bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex patterns of reticulate evolution in opportunistic weeds (Potentilla L., Rosaceae), as revealed by low-copy nuclear markers
Authors: Persson Nannie L. , Eriksson Torsten , Smedmark Jenny E. E. 
Published: March 2020

Abstract
Background
Most cinquefoils (Potentilla L., Rosaceae) are polyploids, ranging from tetraploid (4x) to dodecaploid (12x), diploids being a rare exception. Previous studies based on ribosomal and chloroplast data indicated that Norwegian cinquefoil (P. norvegica L.) has genetic material from two separate clades within Potentilla; the Argentea and the Ivesioid clades – and thus a possible history of hybridization and polyploidization (allopolyploidy). In order to trace the putative allopolyploid origin of the species, sequence data from low-copy, biparentally inherited, nuclear markers were used. Specimens covering the circumpolar distribution of P. norvegica and its two subspecies were included, along with the morphologically similar P. intermedia. Potentilla species of low ploidy level known to belong to other relevant clades were also included.

Results
Gene trees based on three low-copy nuclear markers, obtained by Bayesian Inference and Maximum Likelihood analyses, showed slightly different topologies. This is likely due to genomic reorganizations following genome duplication, but the gene trees were not in conflict with a species tree of presumably diploid taxa obtained by Multispecies Coalescent analysis. The results show that both P. norvegica and P. intermedia are allopolyploids with a shared evolutionary history involving at least four parental lineages, three from the Argentea clade and one from the Ivesioid clade.

Conclusions
This is the first time that reticulate evolution has been proven in the genus Potentilla, and shows the importance of continuing working with low-copy markers in order to properly resolve its evolutionary history. Several hybridization events between the Argentea and Ivesioid clades may have given rise to the species of Wolf’s grex Rivales. To better estimate when and where these hybridizations occurred, other Argentea, Ivesioid and Rivales species should be included in future studies.
Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq
Authors: Martin Cerezo Maria Luisa , Kucka Marek , Zub Karol , Chan Yingguang Frank , Bryk Jarosław 
Published: March 2020

Abstract
Background
Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context.

Results
Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST<0.086.

Conclusion
Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.
An exclusion mechanism is epistatic to an internal detoxification mechanism in aluminum resistance in Arabidopsis
Authors: Wang Yuqi , Yu Wancong , Cao Yu , Cai Yanfei , Lyi Sangbom M. , Wu Weiwei , Kang Yan , Liang Cuiyue , Liu Jiping 
Published: March 2020

AbstractBackgroundInArabidopsis, the aluminum (Al) exclusion mechanism is mainly facilitated by ALMT1-mediated malate exudation and MATE-mediated citrate releases from the root. Recently, we have demonstrated that coordinated functioning between an ALMT1-mediated Al exclusion mechanism, via exudation of malate from the root tip, and a NIP1;2-facilitated internal detoxification mechanism, via removal of Al from the root cell wall and subsequent root-to-shoot Al translocation, plays critical roles in achieving overall Al resistance. However, the genetic relationship betweenALMT1andNIP1;2in these processes remained unclear.ResultsThrough genetic and physiological analyses, we demonstrate that unlikeALMT1andMATE, which function independently and additively,ALMT1andNIP1;2show an epistatic relationship in Al resistance. These results indicate thatALMT1andNIP1;2function in the same biochemical pathway, whereasALMT1andMATEin different ones.ConclusionThe establishment of the epistatic relationship and the coordinated functioning between the ALMT1 and NIP1;2-mediated exclusion and internal detoxification mechanisms are pivotal for achieving overall Al resistance in the non-accumulating Arabidopsis plant. We discuss and emphasize the indispensable roles of the root cell wall for the implementation of the Al exclusion mechanism and for the establishment of an epistatic relationship between the ALMT1-mediated exclusion mechanism and the NIP1;2-facilitated internal detoxification mechanism.
The role of mini-bronchoalveolar lavage fluid in the diagnosis of pulmonary tuberculosis in critically ill patients
Authors: Neves Cynthia Pessoa , Costa Allyson Guimarães , Safe Izabella Picinin , de Souza Brito Alexandra , Jesus Jaquelane Silva , Kritski Afranio Lineu , Lacerda Marcus Vinicius Guimarães , Viveiros Miguel , Cordeiro-Santos Marcelo 
Published: March 2020

