed. RESULTS: A total of 124 children underwent GJ tube placement at an average age of 5.0 y (2 mo-16 y). Of the total, 83 (66%) subjects were neurologically impaired and 108 (87%) had gastroesophageal reflux. Of those, 55 (44%) had undergone prior laparoscopic fundoplication. Persistent reflux symptoms occurred in 22 (17.6%). Subjects underwent an average of 2.75 tube replacements per year and those under 2 y old had almost four. Four children (3.2%) required emergent laparotomy for intestinal perforation due to a GJ tube. These subjects were significantly younger (12 mo) than those without perforations (60.6 mo, P < 0.005). CONCLUSIONS: GJ feeding tubes were associated with notable morbidity ranging from persistent reflux to dislodgement and intestinal perforation. Together with issues of inconvenience with continuous feedings, these complications should be taken into account in children and particularly infants, in whom GJ feedings are being considered as an alternative to fundoplication.

Management of ingested foreign bodies in children: a clinical report of the NASPGHAN Endoscopy Committee.

Foreign body ingestions in children are some of the most challenging clinical scenarios facing pediatric gastroenterologists. Determining the indications and timing for intervention requires assessment of patient size, type of object ingested, location, clinical symptoms, time since ingestion, and myriad other factors. Often the easiest and least anxiety-producing decision is the one to proceed to endoscopic removal, instead of observation alone. Because of variability in pediatric patient size, there are less firm guidelines available to determine which type of object will safely pass, as opposed to the clearer guidelines in the adult population. In addition, the imprecise nature of the histories often leaves the clinician to question the timing and nature of the ingestion. Furthermore, changes in the types of ingestions encountered, specifically button batteries and high-powered magnet ingestions, create an even greater potential for severe morbidity and mortality among children. As a result, clinical guidelines regarding management of these ingestions in children remain varied and sporadic, with little in the way of prospective data to guide their development. An expert panel of pediatric endoscopists was convened and produced the present article that outlines practical clinical approaches to the pediatric patient with a variety of foreign body ingestions. This guideline is intended as an educational tool that may help inform pediatric endoscopists in managing foreign body ingestions in children. Medical decision making, however, remains a complex process requiring integration of clinical data beyond the scope of these guidelines. These guidelines should therefore not be considered to be a rule or to be establishing a legal standard of care. Caregivers may well choose a course of action outside of those represented in these guidelines because of specific patient circumstances. Furthermore, additional clinical studies may be necessary to clarify aspects based on expert opinion instead of published data. Thus, these guidelines may be revised as needed to account for new data, changes in clinical practice, or availability of new technology.

High- and low-dose oral delayed-release mesalamine in children with mild-to-moderately active ulcerative colitis.

OBJECTIVE: The aim of the study was to assess the safety and efficacy of high- and low-dose oral, delayed-release mesalamine in a randomized, double-blind, active control study of children with mild-to-moderately active ulcerative colitis. METHODS: Patients ages 5 to 17 years, with a Pediatric Ulcerative Colitis Activity Index (PUCAI) score of ≥ 10 to ≤ 55 and a truncated Mayo Score of ≥ 1 for both rectal bleeding and stool frequency, were enrolled. They received body weight-dependent doses of oral, delayed-release mesalamine for 6 weeks in a low- (27-71 mg · g(-1) · day(-1)) or high-dose group (53-118 mg · g(-1) · day(-1)). The primary endpoint was treatment success, defined as the proportion of patients who achieved remission (PUCAI score <10) or partial response (PUCAI score ≥ 10 with a decrease from baseline by ≥ 20 points). Secondary endpoints included truncated Mayo Score and global assessment of change of disease activity. RESULTS: The modified intent-to-treat population included 81 of 83 patients enrolled. Treatment success by PUCAI was achieved by 23 of 41 (56%) and 22 of 40 (55%) patients in the mesalamine low- and high-dose groups, respectively (P = 0.924). Truncated Mayo Score (low-dose 30 [73%] and high-dose 28 [70%] patients) and other efficacy results did not differ between the groups. The type and severity of adverse events were consistent with those reported in previous studies of adults with ulcerative colitis and did not differ between groups. CONCLUSIONS: Both low- and high-dose oral, delayed-release mesalamine doses were equally effective as short-term treatment of mild-to-moderately active ulcerative colitis in children, without a specific benefit or risk to using either dose.

Bowel preparation for pediatric colonoscopy: report of the NASPGHAN endoscopy and procedures committee.

