bluuebunny/crossref_metadata_2025_split huggingface dataset:
Body stalk anomaly presenting as an emergency in Ethiopia: a case report
Authors: Jidha Tafese Dejene , Wakjira Tekle , Mekonnen Tigist 
Published: October 2020

Abstract

Background
Body stalk anomaly is a generally lethal malformation of the thorax and/or abdomen. It is often associated with limb defects. The intrathoracic and abdominal organs lie outside the abdominal cavity. These are contained within a sac composed of amnioperitoneal membrane attached directly to the placenta. The umbilical cord may be totally absent or extremely shortened. Severe kyphoscoliosis is often present. This case is reported to highlight this rare malformation and its clinical presentation.

Case presentation
We present a case of a 27-year-old primigravida Oromo woman who had been amenorrheic for 9 months. She presented with an urge to bear down of 10 hours and passage of liquor of the same duration. The patient was referred from a district primary hospital with a diagnosis of preterm labor and hand prolapse. A lower uterine segment cesarean section was performed at Jimma University Medical Center for an indication of active first stage of labor with nonreassuring fetal heart rate pattern (fetal bradycardia) and hand prolapse to effect an anomalous fetus that had only a rudimentary right lower extremity and liver and intestine found outside the abdominal cavity contained within a sac composed of transparent membrane attached directly to the placenta. The umbilical cord was very short, measuring about 7 cm. The fetus had severe scoliosis. It also had a heartbeat upon extraction, which stopped after 5 minutes of delivery. The placenta and fetal body parts together weighed 2400 g.

Conclusion
Termination of pregnancy is usually offered because this abnormality is generally considered lethal. If the pregnancy is continued undetected as in our patient’s case, vaginal delivery is recommended, given the highly lethal nature of this anomaly. Good prenatal screening and counseling are recommended for early detection and management.
NKX6.1 transcription factor: a crucial regulator of pancreatic β cell development, identity, and proliferation
Authors: Aigha Idil I. , Abdelalim Essam M. 
Published: October 2020

AbstractUnderstanding the biology underlying the mechanisms and pathways regulating pancreatic β cell development is necessary to understand the pathology of diabetes mellitus (DM), which is characterized by the progressive reduction in insulin-producing β cell mass. Pluripotent stem cells (PSCs) can potentially offer an unlimited supply of functional β cells for cellular therapy and disease modeling of DM. Homeobox protein NKX6.1 is a transcription factor (TF) that plays a critical role in pancreatic β cell function and proliferation. In human pancreatic islet, NKX6.1 expression is exclusive to β cells and is undetectable in other islet cells. Several reports showed that activation of NKX6.1 in PSC-derived pancreatic progenitors (MPCs), expressing PDX1 (PDX1+/NKX6.1+), warrants their future commitment to monohormonal β cells. However, further differentiation of MPCs lacking NKX6.1 expression (PDX1+/NKX6.1−) results in an undesirable generation of non-functional polyhormonal β cells. The importance of NKX6.1 as a crucial regulator in MPC specification into functional β cells directs attentions to further investigating its mechanism and enhancing NKX6.1 expression as a means to increase β cell function and mass. Here, we shed light on the role of NKX6.1 during pancreatic β cell development and in directing the MPCs to functional monohormonal lineage. Furthermore, we address the transcriptional mechanisms and targets of NKX6.1 as well as its association with diabetes.
Identification of microflora related to growth performance in pigs based on 16S rRNA sequence analyses
Authors: Li Xin-Jian , Wang Mingyu , Xue Yahui , Duan Dongdong , Li Cong , Han Xuelei , Wang Kejun , Qiao Ruimin , Li Xiu-Ling 
Published: October 2020

