bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial structure of the microbiome in the gut of Pomacea canaliculata
Authors: Li Lan-Hua , Lv Shan , Lu Yan , Bi Ding-Qi , Guo Yun-Hai , Wu Jia-Tong , Yue Zhi-Yuan , Mao Guang-Yao , Guo Zhong-Xin , Zhang Yi , Tang Yun-Feng 
Published: December 2019

Abstract
Background
Gut microbes can contribute to their hosts in food digestion, nutrient absorption, and inhibiting the growth of pathogens. However, only limited studies have focused on the gut microbiota of freshwater snails. Pomacea canaliculata is considered one of the worst invasive alien species in the world. Elucidating the diversity and composition of the microbiota in the gut of P. canaliculata snails may be helpful for better understanding the widespread invasion of this snail species. In this study, the buccal masses, stomachs, and intestines were isolated from seven P. canaliculata snails. The diversity and composition of the microbiota in the three gut sections were then investigated based on high-throughput Illumina sequencing targeting the V3-V4 regions of the 16S rRNA gene.

Results
The diversity of the microbiota was highest in the intestine but lowest in the buccal mass. A total of 29 phyla and 111 genera of bacteria were identified in all of the samples. In general, Ochrobactrum, a genus of putative cellulose-degrading bacteria, was the most abundant (overall relative abundance: 13.6%), followed by Sediminibacterium (9.7%), Desulfovibrio (7.8%), an unclassified genus in the family Aeromonadaceae (5.4%), and Cloacibacterium (5.4%). The composition of the microbiota was diverse among the different gut sections. Ochrobactrum (relative abundance: 23.15% ± 7.92%) and Sediminibacterium (16.95 ± 5.70%) were most abundant in the stomach, an unclassified genus in the family Porphyromonadaceae (14.28 ± 7.29%) and Leptotrichia (8.70 ± 4.46%) were highest in the buccal mass, and two genera in the families Aeromonadaceae (7.55 ± 4.53%) and Mollicutes (13.47 ± 13.03%) were highest in the intestine.

Conclusions
The diversity and composition of the microbiome vary among different gut sections of P. canaliculata snails. Putative cellulose-degrading bacteria are enriched in the gut of P. canaliculata.
Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)
Authors: Ji Yunheng , Yang Lifang , Chase Mark W. , Liu Changkun , Yang Zhenyan , Yang Jin , Yang Jun-Bo , Yi Ting-Shuang 
Published: December 2019

AbstractBackgroundParis(Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships withinParishave long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus.ResultsAll 29 species currently recognized inPariswere sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification ofPariswere explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated thatParismay have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary.ConclusionsOur results provide important insights for clarifying some of the long-standing taxonomic debates inParis. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification inParis. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.
Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs
Authors: Rahimi Yousef , Bihamta Mohammad Reza , Taleei Alireza , Alipour Hadi , Ingvarsson Pär K. 
Published: December 2019