Pediatric bowel preparation protocols used before colonoscopy vary greatly, with no identified standard practice. The present clinical report reviews the evidence for several bowel preparations in children and reports on their use among North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition members. Publications in the pediatric literature for bowel preparation regimens are described, including mechanisms of action, efficacy and ease of use, and pediatric studies. A survey distributed to pediatric gastroenterology programs across the country reviews present national practice, and cleanout recommendations are provided. Finally, further areas for research are identified.

A description of cases of severe physical abuse in the elderly and 1-year mortality.

We conducted a case-control study to evaluate severe physical abuse of the elderly treated in two Chicago area Level I trauma centers. This report details whether physicians are adequately reporting cases of abuse to Adult Protective Services (APS), and assesses 1 year. The failure to report two-thirds of the cases and the substantially higher risk of death during the first year after hospitalization indicates the need for improved identification, reporting, and intervention. It is important that clinicians understand the complexity of elder abuse in order to better identify suspected victims and report these cases to professionals in APS.

Solid pseudopapillary tumor of pancreas in a male child: a diagnosis by fine needle aspiration cytology.

Solid pseudopapillary tumor (SPT) is an uncommon pancreatic neoplasm with low malignant potential. It occurs predominantly in young women. It is very rare in males and nonrelated pediatrics. In children, SPT commonly present as abdominal mass and pain. A 10-year-old male presented with progressively growing palpable tumor in upper abdomen. SPT of pancreas is diagnosed on preoperative fine needle aspiration cytology. This was subsequently confirmed by histopathology and immunohistochemistry. Due to rarity, SPT is not the first option to rule out, especially in children. Preoperative cytological diagnosis of SPT helps in management of this surgically curable neoplasm with good prognosis.

Primary intratesticular rhabdomyosarcoma in pediatrics.

Testicular sarcomas constitute only 1-2% of all testicular tumors and are mostly associated with germ cell tumor. Primary intratesticular rhabdomyosarcoma is rare and only 14 cases have been reported in the literature till date. It should be differentiated from germ cell tumor with sarcomatous component, other intratesticular spindle-cell sarcomas and paratesticular rhabdomyosarcoma. Accurate diagnosis and early treatment is essential as it is an aggressive tumor with high metastatic potential and poor prognosis. Orchidectomy is the treatment of choice. Chemo-radiotherapy is recommended in case of recurrence and metastasis.

Seroprevalence of canine distemper virus (CDV) in the free-roaming dog (Canis familiaris) population surrounding Chitwan National Park, Nepal.

Canine distemper virus (CDV) is a global multi-host pathogen that is capable of causing considerable mortality in a range of species and is important in the field of conservation medicine. Nepal's Chitwan National Park is a protected area providing habitat for 32% of the country's mammal species including endangered carnivores such as the Bengal tiger (Panthera tigris tigris) that are susceptible to CDV. The presence of free-roaming dogs around protected areas could represent a source of infectious disease for transmission to local wildlife. A cross-sectional demographic and canine distemper virus seroprevalence study of 100 free-roaming dogs from the Chitwan National Park buffer zone and surrounding area was conducted in November 2019. The overall seroprevalence indicating past exposure to canine distemper virus was 80.0% (95% CI: 70.8-87.3). Of the host variables assessed, sex and age were positively associated with seroprevalence at the univariable level, with male dogs demonstrating lower seroprevalence than females (OR = 0.32, 95% CI: 0.11-0.91) and adult dogs demonstrating higher seroprevalence than juveniles (OR = 13.94, 95% CI: 1.37-142.29). The effect of sex was no longer significant at the multivariable level, but the direction of the effect remained the same. The effect of age remained significant after multivariable analysis (OR = 9.00, 95% CI: 1.03-192.75). No spatial associations were demonstrated in relation to the buffer zone area or boundary of Chitwan National Park. Free-roaming dog neutering and vaccination programmes can provide a useful baseline for future CDV studies in the region, and a proxy to monitor disease threats to susceptible wildlife.

Refining the evolutionary tree of the horse Y chromosome.

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.

Transforming growth factor beta 2: a predictive marker for breast cancer.