Abstract
Intestinal microorganisms have been shown to be important factors affecting the growth performance of pigs. Therefore, to investigate the effect of the intestinal microflora structure on the growth performance of pigs, samples from Duroc (n = 10), Landrace (n = 9) and Yorkshire (n = 21) pigs under the same diet and feeding conditions were collected. The fecal microbial composition was profiled via 16S ribosomal RNA (rRNA) gene sequencing. We also analyzed their growth performance. We found that Duroc and Landrace pigs had significant differences in average daily gain (ADG), feed efficiency ratio (FER), growth index (GI), and number of days taken to reach 100 kg (P < 0.05). Moreover, through analysis of the intestinal flora, we also identified 18 species of intestinal flora with significant differences between Duroc and Landrace pigs (P < 0.05). To eliminate the influence of genetic background, the differential intestinal flora of 21 Yorkshire pigs with differences in growth performance was analyzed. The results showed that there were significant correlations between Barnesiella, Dorea, Clostridium and Lactobacillus and pig growth performance. To explore the effect of the intestinal flora on the growth performance of pigs at the molecular level, Lactobacillus, which is the most abundant in the intestine, was selected for isolation and purification and cocultured with intestinal epithelial cells. qPCR was used to determine the effect of Lactobacillus on MC4R gene expression in intestinal epithelial cells. The results showed that Lactobacillus inhibited MC4R gene expression in these cells. The results provide a useful reference for further study of the relationship between the intestinal flora and pig growth performance.
Impact of systematic screening for AmpC-hyperproducing Enterobacterales intestinal carriage in intensive care unit patients
Authors: Manquat Elsa , Le Dorze Matthieu , Pean De Ponfilly Gauthier , Benmansour Hanaa , Amarsy Rishma , Cambau Emmanuelle , Soyer Benjamin , Chousterman Benjamin Glenn , Jacquier Hervé 
Published: October 2020

Abstract
Background
Empirical antimicrobial therapy (EAT) is a challenge for community-acquired, hospital-acquired and ventilator-associated pneumonia, particularly in the context of the increasing occurrence of third-generation cephalosporin-resistant Enterobacterales (3GCR-E), including extended-spectrum beta-lactamase Enterobacterales (ESBL-E) and high-level expressed AmpC cephalosporinase-producing Enterobacterales (HLAC-E). To prevent the overuse of broad-spectrum antimicrobial therapies, such as carbapenems, we assessed the performance of screening for intestinal carriage of HLAC-E in addition to ESBL-E to predict 3GCR-E (ESBL-E and/or HLAC-E) presence or absence in respiratory samples in ICU, and to evaluate its potential impact on carbapenem prescription.

Materials and methods
This monocentric retrospective observational study was performed in a surgical ICU during a 4-year period (January 2013–December 2016). Patients were included if they had a positive culture on a respiratory sample and a previous intestinal carriage screening performed by rectal swabbing within 21 days. Sensitivity, specificity, positive (PPV) and negative (NPV) predictive values and likelihood ratios were calculated for the screening for intestinal carriage of ESBL-E, HLAC-E and 3GCR-E (ESBL-E and/or HLAC-E) as predictor of their absence/presence in respiratory samples. Impact of HLAC-E and ESBL-E reporting on EAT was also studied.

Results
765 respiratory samples, retrieved from 468 patients, were analyzed. ESBL-E prevalence was 23.8% in rectal swab and 4.4% in respiratory samples. HLAC-E prevalence was 9.0% in rectal swabs and 3.7% in respiratory samples. Overall, the 3GCR-E prevalence was 31.8% in rectal swabs and 7.7% in respiratory samples. NPVs were 98.8%, 98.0% and 96.6% for ESBL-E, HLAC-E and 3GCR-E, respectively. Over the study period, empirical antimicrobial therapy was initiated for 315 episodes of respiratory infections: 228/315 (72.4%) were associated with negative intestinal carriage screening for both HLAC-E and ESBL-E, of whom 28/228 (12.3%) were treated with carbapenems. Of 23/315 (7.3%) cases with screening for positive intestinal carriage with HLAC-E alone, 10/23 (43.5%) were treated with carbapenems.