Abstract
Background
The detection of Mycobacterium tuberculosis (MTB) in the intensive care unit (ICU) presents several challenges, mainly associated to the clinical state of the patient. The presence of HIV infection further aggravates this scenario, requiring a reliable collection method, with better performance in the microbiological/molecular techniques to be used. We evaluated the performance of two methods for sample collection, mini bronchoalveolar lavage (Mini-BAL) and endotracheal aspirate (ETA), for diagnosis of pulmonary tuberculosis (PTB) in critically ill patients.

Methods
This prospective study involved 26 HIV positive ICU internalized patients, with presumptive PTB who required mechanical ventilation. Two samples were obtained prospectively from 26 HIV ICU patients with presumptive PTB by Mini-BAL and ETA. The samples were processed for smear microscopy, Löwenstein-Jensen medium and the BACTEC Mycobacteria Growth Indicator Tube 960 system®. We define as confirmed PTB patients with positive MTB culture. Furthermore, all samples obtained through the Mini-BAL were analyzed by Xpert® MTB/RIF.

Results
Our results demonstrated that the respiratory samples obtained by Mini-BAL were able to increase MTB detection in critically ill patients with presumptive PTB. The Mini-BAL allowed 30% increased recovery and guaranteed enough sample volume for processing in all methods. In addition, the larger volume of the samples obtained with this technique enabled the Xpert® MTB/RIF molecular test for diagnosis of TB.

Conclusions
The Mini-BAL showed be an acceptable alternative to ETA in this population, since these critically ill and often-immunocompromised patients are more likely to develop complications related to invasive procedures.
Case reports of latent HBV hepatitis in patients after neurosurgical treatment for hypothalamic and pituitary tumors
Authors: Niizuma Kuniyasu , Ogawa Yoshikazu , Kogure Takayuki , Tominaga Teiji 
Published: March 2020

Abstract
Background
Hepatitis B virus (HBV) infection is a major public health problem worldwide. More than 2 billion people have been exposed to HBV, and about 257 million individuals are chronic carriers of HBV. HBV reactivation has been increasingly reported in HBV carriers who have undergone immunosuppression or chemotherapy, resulting in mortality. Treatment of hypothalamic/pituitary tumors in HBV carriers requires extensive care to avoid HBV reactivation as steroid therapy is required after surgery for hypothalamic/pituitary tumors.

Case presentation
This retrospective review identified 5 patients, who were HBV carriers positive for hepatitis B surface antigen among 1352 patients with surgically treated hypothalamic/pituitary tumor in Kohnan Hospital between February 2007 and April 2017. Transsphenoidal surgery was performed with particular attention to prevent damage to the pituitary gland, with delicate manipulation to minimize postoperative steroid coverage. All patients received nucleot(s)ide analogue to control HBV-DNA levels before the surgery. As a result, all patients had a good clinical course. Blood examinations found a transient increase of liver enzymes and HBV-DNA levels in all patients, which started to decrease within 2 weeks after surgery. No specific treatment other than nucleot(s)ide analogues was needed to maintain liver function, and all patients returned to their previous activities including reinstatement.

Conclusion
Initiation of nucleot(s)ide analogues administration prior to the surgery for hypothalamic/pituitary tumors can be an effective strategy for preventing reactivation in HBV carriers. Appropriate screening of the patient’s HBV phase, optimal timing of nucleot(s)ide analogues -administration, and administration period of nucleot(s)ide analogues need to be established.
A ruptured posterior communicating artery aneurysm presenting as tentorial and spinal isolated subdural hemorrhage: a case report and literature review
Authors: Al-Abdulwahhab Abdulrahman Hamad , Al-Sharydah Abdulaziz Mohammad , Al-Suhibani Sari Saleh , Almulhim Abdullah Salman , Al-Dhafeeri Obaied M. , Al-Jubran Saeed A. 
Published: March 2020

