bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symbiosis of the millipede parasitic nematodes Rhigonematoidea and Thelastomatoidea with evolutionary different origins
Authors: Nagae Seiya , Sato Kazuki , Tanabe Tsutomu , Hasegawa Koichi 
Published: June 2021

AbstractBackgroundHow various host–parasite combinations have been established is an important question in evolutionary biology. We have previously described two nematode species,Rhigonema naylaeandTravassosinema claudiae, which are parasites of the xystodesmid millipedeParafontaria laminatain Aichi Prefecture, Japan.Rhigonema naylaebelongs to the superfamily Rhigonematoidea, which exclusively consists of parasites of millipedes.T. claudiaebelongs to the superfamily Thelastomatoidea, which includes a wide variety of species that parasitize many invertebrates. These nematodes were isolated together with a high prevalence; however, the phylogenetic, evolutionary, and ecological relationships between these two parasitic nematodes and between hosts and parasites are not well known.ResultsWe collected nine species (11 isolates) of xystodesmid millipedes from seven locations in Japan, and found that all species were co-infected with the parasitic nematodes Rhigonematoidea spp. and Thelastomatoidea spp. We found that the infection prevalence and population densities of Rhigonematoidea spp. were higher than those of Thelastomatoidea spp. However, the population densities of Rhigonematoidea spp. were not negatively affected by co-infection with Thelastomatoidea spp., suggesting that these parasites are not competitive. We also found a positive correlation between the prevalence of parasitic nematodes and host body size. In Rhigonematoidea spp., combinations of parasitic nematode groups and host genera seem to be fixed, suggesting the evolution of a more specialized interaction between Rhigonematoidea spp. and their host. On the other hand, host preference of Thelastomatoidea spp. was not specific to any millipede species, indicating a non-intimate interaction between these parasites and their hosts.ConclusionsThe two nematode superfamilies, Rhigonematoidea and Thelastomatoidea, have phylogenetically distinct origins, and might have acquired xystodesmid millipede parasitism independently. Currently, the two nematodes co-parasitize millipedes without any clear negative impact on each other or the host millipedes. Our study provides an example of balanced complex symbioses among parasitic nematodes and between parasitic nematodes and host millipedes, which have been established over a long evolutionary history.
Molecular genetic diversity and population structure analyses of rutabaga accessions from Nordic countries as revealed by single nucleotide polymorphism markers
Authors: Yu Zhiyu , Fredua-Agyeman Rudolph , Hwang Sheau-Fang , Strelkov Stephen E. 
Published: June 2021

Abstract
Background
Rutabaga or swede (Brassica napus ssp. napobrassica (L.) Hanelt) varies in root and leaf shape and colour, flesh colour, foliage growth habits, maturity date, seed quality parameters, disease resistance and other traits. Despite these morphological differences, no in-depth molecular analyses of genetic diversity have been conducted in this crop. Understanding this diversity is important for conservation and broadening the use of this resource.

Results
This study investigated the genetic diversity within and among 124 rutabaga accessions from five Nordic countries (Norway, Sweden, Finland, Denmark and Iceland) using a 15 K single nucleotide polymorphism (SNP) Brassica array. After excluding markers that did not amplify genomic DNA, monomorphic and low coverage site markers, the accessions were analyzedwith 6861 SNP markers. Allelic frequency statistics, including polymorphism information content (PIC), minor allele frequency (MAF) and mean expected heterozygosity ($$ \overline{H} $$

H
¯

e) and population differentiation statistics such as Wright’s F-statistics (FST) and analysis of molecular variance (AMOVA) indicated that the rutabaga accessions from Norway, Sweden, Finland and Denmark were not genetically different from each other. In contrast, accessions from these countries were significantly different from the accessions from Iceland (P < 0.05). Bayesian analysis with the software STRUCTURE placed 66.9% of the rutabaga accessions into three to four clusters, while the remaining 33.1% constituted admixtures. Three multivariate analyses: principal coordinate analysis (PCoA), the unweighted pair group method with arithmetic mean (UPGMA) and neighbour-joining (NJ) clustering methods grouped the 124 accessions into four to six subgroups.