Conclusion
Systematic screening and reporting of HLAC-E in addition to ESBL-E in intestinal carriage screening could help to predict the absence of 3GCR-E in respiratory samples of severe surgical ICU patients. This could improve the appropriateness of EAT in ICU patients with HAP and may prevent the overuse of carbapenems.
Assessing risk of bias in human environmental epidemiology studies using three tools: different conclusions from different tools
Authors: Eick Stephanie M. , Goin Dana E. , Chartres Nicholas , Lam Juleen , Woodruff Tracey J. 
Published: October 2020

Abstract

Background
Systematic reviews are increasingly prevalent in environmental health due to their ability to synthesize evidence while reducing bias. Different systematic review methods have been developed by the US National Toxicology Program’s Office of Health Assessment and Translation (OHAT), the US Environmental Protection Agency’s (EPA) Integrated Risk Information System (IRIS), and by the US EPA under the Toxic Substances Control Act (TSCA), including the approach to assess risk of bias (ROB), one of the most vital steps which is used to evaluate internal validity of the studies. Our objective was to compare the performance of three tools (OHAT, IRIS, TSCA) in assessing ROB.

Methods
We selected a systematic review on polybrominated diphenyl ethers and intelligence quotient and/or attention deficit hyperactivity disorder because it had been endorsed by the National Academy of Sciences. Two reviewers followed verbatim instructions from the tools and independently applied each tool to assess ROB in 15 studies previously identified. We documented the time to apply each tool and the impact the ROB ratings for each tool had on the final rating of the quality of the overall body of evidence.

Results
The time to complete the ROB assessments varied widely (mean = 20, 32, and 40 min per study for the OHAT, IRIS, and TSCA tools, respectively). All studies were rated overall “low” or “uninformative” using IRIS, due to “deficient” or “critically deficient” ratings in one or two domains. Similarly, all studies were rated “unacceptable” using the TSCA tool because of one “unacceptable” rating in a metric related to statistical power. Approximately half of the studies had “low” or “probably low ROB” ratings across all domains with the OHAT and Navigation Guide tools.

Conclusions
Tools that use overall ROB or study quality ratings, such as IRIS and TSCA, may reduce the available evidence to assess the harms of environmental exposures by erroneously excluding studies, which leads to inaccurate conclusions about the quality of the body of evidence. We recommend using ROB tools that circumvents these issues, such as OHAT and Navigation Guide.

Systematic review registration
This review has not been registered as it is not a systematic review.
Contamination of SARS-CoV-2 in patient surroundings and on personal protective equipment in a non-ICU isolation ward for COVID-19 patients with prolonged PCR positive status
Authors: Wei Li , Huang Wenzhi , Lu Xiaojun , Wang Yantong , Cheng Linzhi , Deng Rong , Long Haiyan , Zong Zhiyong 
Published: October 2020

AbstractObjectivesWe performed an environmental sampling study to investigate the environmental contamination of SARS-CoV-2 by COVID-19 patients with prolonged PCR positive status of clinical samples.MethodsWe sampled the air from rooms for nine COVID-19 patients with illness or positive PCR > 30 days, before and after nasopharyngeal/oropharyngeal swabbing and before and after nebulization treatment. We also sampled patients’ surroundings and healthcare workers’ personal protection equipment (PPE) in a non-ICU ward. SARS-CoV-2 was detected by PCR.ResultsEighty-eight samples were collected from high-touch surfaces and floors in patient rooms and toilets, with only the bedsheets of two patients and one toilet positive for SARS-CoV-2. All air samples (n = 34) were negative for SARS-CoV-2. Fifty-five samples collected from PPE were all negative.ConclusionContamination of near-patient surroundings was uncommon for COVID-19 patients with prolonged PCR positive status if environmental cleaning/disinfection were performed rigorously. Airborne transmission of SARS-CoV-2 was unlikely in these non-ICU settings.
Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission
Authors: Ott Emanuel , Kawaguchi Yuko , Kölbl Denise , Rabbow Elke , Rettberg Petra , Mora Maximilian , Moissl-Eichinger Christine , Weckwerth Wolfram , Yamagishi Akihiko , Milojevic Tetyana 
Published: October 2020