AbstractBackgroundIdentification of loci for agronomic traits and characterization of their genetic architecture are crucial in marker-assisted selection (MAS). Genome-wide association studies (GWAS) have increasingly been used as potent tools in identifying marker-trait associations (MTAs). The introduction of new adaptive alleles in the diverse genetic backgrounds may help to improve grain yield of old or newly developed varieties of wheat to balance supply and demand throughout the world. Landraces collected from different climate zones can be an invaluable resource for such adaptive alleles.ResultsGWAS was performed using a collection of 298 Iranian bread wheat varieties and landraces to explore the genetic basis of agronomic traits during 2016–2018 cropping seasons under normal (well-watered) and stressed (rain-fed) conditions. A high-quality genotyping by sequencing (GBS) dataset was obtained using either all original single nucleotide polymorphism (SNP, 10938 SNPs) or with additional imputation (46,862 SNPs) based on W7984 reference genome. The results confirm that the B genome carries the highest number of significant marker pairs in both varieties (49,880, 27.37%) and landraces (55,086, 28.99%). The strongest linkage disequilibrium (LD) between pairs of markers was observed on chromosome 2D (0.296). LD decay was lower in the D genome, compared to the A and B genomes. Association mapping under two tested environments yielded a total of 313 and 394 significant (−log10P>3) MTAs for the original and imputed SNP data sets, respectively. Gene ontology results showed that 27 and 27.5% of MTAs of SNPs in the original set were located in protein-coding regions for well-watered and rain-fed conditions, respectively. While, for the imputed data set 22.6 and 16.6% of MTAs represented in protein-coding genes for the well-watered and rain-fed conditions, respectively.ConclusionsOur finding suggests that Iranian bread wheat landraces harbor valuable alleles that are adaptive under drought stress conditions. MTAs located within coding genes can be utilized in genome-based breeding of new wheat varieties. Although imputation of missing data increased the number of MTAs, the fraction of these MTAs located in coding genes were decreased across the different sub-genomes.
Effectiveness, benefit harm and cost effectiveness of colorectal cancer screening in Austria
Authors:   on behalf of the Austrian Colorectal Cancer Screening Model Group, Jahn Beate , Sroczynski Gaby , Bundo Marvin , Mühlberger Nikolai , Puntscher Sibylle , Todorovic Jovan , Rochau Ursula , Oberaigner Willi , Koffijberg Hendrik , Fischer Timo , Schiller-Fruehwirth Irmgard , Öfner Dietmar , Renner Friedrich , Jonas Michael , Hackl Monika , Ferlitsch Monika , Siebert Uwe 
Published: December 2019

Abstract
Background
Clear evidence on the benefit-harm balance and cost effectiveness of population-based screening for colorectal cancer (CRC) is missing. We aim to systematically evaluate the long-term effectiveness, harms and cost effectiveness of different organized CRC screening strategies in Austria.

Methods
A decision-analytic cohort simulation model for colorectal adenoma and cancer with a lifelong time horizon was developed, calibrated to the Austrian epidemiological setting and validated against observed data. We compared four strategies: 1) No Screening, 2) FIT: annual immunochemical fecal occult blood test age 40–75 years, 3) gFOBT: annual guaiac-based fecal occult blood test age 40–75 years, and 4) COL: 10-yearly colonoscopy age 50–70 years. Predicted outcomes included: benefits expressed as life-years gained [LYG], CRC-related deaths avoided and CRC cases avoided; harms as additional complications due to colonoscopy (physical harm) and positive test results (psychological harm); and lifetime costs. Tradeoffs were expressed as incremental harm-benefit ratios (IHBR, incremental positive test results per LYG) and incremental cost-effectiveness ratios [ICER]. The perspective of the Austrian public health care system was adopted. Comprehensive sensitivity analyses were performed to assess uncertainty.

Results
The most effective strategies were FIT and COL. gFOBT was less effective and more costly than FIT. Moving from COL to FIT results in an incremental unintended psychological harm of 16 additional positive test results to gain one life-year. COL was cost saving compared to No Screening. Moving from COL to FIT has an ICER of 15,000 EUR per LYG.

Conclusions
Organized CRC-screening with annual FIT or 10-yearly colonoscopy is most effective. The choice between these two options depends on the individual preferences and benefit-harm tradeoffs of screening candidates.
Magnetic resonance enterography, colonoscopy, and fecal calprotectin correlate in colonic Crohn’s disease
Authors: Somwaru Alexander S. , Khanijow Vikesh , Katabathina Venkat S. 
Published: December 2019

Abstract
Background
Fecal calprotectin (FCP), magnetic resonance enterography (MRE), and colonoscopy are complementary biometric tests that are used to assess patients with Crohn’s Disease (CD). While prior studies have evaluated the association between combinations of these tests, no study has established a correlation between all three: FCP, MRE, and colonoscopy. We prospectively investigated if there is correlation between these three tests, which may result in improved clinical outcomes that can then be used to streamline patient monitoring and treatment modification.