Conclusion
Overall, the correlation of the accessions with their geographic origin was very low, except for the accessions from Iceland. Thus, Icelandic rutabaga accessions can offer valuable germplasm for crop improvement.
Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs
Authors: Wang Liyuan , Zhang Yawen , Zhang Bo , Zhong Haian , Lu Yunfeng , Zhang Hao 
Published: June 2021

Abstract
Background
Lower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence. One such breed, the Nanyang black pig, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model in which to investigate lipid position trait mechanisms in pigs. An understanding of lipid deposition in pigs might improve pig meat traits in future breeding and promote the selection progress of pigs through modern molecular breeding techniques. Here, transcriptome and tandem mass tag-based quantitative proteome (TMT)-based proteome analyses were carried out using longissimus dorsi (LD) tissues from individual Nanyang black pigs that showed high levels of genetic variation.

Results
A large population of Nanyang black pigs was phenotyped using multi-production trait indexes, and six pigs were selected and divided into relatively high and low lipid deposition groups. The combined transcriptomic and proteomic data identified 15 candidate genes that determine lipid deposition genetic divergence. Among them, FASN, CAT, and SLC25A20 were the main causal candidate genes. The other genes could be divided into lipid deposition-related genes (BDH2, FASN, CAT, DHCR24, ACACA, GK, SQLE, ACSL4, and SCD), PPARA-centered fat metabolism regulatory factors (PPARA, UCP3), transcription or translation regulators (SLC25A20, PDK4, CEBPA), as well as integrin, structural proteins, and signal transduction-related genes (EGFR).

Conclusions
This multi-omics data set has provided a valuable resource for future analysis of lipid deposition traits, which might improve pig meat traits in future breeding and promote the selection progress in pigs, especially in Nanyang black pigs.
De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance
Authors: Wang Jie , Li Shiming , Lan Lei , Xie Mushan , Cheng Shu , Gan Xiaolong , Huang Gang , Du Guohua , Yu Kang , Ni Xuemei , Liu Baolong , Peng Guoxiong 
Published: June 2021

Abstract
Background
Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity.

Results
Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11.

Conclusions
A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.
Neuroendocrine carcinoma of the common bile duct associated with congenital bile duct dilatation: a case report
Authors: Kiya Yoshitaka , Nagakawa Yuichi , Takishita Chie , Osakabe Hiroaki , Nishino Hitoe , Akashi Masanori , Yamaguchi Hiroshi , Nagao Toshitaka , Oono Ryo , Katsumata Kenji , Tsuchida Akihiko 
Published: June 2021

Abstract
Background
Cholangiocarcinoma is frequently observed in patients with congenital bile duct dilatation (CBDD). Most cholangiocarcinomas are adenocarcinomas. Other types, especially neuroendocrine carcinomas (NECs), are rare. To the best of our knowledge, this is the third reported case of an NEC of the common bile duct associated with CBDD and the first to receive adjuvant chemotherapy for advanced disease.

Case presentation

A 29-year-old woman presented with upper abdominal pain. Preoperative imaging indicated marked dilatation of the common bile duct and a tumor in the middle portion of the common bile duct. She was suspected of having distal cholangiocarcinoma associated with CBDD and underwent pylorus-preserving pancreaticoduodenectomy. Pathological and immunohistological findings led to a final diagnosis of large-cell NEC (pT3aN1M0 pStageIIB). The postoperative course was uneventful, and she was administered cisplatin and irinotecan every 4 weeks (four cycles) as adjuvant chemotherapy. She has remained recurrence-free for 16 months.

Conclusions
NEC might be a differential diagnosis in cases of cholangial tumor associated with congenital bile duct dilatation. This presentation is rare and valuable, and to establish better treatment for NEC, further reports are necessary.
Immunological and virological discordance among people living with HIV on highly active antiretroviral therapy in Tigray, Northern Ethiopia
Authors: Hailu Genet Gebrehiwet , Wasihun Araya Gebreyesus 
Published: June 2021

Abstract
Background
People living with human immunodeficiency virus (HIV) with immuno-virological discordant responses are at an increased risk to develop acquired immunodeficiency syndrome (AIDS) and severe non AIDS events which are risk factors for death. This study was aimed to assess prevalence of immuno- virological discordant responses and associated risk factors among highly active antiretroviral therapy (HAART) users in Tigray, Northern Ethiopia.

Methods
A cross sectional study was conducted from September to December 30, 2016 on 260 people living with HIV who started first line HAART from January 2008 to March 2016 at Mekelle hospital and Ayder comprehensive specialized hospital. Baseline and follow-up clinical data and CD4+ result were collected from patient charts. Besides, socio-demographic data and blood samples for CD4 + count and viral load measurement were collected during data collection period. Fisher’s exact test, bivariate and multivariate logistic regressions were used for data analysis. P-value < 0.05 with 95% CI was considered as statistically significant.