AbstractBackgroundThe extraordinarily resistant bacteriumDeinococcus radioduranswithstands harsh environmental conditions present in outer space.Deinococcus radioduranswas exposed for 1 year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. In addition, a ground-based simulation experiment with conditions, mirroring those from low Earth orbit, was performed.MethodsWe monitoredDeinococcus radioduranscells during early stage of recovery after low Earth orbit exposure using electron microscopy tools. Furthermore, proteomic, transcriptomic and metabolomic analyses were performed to identify molecular mechanisms responsible for the survival ofDeinococcus radioduransin low Earth orbit.ResultsD. radioduranscells exposed to low Earth orbit conditions do not exhibit any morphological damage. However, an accumulation of numerous outer-membrane-associated vesicles was observed. On levels of proteins and transcripts, a multi-faceted response was detected to alleviate cell stress. The UvrABC endonuclease excision repair mechanism was triggered to cope with DNA damage. Defense against reactive oxygen species is mirrored by the increased abundance of catalases and is accompanied by the increased abundance of putrescine, which works as reactive oxygen species scavenging molecule. In addition, several proteins and mRNAs, responsible for regulatory and transporting functions showed increased abundances. The decrease in primary metabolites indicates alternations in the energy status, which is needed to repair damaged molecules.ConclusionLow Earth orbit induced molecular rearrangements trigger multiple components of metabolic stress response and regulatory networks in exposed microbial cells. Presented results show that the non-sporulating bacteriumDeinococcus radioduranssurvived long-term low Earth orbit exposure if wavelength below 200 nm are not present, which mirrors the UV spectrum of Mars, where CO2effectively provides a shield below 190 nm. These results should be considered in the context of planetary protection concerns and the development of new sterilization techniques for future space missions.
More pilot trials could plan to use qualitative data: a meta-epidemiological study
Authors: Baldeh Tejan , MacDonald Tonya , Kosa Sarah Daisy , Lawson Daeria O. , Stalteri Rosa , Olaiya Oluwatobi R. , Alotaibi Ahlam , Thabane Lehana , Mbuagbaw Lawrence 
Published: October 2020

Abstract

Background
Pilot trials often use quantitative data such as recruitment rate and retention rate to inform the design and feasibility of a larger trial. However, qualitative data such as patient, healthcare provider, and research staff perceptions of an intervention may also provide insights for a larger trial.

Methods
As part of a larger study investigating the reporting of progression criteria in pilot studies, we sought to determine how often pilot studies planned to use qualitative data to inform the design and feasibility of a larger trial and the factors associated with plans to use qualitative data. We searched for protocols of pilot studies of randomized trials in PubMed between 2013 and 2017.

Results
We included 227 articles. Only 92 (40.5%; 95% confidence interval [CI] 34.1–47.2) reported plans to collect qualitative data. The factors associated with collecting qualitative data were large studies (defined as sample size ≥ 60; adjusted odds ratio [aOR] 2.77; 95% CI 1.47–5.23; p = 0.002) and studies from Europe (aOR 3.86; 95% CI 1.68–8.88; p = 0.001) compared to North America and the rest of the world. Pilot trials with pharmacological interventions were less likely to plan to collect qualitative data (aOR 0.20; 95% CI 0.07–0.58; p = 0.003).

Conclusions
Qualitative data is not used enough in pilot trials. Large pilot trials, pilot trials from Europe, and pilot trials of non-pharmacological interventions are more likely to plan for qualitative data.
Trichoderma: a beneficial antifungal agent and insights into its mechanism of biocontrol potential
Authors: Mukhopadhyay Ria , Kumar Deepak 
Published: October 2020

Abstract

Background
Agriculture is an indispensable part of any country to feed the millions of people but it is under constant threat of pests. To protect the crops from this huge yield loss recently, chemical pesticides are used. Though chemical pesticides have shown effective results in killing the crop pests, it causes negative impact on the environment as well as humans. So to find an eco-friendly alternative, biological control methods are being used.