AbstractBackgroundRuptured intracranial aneurysms are often associated with subarachnoid or intraparenchymal hemorrhage. However, the prevalence of subdural hemorrhage post aneurysmal rupture is low and rarely reported in scientific studies. Here, we report an unusual case of a ruptured posterior communicating artery aneurysm resulting in an isolated subdural hematoma located in the tentorial and spinal canal without subarachnoid or intraparenchymal hemorrhage.Case presentationIn this case, a 34-year-old woman with no history of trauma or coagulopathy was diagnosed with a subdural hematoma in the tentorium cerebellum tracing to the subdural space of the spinal column. Computed tomography angiography was used to identify the source of the bleeding, which revealed a ruptured left-sided posterior communicating artery saccular aneurysm. The aneurysm was clipped, and the hematoma was evacuated. The patient recovered without any neurological complications.ConclusionsOur results suggest that a diagnosis of ruptured intracranial aneurysm should be considered in patients with nontraumatic subdural hematoma. Prompt diagnostic imaging and interventional diagnostic procedures are required to ensure proper management of these patients and to avoid unnecessary complications.
Healthcare professionals’ perceptions and experiences of using a cold cot following the loss of a baby: a qualitative study in maternity and neonatal units in the UK
Authors: Smith Paula , Vasileiou Konstantina , Jordan Abbie 
Published: March 2020

Abstract
Background
Best practice in perinatal bereavement care suggests offering parents the opportunity to spend time with their baby. Cold cots facilitate this purpose by reducing the deterioration of the body and evidence indicates their wide availability in maternity and neonatal units in the UK. This study aimed to examine healthcare professionals’ perceptions and experiences of using a cold cot following the loss of a baby.

Methods
A qualitative cross-sectional study was designed. In-depth, semi-structured interviews were conducted with 33 maternity and neonatal unit healthcare professionals who worked across three UK hospital settings. Data were analysed using inductive reflexive thematic analysis.

Results
Findings revealed that staff had predominantly positive views about, and experiences of, using a cold cot. The technology was highly valued because it facilitated parents to spend time with their baby and participants reported that it was generally easy to use and smoothly embedded into the clinical environment. Cold cots were deemed useful when mothers were medically unwell and needed time to recover, when parents struggled to say goodbye to their baby, wished to take the baby home, or wanted their baby to stay in the unit instead of going straight to the mortuary. The use of technology was further perceived to be relevant in scenarios of unexpected loss, post-mortem examination and with babies of late gestations or neonates. Despite staff expressing comfort with the delay of visual and olfactory body changes, the coldness of the baby’s body that was accelerated with the use of a cold cot was a major concern as it connoted and possibly exacerbated the reality of death.

Conclusions
Cold cots allow the materialisation of modern bereavement care practices that recognise the importance of continuing bonds with the deceased that is made possible through the creation of memories within an extremely restricted timeframe. Simultaneously, the body coldness concentrates the ambivalence toward an inherently paradoxical death, that of a baby. Training in perinatal bereavement care, including the use of cold cots, would help staff support bereaved parents whilst acknowledging dilemmas and managing contradictions encompassed in death at the time or near the time of birth.
In their own words: a qualitative study of factors promoting resilience and recovery among postpartum women with opioid use disorders
Authors: Goodman Daisy J. , Saunders Elizabeth C. , Wolff Kristina B. 
Published: March 2020

Abstract
Background
Opioid use disorder (OUD) is associated with substantial morbidity and mortality for women, especially during the perinatal period. Opioid overdose has become a significant cause of maternal death in the United States, with rates highest in the immediate postpartum year. While pregnancy is a time of high motivation for healthcare engagement, unique challenges exist for pregnant women with OUD seeking both substance use treatment and maternity care, including managing change after birth. How women successfully navigate these barriers, engage in treatment, and abstain from substance use during pregnancy and postpartum is poorly understood. The aim of this study is to explore the experiences of postpartum women with OUD who successfully engaged in both substance use treatment and maternity care during pregnancy, to understand factors contributing to their ability to access care and social support.

Methods
We conducted semi-structured, in-depth interviews with postpartum women in sustained recovery (n = 10) engaged in a substance use treatment program in northern New England. Interviews were analyzed using grounded theory methodology.