Result
Among the 260 study participants, 8.80% (95% Confidence Interval (CI) =8.77–8.84%) and 2.70% (95% CI = 2.68–2.72%) had virological and immunological discordant responses, respectively with an overall immuno-virological discordance response of 11.50% (95% CI = 11.46–11.54%). The median age of the study participants at HAART initiation was 35 (IQR: 28–44 years). More than half (58.1%) of the study participants were females. Age at or below 35 years old at HAART initiation (AOR ((95% CI) = 4.25(1.48–12.23), p = 0.007)), male gender ((Adjusted Odds Ratio (AOR) (95% CI) =1.71(1.13–1.10), p = 0.029)), type of regimen given ((AOR(95% CI) = 0.30 (0.10–0.88), p = 0.028)) and good treatment adherence ((AOR (95% CI) = 0.12 (0.030–0.0.48), p = 0.003)) were associated risk factors for virological discordant response. Likewise, immunological discordant response was associated with tuberculosis co-infections (p = 0.016), hepatitis B virus co-infections (p = 0.05) and low CD4+ count (≤100 cells/μl) at baseline (p = 0.026).

Conclusions
Over all, immuno-virological discordance response was 11.5% in the study area. Males, low baseline CD4+ count, poor/fair treatment adherence, and TB and HBV co-infections were significantly associated with higher immuno-virological discordance. We recommend that decision of patient treatment outcome, regimen change and patient management response should be done using trends of both viral load and CD4+ count concurrently.
Isolation and characterization of Listeria monocytogenes among women attending Jimma University medical center, Southwest Ethiopia
Authors: Girma Lencho , Geteneh Alene , Amenu Demisew , Kassa Tesfaye 
Published: June 2021

Abstract
Background
Listeria monocytogenes (LM) has come to be a major public health issue of at-risk groups, causing high morbidity and mortality. Despite this data, studies are very limited in developing countries like Ethiopia. Thus, we aimed to isolate and characterize LM in terms of antibiogram and biofilm formation among pregnant women with fever, women with a history of spontaneous abortion, women with a history of fetal loss, and women with preterm delivery at Jimma University Medical Center (JUMC), southwest Ethiopia.

Methods
A cross-sectional study was done among 144 women from June to August 2019. Isolates were tested for antibiotic susceptibility and biofilm formation using disc diffusion and microtiter plate method, respectively. Data were collected using a structured questionnaire, entered into Epidata 3.1 and logistic regression was done by SPSS v25.0.

Results
LM was isolated in 8 (5.56%) of 144 screened women. The isolation rate of LM was relatively higher among women with a history of fetal loss (9.7%), followed by women with preterm delivery (6.25%). One of the six cord blood was positive for LM, indicating that the transplacental transmission rate at JUMC was 16.7%. More than 2% of women with an ongoing pregnancy were found to have LM septicemia, which could hurt their fetus. All of the isolates tested were susceptible to Ampicillin. However, all of the isolates were resistant to Penicillin and Meropenem and were biofilm producers.

Conclusions
The high magnitude of pregnancy-related listeriosis in the current study setting appears that implementation of educational programs targeting risk reduction and more studies to identify sources of LM are warranted. The choice of antibiotics should be after susceptibility testing.
Comparison between RT-qPCR for SARS-CoV-2 and expanded triage in sputum of symptomatic and asymptomatic COVID-19 subjects in Ecuador
Authors: Torres Ariel , Fors Martha , Rivero Tamaris , Pantoja Karina , Ballaz Santiago 
Published: June 2021

Abstract
Background
The quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) effectively detects the SARS-COV-2 virus. SARS-CoV-2 Nevertheless, some critical gaps remain in the identification and monitoring of asymptomatic people.

Methods
This retrospective study included 733 asymptomatic and symptomatic COVID-19 subjects, who were submitted to the RT-qPCR test. The objective was to assess the efficacy of an expanded triage of subjects undergoing the RT-qPCR test for SARS-COV-2 to identify the largest possible number of COVID-19 cases in a hospital setting in Ecuador. SARS-CoV-2 Firstly, the sensitivity and specificity as well as the predictive values of an expanded triage method were calculated. In addition, the Kappa coefficient was also determined to assess the concordance between laboratory test results and the expanded triage.

Results
Of a total of 733 sputum samples; 229 were RT-qPCR-positive (31.2%) and mortality rate reached 1.2%. Overall sensitivity and specificity were 86.0% (95% confidence interval: 81.0–90.0%) and 37.0% (95% confidence interval: 32.0–41.0%) respectively, with a diagnostic accuracy of 52.0% and a Kappa coefficient of 0.73. An association between the positivity of the test and its performance before 10 days was found.