Main body
Biological control is a great renaissance of interest and research in microbiological balance to control soil-borne plant pathogens and leads to the development of a better farming system. In biological control, genus Trichoderma serves as one of the best bioagents, which is found to be effective against a wide range of soil and foliar pathogens. Genus Trichoderma is a soil inhabiting green filamentous fungus, which belongs to the division Ascomycota. The efficacy of Trichoderma depends on many abiotic parameters such as soil pH, water retention, temperature and presence of heavy metals. The biocontrol potential of Trichoderma spp. is due to their complex interaction with plant pathogens either by parasitizing them, secreting antibiotics or by competing for space and nutrients. During mycoparasitic interactions, production of hydrolytic enzymes such as glucanase, chitinase and protease and also signalling pathways are initiated by Trichoderma spp. and the important ones are Heterotrimeric G protein, MAP kinase and cAMP pathway. G protein and MAPK are mainly involved in secretion of antifungal metabolites and the formation of infection structures. cAMP pathway helps in the condition and coiling of Trichoderma mycelium on pathogenic fungi and inhibits their proliferation.

Short conclusion
Trichoderma being an efficient biocontrol agent, their characteristics and mechanisms should be well understood to apply them in field conditions to restrict the proliferation of phytopathogens.
Zinner’s syndrome, radiological diagnosis for a rare syndrome with non-specific clinical presentation: case report
Authors: Soliman Ahmed Atef , Alshukami Anwar Ali , AlZuber Walaa Hussein 
Published: October 2020

Abstract

Background
Zinner’s syndrome is a rare congenital malformation involving the seminal vesicle that mostly shows cystic transformation. Embryogenesis of the kidney, ureter, seminal vesicle, and vas deferens can be altered if an insult occurs during the first trimester mainly between the 4th and the 13th gestational week. Cystic lesions of the seminal vesicle may present with a mass effect. Associated ipsilateral renal agenesis is a characteristic feature in more than 50% of patients as the seminal vesicles and ureteral buds originate from the mesonephric (Wolffian) duct. For management, the transrectal ultrasound provides good visualization of the seminal vesicles and the rest of the pelvic structures providing a good guidance for aspiration of the cysts.

Case presentation
We present a case of a seminal vesicle fluid-filled tubular lesion. The patient first complained of vague abdominal pain with lower abdominal fullness. He was clinically evaluated, and radiological evaluation was performed using different modalities, and finally, the patient took his decision to live with it without any intervention at present.

Conclusions
The combination of seminal vesicle cysts and ipsilateral renal agenesis, is a rare urological anomaly with an insult during the 1st trimester is to be considered as the first suspicion. Usual manifestations are caused by the seminal vesicle cysts that cause mass effect and irritation to the surroundings in the form of urinary bladder irritation and in sometimes obstruction as well as pain/discomfort in the perineum and scrotum. Epididymitis is frequently occurring as a complication. Treatment mainly consists of removing the seminal vesicle cyst/tubular lesion.
In-vitro antioxidant, anti-cancer, and anti-inflammatory activities of selected medicinal plants from western Nepal
Authors: Pandey Bishnu Prasad , Adhikari Kapil , Pradhan Suman Prakash , Shin Hee Jeong , Lee Eun Kyeong , Jung Hye Jin 
Published: October 2020

Abstract

Background
This study was focused on the measurement of anticancer properties of six medicinal plants from western Nepal in three cell lines; HeLa, Hep3B, and HCT116, and anti-inflammatory properties in RAW 264.7 cell line through NO, PGE2, and TNF-α production. In addition, the phytochemical screening, total phenolic, flavonoid content, and antioxidant properties were evaluated.

Results
The qualitative phytochemical analysis revealed the presence of different secondary metabolite and range of total phenolic and total flavonoid content. The highest antioxidant activities were observed in Bergenia pacumbis against both DPPH (IC50 = 25.97 ± 0.19 μg/mL) and ABTS (IC50 = 14.49 ± 0.40 μg/mL). Furthermore, the highest antiproliferative effect against cervical, liver, and colon cancer cell lines were observed in Melia azedarach as IC50 values of 10.50, 5.30, and 1.57 μg/mL respectively, while the strongest anti-metastatic potential on liver cancer cell line was found in Pleurospermum benthamii. In addition, P. benthamii showed the most potent anti-inflammatory effect in RAW264.7 murine macrophage cells.

Conclusion
This study provided the evidence for M. azedarach and P. benthamii to have great anticancer potential and finding builds the enough scientific backgrounds in future to isolate and purify the bioactive compounds for further applications.