Results
Despite multiple barriers, women identified pregnancy as a change point from which they were able to develop self-efficacy and exercise agency in seeking care. A shift in internal motivation enabled women to disclose need for OUD treatment to maternity care providers, a profoundly significant moment. Concurrently, women developed a new capacity for self-care, demonstrated through managing relationships with providers and family members, and overcoming logistical challenges which had previously seemed overwhelming. This transformation was also expressed in making decisions based on pregnancy risk, engaging with and caring for others, and providing peer support. Women developed resilience through the interaction of inner motivation and their ability to positively utilize or transform external factors.

Conclusions
Complex interactions occurred between individual-level changes in treatment motivation due to pregnancy, emerging self-efficacy in accessing resources, and engagement with clinicians and peers. This transformative process was identified by women as a key factor in entering recovery during pregnancy and sustaining it postpartum. Clinicians and policymakers should target the provision of services which promote resilience in pregnant women with OUD.
Severe sepsis caused by serious gastrointestinal infection in sJIA patients treated with IL-6 receptor antagonist: a case report
Authors: Xu Meng , Liu Congcong , Guo Lishuang , Yang Sirui 
Published: March 2020

Abstract
Background
Interleukin (IL)-6 plays an essential role in the pathogenesis of systemic juvenile idiopathic arthritis (sJIA). Tocilizumab (TCZ), a kind of biological agent against both membrane and soluble IL-6 receptor, is the only biological agent approved for the treatment of sJIA in China. Infections are the most common adverse events during TCZ therapy, and most of infections are mild or moderate. Severe sepsis originated from gastrointestinal infection is rarely reported.

Case presentation
In this article, we reported two 13-year-old sJIA patients who suffered from life-threatening infections after TCZ administration. Within one day, both of them presented rapidly progressive conditions that included fever, abdominal pain, dizziness, diarrhea and vomiting, and laboratory tests showed multi-organ dysfunctions. They were diagnosed with severe sepsis and septic shock that were supposed to be caused by the pathogens from the gastrointestinal tract, and they were eventually rescued by timely treatment. In addition, we also reviewed the literature about serious gastrointestinal infections and sepsis in sJIA patients receiving TCZ therapy.

Conclusions
In summary, for sJIA patients with TCZ therapy, invading pathogens from the gastrointestinal tract can cause an intensely systemic infection that may even be fatal. Therefore, it is essential to pay attention to the gastrointestinal management of sJIA patients as well as remind them of their intestinal hygiene.
Risk factors for viral hepatitis A infection in Gampaha District, Sri Lanka: an unmatched case control study
Authors: Ariyarathna Nalin , Abeysena Chrishantha 
Published: March 2020

Abstract
Background
Hepatitis A virus (HAV) is one of the commonest food and water borne infectious diseases. The objective of the study was to determine the risk factors of HAV infection in the Gampha District in Sri Lanka.

Methods
This was an unmatched case control study conducted between January 2015 and November 2016 comprising of 504 participants with a case control ratio of 1:1. The study population included individuals of age 1 year and above who were permanent residents of the district. Cases included participants admitted to four secondary care state hospitals with an acute HAV diagnosed by detecting serum anti-HAV IgM antibodies. Controls were randomly selected individuals from the community with serum negative for Anti-HAV IgM and IgG. An interviewer administered questionnaire was used for the data collection and multiple logistic regression was applied to determine the independent risk factors. The results are expressed as adjusted odds ratios (AOR) and 95% confidence intervals (CI).

Results
Risk factors for HAV infection were poor knowledge regarding hepatitis (AOR;3.98, 95% CI = 1.97–8.05), unhygienic sanitary practices (OR = 2.73; 95% CI = 1.42–5.23), unhygienic practices related to drinking water (OR = 2.67; 95% CI = 1.37–5.21), residing in urban areas (OR = 5.94; 95% CI = 2.98–11.86) and lower family income (OR = 2.83; 95% CI = 1.30–6.13).