Methods
One hundred fifty-six patients with colonic CD were prospectively examined between March 2017 and December 2018. FCP levels, MRE, and colonoscopy were assessed in parallel on all 156 patients. Clinical CD activity was measured with the Crohn’s Disease Activity Index (CDAI). CD activity with FCP was measured with a quantitative immunoassay. CD activity on MRE was measured with the Magnetic Resonance Index of Activity (MaRIA). CD activity on colonoscopy was measured with the Crohn’s Disease Endoscopic Index of Severity (CDEIS).

Results
One hundred twelve patients (72%) had active disease (Crohn’s Disease Activity Index > 150) and 44 patients (28%) were in clinical remission disease (Crohn’s Disease Activity Index < 150). FCP levels, MaRIA, and CDEIS are highly correlated with positive and significant Pearson and Spearman coefficients, respectively (P < 0.0001), in univariate analyses. Regression analysis (multivariate analyses) demonstrates significant, positive correlation between FCP and MaRIA (r = 1.07, P < 0.0001) and between FCP and CDEIS (r = 0.71, P = 0.03), and between.
MaRIA and CDEIS (r = 0.63, P = 0.01).

Conclusions
FCP levels significantly correlate with the degree of active inflammation in patients with colonic Crohn’s Disease. Improved clinical results may be achieved by using a biometric strategy that incorporates FCP, colonoscopy, and MRE together. This strategy may in-turn be used in the future to streamline monitoring disease activity and adjustment of therapy to improve long term patient outcomes.
Flexitrate regional citrate anticoagulation in continuous venovenous hemodiafiltration: a retrospective analysis
Authors: Lenga Ilan , Hopman Wilma M. , O’Connell Adam J. , Hume Francesca , Wei Charles C. Y. 
Published: December 2019

Abstract
Background
Flexitrate, an innovative regional citrate anticoagulation (RCA) protocol, was compared to traditional RCA (tRCA) and Heparin anticoagulation protocols in intensive care patients treated with continuous renal replacement therapy (CRRT).

Methods
A single-center, retrospective, cohort study, was done in a 26-bed intensive care unit in a large community hospital. Eighty dialysis sessions (Flexitrate = 2852 h, tRCA = 3580 h and Heparin = 2026 h), performed in 53 patients, were evaluated for filter life, RCA control, and metabolic control.

Results
In the Flexitrate cohort, 3.8% of filters clotted, compared to 16.9% with tRCA and 28.3% with Heparin (p < 0.001 for Flexitrate compared to either tRCA or Heparin). Filter survival was significantly improved with Flexitrate compared to tRCA (HR 0.24, p = 0.018) or Heparin (HR 0.14, p = 0.004).
Anticoagulation control was superior with Flexitrate with Patient Ionized Calcium out of target a median of 16% of the time, compared to 27% for tRCA (p < 0.001). Filter Ionized Calcium was out of target a median of 6.8% of the time, compared to 23% for tRCA (p = 0.03).
Flexitrate produced significantly less alkalosis, hypernatremia, and hypocalcemia than tRCA, and overall metabolic control was comparable to Heparin anticoagulation. The only adverse metabolic outcome with Flexitrate was increased hypomagnesemia.

Conclusions
The Flexitrate protocol extended filter life, delivered more consistent anticoagulation, and provided superior metabolic control compared to a tRCA protocol. Filter life was superior to Heparin anticoagulation, with similar metabolic control. A randomized control trial comparing these protocols is recommended.
Oral health and Candida carriage in socioeconomically disadvantaged US pregnant women
Authors: Xiao Jin , Fogarty Colleen , Wu Tong Tong , Alkhers Naemah , Zeng Yan , Thomas Marie , Youssef Moustafa , Wang Lin , Cowen Lauren , Abdelsalam Hossam , Nikitkova Anna 
Published: December 2019