Conclusions
The clinical sensitivity for COVID-19 detection was within acceptable standards, but the specificity still fell below the values of reference. The lack of symptoms did not always mean to have a negative SARS-COV-2 RT-qPCR test. The expanded triage identified a still unnoticed percentage of asymptomatic subjects showing positive results for the SARS-COV-2 RT-qPCR test. The study also revealed a significant relationship between the number of RT-qPCR-positive cases and the performance of the molecular diagnosis within the first 10 days of COVID-19 in the symptomatic group.
Food and Drug Administration approvals in phase 3 Cancer clinical trials
Authors: Abi Jaoude Joseph , Kouzy Ramez , Ghabach Marc , Patel Roshal , Pasalic Dario , Ghossain Elie , Miller Austin B. , Lin Timothy A. , Verma Vivek , Fuller C. David , Subbiah Vivek , Minsky Bruce D. , Ludmir Ethan B. , Taniguchi Cullen M. 
Published: June 2021

Abstract
Background
Phase 3 oncologic randomized clinical trials (RCTs) can lead to Food and Drug Administration (FDA) approvals. In this study, we aim to identify trial-related factors associated with trials leading to subsequent FDA drug approvals.

Methods
We performed a database query through the ClinicalTrials.gov registry to search for oncologic phase 3 RCTs on February 2020. We screened all trials for therapeutic, cancer-specific, phase 3, randomized, multi-arm trials. We then identified whether a trial was used for subsequent FDA drug approval through screening of FDA approval announcements.

Results
In total, 790 trials were included in our study, with 225 trials (28.4%) generating data that were subsequently used for FDA approvals. Of the 225 FDA approvals identified, 65 (28.9%) were based on trials assessing overall survival (OS) as a primary endpoint (PEP), two (0.9%) were based on trials with a quality of life (QoL) PEP, and 158 approvals (70.2%) were based on trials with other PEP (P = 0.01). FDA approvals were more common among industry funded-trials (219, 97.3%; P < 0.001), and less common among trials sponsored by national cooperative groups (21, 9.3%; P < 0.001). Finally, increased pre-hoc power and meeting patients’ accrual target were associated with FDA approvals (P < 0.001).

Conclusions
The majority of FDA approvals are based on data generated from trials analyzing surrogate primary endpoints and trials receiving industry funding. Additional studies are required to understand the complexity of FDA approvals.
A survey on COVID-19 vaccine acceptance and concern among Malaysians
Authors: Syed Alwi S. A. R. , Rafidah E. , Zurraini A. , Juslina O. , Brohi I. B. , Lukas S. 
Published: June 2021

Abstract
Background
Vaccination is an effective way to curtail the burden of COVID-19 in which success depends on a high acceptance of the vaccine. However, addressing concerns among vaccine-hesitant individuals is essential to avoid failure of the immunisation programme. This study sought to assess the concerns and acceptance rates regarding the COVID-19 vaccine among Malaysians.

Methods
An online questionnaire was distributed to 1411 respondents via a snowball sampling method among Malaysians aged 18 years and above.

Results
The majority of the respondents were young adults (40.7%), female (62.8%), Malay (63.8%), Muslim (72.3%), married (52.9%), with tertiary education (86.8%) and without medical illness (85%). Social media (97.4%) was the primary source of information regarding COVID-19. The overall acceptance rate was high (83.3%), with the lowest rates among the elderly aged 60 years and above (63.4%) and pensioners (64.6%). Hesitance was caused by concerns regarding side effects (95.8%), safety (84.7%), lack of information (80.9%), effectiveness (63.6%) and religious (20.8%) and cultural factors related to the COVID-19 vaccine (6.8%). Respondents with diabetes mellitus (24.7%) and hypercholesterolemia (23%) were more hesitant to accept the COVID-19 vaccine, at 16.1 and 15.8%, respectively. Predictors of COVID-19 vaccine hesitance were age, religion, and current residence.

Conclusions
The results indicate a high rate of acceptance of the COVID-19 vaccine among Malaysians. Thus, the Malaysian government and other related agencies should increase their campaign and prepare to implement the COVID-19 mass immunisation programme among Malaysians. However, despite the high acceptance rate, it remains important to address concerns among hesitant individuals by building trust in vaccine safety and effectiveness through adequate information regarding the vaccine.