Conclusions
The independent modifiable risk factors for HAV infection were poor knowledge regarding hepatitis, unhygienic sanitary practices, and unhygienic practices related to drinking water. Community awareness must be raised on hygienic practices and safe water drinking practices. Inequities of social determinates of health must be addressed.
Global trends and gaps in research related to latent tuberculosis infection
Authors: Chaw Liling , Chien Lung-Chang , Wong Justin , Takahashi Ken , Koh David , Lin Ro-Ting 
Published: March 2020

Abstract
Background
There is a global commitment to eliminating tuberculosis (TB). It is critical to detect and treat cases of latent TB infection (LTBI), the reservoir of new TB cases. Our study assesses trends in publication of LTBI-related research.

Methods
We used the keywords (“latent tuberculosis” OR “LTBI” OR “latent TB”) to search the Web of Science for LTBI-related articles published 1995–2018, then classified the results into three research areas: laboratory sciences, clinical research, and public health. We calculated the proportions of LTBI-related articles in each area to three areas combined, the average rates of LTBI-related to all scientific and TB-related articles, and the average annual percent changes (AAPC) in rates for all countries and for the top 13 countries individually and combined publishing LTBI research.

Results
The proportion of LTBI-related articles increased over time in all research areas, with the highest AAPC in laboratory (38.2%/yr), followed by public health (22.9%/yr) and clinical (15.1%/yr). South Africa (rate ratio [RR] = 8.28, 95% CI 5.68 to 12.08) and India (RR = 2.53, 95% CI 1.74 to 3.69) had higher RRs of overall TB-related articles to all articles, but did not outperform the average of the top 13 countries in the RRs of LTBI-related articles to TB-related articles. Italy (RR = 1.95, 95% CI 1.45 to 2.63), Canada (RR = 1.73, 95% CI 1.28 to 2.34), and Spain (RR = 1.53, 95% CI 1.13 to 2.07) had higher RRs of LTBI-related articles to TB-related articles.

Conclusions
High TB burden countries (TB incidence > 100 per 100,000 population) published more overall TB-related research, whereas low TB burden countries showed greater focus on LTBI. Given the potential benefits, high TB burden countries should consider increasing their emphasis on LTBI-related research.
Predictors of lost to follow-up in a “test and treat” programme among adult women with high-risk sexual behavior in Kampala, Uganda
Authors: Kamacooko Onesmus , Mayanja Yunia , Bagiire Daniel , Namale Gertrude , Hansen Christian Holm , Seeley Janet 
Published: March 2020

Abstract
Background
Immediate uptake of antiretroviral therapy (ART) after an HIV-positive diagnosis (Test and Treat) is now being implemented in Uganda. Data are limited on lost to follow-up (LTFU) in high-risk cohorts that have initiated ‘Test and Treat’. We describe LTFU in a cohort of women of high-risk sexual behaviour who initiated ART under “Test and Treat”.

Methods
We performed a retrospective cohort study of participant records at the Good Health for Women Project (GHWP) clinic, a clinic in Kampala for women at high-risk of HIV-infection. We included HIV positive women ≥18 years who initiated ART at GHWP between August 2014 and March 2018. We defined LTFU as not taking an ART refill for ≥3 months from the last clinic appointment among those not registered as dead or transferred to another clinic. We used the Kaplan-Meier technique to estimate time to LTFU after ART initiation. Predictors of LTFU were assessed using a multivariable Cox proportional hazards model.

Results
The mean (±SD) age of the 293 study participants was 30.3 (± 6.5) years, with 274 (94%) reporting paid sex while 38 (13%) had never tested for HIV before enrolment into GHWP. LTFU within the first year of ART initiation was 16% and the incidence of LTFU was estimated at 12.7 per 100 person-years (95%CI 9.90–16.3). In multivariable analysis, participants who reported sex work as their main job at ART initiation (Adjusted Hazards Ratio [aHR] =1.95, 95%CI 1.10–3.45), having baseline WHO clinical stage III or IV (aHR = 2.75, 95% CI 1.30–5.79) were more likely to be LTFU.

Conclusion
LTFU in this cohort is high. Follow up strategies are required to support women on Test and Treat to remain on treatment, especially those who engage in sex work and those who initiate ART at a later stage of disease.