Dual role of TGF-beta signaling in breast tumorigenesis as an inhibitor in early stages and promoter in advanced stages has been well established and known as TGF-beta switch. However, the biological mechanisms needs to be explored. Aim of the present study was to look for the usefulness of TGF-beta as a predictive marker for breast cancer and to offer a better predictability to identify patients likely to benefit from antiTGF-beta strategies. Circulatory as well as transcript levels of TGF-beta2 were estimated from 118 pretherapeutic breast cancer patients using ELISA and q-PCR with ddCt method. Multifactorial analysis was performed to correlate the results to clinico-pathological prognosticators and Kaplan-Meier survival analysis with a median follow-up of 49 months was also evaluated. Circulating TGF-beta2 was similar in control and breast cancer patients. TGF-beta2 was significantly upregulated in advanced tumors compared to early tumors. An inverse correlation was observed between TGF-beta2 protein and mRNA; nevertheless both exhibited significant correlations with clinico-pathological prognosticators. Higher expression of TGF-beta2 mRNA was connected to an early relapse in advanced stage than early stage patients. It is the first report to evaluate circulatory and transcript levels exhibiting TGF-beta switch and confirming the utility of TGF-beta2 as an important predictive marker for breast cancer.

FGF5 and EPAS1 gene polymorphisms are associated with high-altitude adaptation in Nepalese goat breeds.

Several studies have reported the gene polymorphisms associated with high-altitude adaptation in goats. The FGF5 gene is a regulator in the hair-growth and a SNP c.-253G>A located within 5'UTR has been reported to cause long-haired phenotype. The EPAS1 gene is a transcription factor for various genes that have hypoxia-adaptive functions and a nonsynonymous SNP (Q579L) located in exon 5 has been reported to be associated with the mean corpuscular hemoglobin concentration. Nepal has large difference in altitudes in the north-south direction and four indigenous goat breeds are bred depending on the altitude. We used a total of 130 animals in Nepal, Chyangra (n = 37), Sinhal (n = 24), Khari (n = 33), and Terai (n = 36), and genotyped these two gene polymorphisms to compare the gene frequencies among the breeds and investigate the associations between breeding altitudes and allele frequencies. The genotyping results revealed that the mutant allele frequency in both polymorphisms tended to increase, as the breeding altitude of each population increased. In addition, correlation coefficients showed a relatively strong positive correlation between the breeding altitude and the mutant allele frequencies (r = 0.87 in FGF5 and r = 0.68 in EPAS1). These results suggested that both polymorphisms would significantly contribute to the high-altitude adaptation in Nepalese goat breeds.

Split Versus Non-Split Morning Dosing Regimen for Assessment of Quality of Bowel Preparation for Colonoscopy.

BACKGROUND: Different bowel preparation regimens are available. Currently we are giving the entire preparation on the day of colonoscopy. Multiple studies have shown splitting the regimen might improve the quality of bowel preparation with lesser side effects and better compliance. The study was done to compare the efficacy and tolerability of split bowel preparation regimen with non-split dosing regimen. METHODS: Single centered observational comparative study was done in a tertiary care hospital. One hundred ninety eight patients requiring elective colonoscopy were assigned to receive one of the two preparations (split versus morning) prior to colonoscopy. Main outcomes were bowel preparation quality and patient compliance and tolerability. RESULTS: There was no significant difference between the two regimen for the mean total Boston Bowel Preparation Scale (6.79VS 6.74,P value -0.777).Patient compliance was better for split dosing compared to single dosing (99 vs 5 p value-<0.001).There were more side effects in the single dosage compared to split dosing except for sleep disturbance which was more in split dosing. CONCLUSIONS: The study found that split-dose and single dose polyethylene glycol solution for bowel preparation before colonoscopy had similar efficacy in the quality of bowel preparation. Split-dose polyethylene glycol appears to be superior to single-dose PEG for patient compliance and side effects.

Frequency and methods of gastrojejunal tube replacement in children.

Gastrojejunal (GJ) tubes are increasingly used for enteral feeding in children in whom gastric feeding either is not tolerated or is contraindicated. The most common complications associated with GJ tube use are mechanical failure (clogging, cracking, deterioration) and dislodgement. Less common, but more significant, complications are bowel perforation, aspiration, and feeding intolerance. Some of these complications may be prevented by replacing GJ tubes at regular intervals. Methods to direct a GJ tube include 1) guidewire, 2) gastroduodenoscopy-guidewire, 3) esophagogastroduodenoscopy-forceps, and 4) fluoroscopy-guidewire. Clinical experience to determine the ideal method and optimal timing of GJ tube replacement is evolving. GJ tube replacement using a guidewire through the prior GJ tube, without endoscopy, fluoroscopy, or sedation, is the least risky method, but is also the least likely to be successful.