AbstractBackgroundDespite the well-documented associations between poor maternal oral health and increased risk for adverse birth outcomes and dental caries in children after birth, prenatal oral health care is under-utilized, especially among the underserved population. In addition, oralCandidahas recently been suggested as a potential culprit for children’s dental caries, with evident maternal contributions. Therefore, this study aimed to obtain epidemiological data on the oral health and oralCandidacarriage in a cohort of underserved US pregnant women, and reveal factors associated with their oralCandidacarriage.MethodsDemographic-medical-oral hygiene practice data were collected. Comprehensive oral examination was conducted. Caries status and plaque index were recorded. Oral samples (saliva, plaque and swab) were processed to identifyCandidaspecies andStreptococcus mutansby culturing-dependent and -independent methods. Multiple logistic regression analyses were used to identify factors associated with oralCandidacarriage and caries severity.ResultsEighty-two socioeconomically disadvantaged women (48 pregnant and 34 non-pregnant) were enrolled. More pregnant women (79.1%) had > = 1 untreated decayed tooth when compared to their non-pregnant counterparts (47.1%) (p = 0.01). The average number of decayed teeth in pregnant and non-pregnant women was 3.9 and 3.1 (p > 0.05). Caries severity was positively associated with race (African American vs. white), plaque index and salivaryCandida albicanslevel.C. albicanswas the most predominant/abundantCandidastrain, with cheek and tonsil as the most common colonized sites. The detection ofC. albicanswas 56%/56% in saliva and 40%/47% in plaque of the pregnant and non-pregnant groups, respectively. Study women’s oralCandidacarriage is positively associated with hypertension [p = 0.03, odds ratio = 14.47(1.28, 163.51)], decayed teeth number [p = 0.04, odds ratio = 1.31 (1.01,1.69)] and salivaryS. mutanslevel [p = 0.03, odds ratio = 4.80 (1.18–19.43)].ConclusionsSocioeconomically disadvantaged US women are in need of improved prenatal oral health, a large proportion of them have untreated decayed teeth and high carriage of oralCandida. Due to the observed significant association between the decayed teeth number and oralCandidacarriage, providing oral health care during pregnancy (including limiting decayed teeth) will not only improve women’s oral health, but also present as a promising approach to reduce oralCandidacarriage in women.
Treatment of consistent BRAF/HRAS gene mutation and MYC amplification radiation-induced abdominal wall angiosarcoma with low-dose apatinib: a case report
Authors: Guan Jieshan , Luo Zhijie , Xiao Zhiwei , Xie Yubin , Lin Lizhu 
Published: December 2019

Abstract
Background
An extremely rare condition, radiation-induced angiosarcoma is characterized by a poor prognosis, high recurrence rate and lack of effective treatment. Herein, we present a case report of a 48-year-old female patient with radiation-induced abdominal wall angiosarcoma who showed a dramatic response to low-dose apatinib.

Case presentation
The patient, who was diagnosed with cervical squamous cell carcinoma 20 years ago, had received radiotherapy and chemotherapy after operation. Angiosarcomas of the abdominal wall appeared 9 years later. After repeated surgical operations and intravenous chemotherapy for the angiosarcomas, the patient developed tumor recurrence and pulmonary metastasis. The abdominal wall tumors showed repeated rupture and bleeding, with poor wound healing. On evaluation, laboratory findings detected the negative serum tumor markers CEA, CA 125, CA 15–3 and CA 19–9. Imaging showed multiple subcutaneous nodules and masses in the abdominal wall, accompanied by suspected small subpleural nodule at the lower lobe of the right lung. Immunohistochemistry of previous surgical pathology indicated that CD31, ERG and Vim were positive. The result of whole exome sequencing suggested the mutations of BRAF and HRAS, and the amplification of MYC. Based on the above results, the patient was clinically diagnosed with radiation-induced angiosarcoma of the abdominal wall with pulmonary metastasis. The patient was treated with low-dose apatinib and rejected reoperation or chemotherapy.

Results
At the 6-month follow-up visit, the abdominal wall lesions that had previously ruptured stopped bleeding and showed significant shrinkage. Imaging showed that most of the abdominal wall lesions had partially regressed, and some of the lesions on the abdominal wall and the suspected lesion of subpleural nodule at the lower lobe of the right lung had disappeared.

Conclusions
We described this case and reviewed the literature on radiation-related angiosarcoma. Importantly, this case suggests that apatinib may be an effective and sensitive treatment for radiation-induced angiosarcoma even at the lowest dosage, without aggravating the bleeding of lesions.
Fatal myositis and spontaneous haematoma induced by combined immune checkpoint inhibitor treatment in a patient with pancreatic adenocarcinoma
Authors: Liu Yuan , Liu Zhi , Zeng Xuejun , Bai Chunmei , Chen Lin , Lin Songbai , Tian Xinlun 
Published: December 2019

Abstract
Background
Immune checkpoint inhibitors (ICIs) have achieved unprecedented success in cancer treatment over the past decade. The application of ICIs hasled to the discovery of various types of immune-related adverse events (irAEs). Here, we report a case of fatal myositis and spontaneous haematoma following concurrent treatment of nivolumab and ipilimumab for pancreatic adenocarcinoma.

Case presentation
A 71-year-old gentleman with pancreatic adenocarcinoma underwent the Whipple procedure in September 2014. The patient received 8 cycles of adjuvant chemotherapy with gemcitabineand achieved a complete responsein April 2015. Treatment with the PD-1 inhibitor nivolumab was started due to suspected tumour recurrence in November 2015. In August 2016, the CTLA-4 inhibitor ipilimumab was added to nivolumab for 2 cycles. Eight weeks after the last dose, the patient developed severe myositis complicated with spontaneous haematomain skeletalmuscle. Pathology of the skeletal muscle autopsy revealed lymphocytic infiltration. Intense immunosuppressive therapy, including high-dose corticosteroids and methotrexate, resulted in clinical success in the treatment of myositis. However, the patient died of cancer recurrence.

Conclusion
Myositis due to immunotherapy can be a fatal adverse event of ICIs, which requires close monitoring and cautious management.
Clinical significance of neutrophil-to-lymphocyte ratio as a predictor of lymph node metastasis in gastric cancer
Authors: Kosuga Toshiyuki , Konishi Tomoki , Kubota Takeshi , Shoda Katsutoshi , Konishi Hirotaka , Shiozaki Atsushi , Okamoto Kazuma , Fujiwara Hitoshi , Kudou Michihiro , Arita Tomohiro , Morimura Ryo , Murayama Yasutoshi , Kuriu Yoshiaki , Ikoma Hisashi , Nakanishi Masayoshi , Otsuji Eigo 
Published: December 2019

Abstract
Background
Precise staging is indispensable to select the appropriate treatment strategy for gastric cancer (GC); however, the diagnostic accuracy of conventional modalities needs to be improved. This study investigated the clinical significance of the preoperative neutrophil-to-lymphocyte ratio (NLR) for the prediction of pathological lymph node metastasis (pN+) in GC.

Methods
This was a retrospective study of 429 patients with GC who underwent curative gastrectomy. The predictive ability of NLR for pN+ was examined in comparison with that of computed tomography.

Results
The preoperative NLR ranged from 0.6 to 10.8 (median, 2.0), and the optimal cut-off value for predicting pN+ was 1.6 according to the receiver operating characteristic curve with the maximal Youden index. Multivariate analysis identified a NLR ≥ 1.6 (odds ratio (OR) 3.171; 95% confidence interval (CI) 1.448–7.235, p = 0.004) and cN+ (OR 2.426; 95% CI 1.221–4.958, p = 0.011) to be independent factors associated with pN+ in advanced GC (cT2-T4). On the other hand, a NLR ≥ 1.6 was not useful for predicting pN+ in early GC (cT1). In advanced GC, a NLR ≥ 1.6 detected pN+ with a higher sensitivity (84.9%) and negative predictive value (NPV) (63.9%) than conventional modalities (50.0 and 51.7%, respectively). When the subjects were limited to those with advanced GC with cN0, the sensitivity and NPV of a NLR ≥ 1.6 for pN+ increased further (90.7 and 81.0%, respectively).

Conclusion
The preoperative NLR may be a useful complementary diagnostic tool for predicting pN+ in advanced GC because of its higher sensitivity and NPV than conventional modalities.