bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of a multidisciplinary team-led school-based human papillomavirus vaccination health-promotion programme on improving vaccine acceptance and uptake among female adolescents
Authors: Chau Janita Pak Chun , Lo Suzanne Hoi Shan , Choi Kai Chow , Lee Vivian Wing Yan , Lui Grace Chung Yan , Chan Kam Ming , Lau Alexander Yuk Lun
Published: September 2020

Introduction:

Evidence has consistently shown the high efficacy of human papillomavirus (HPV) vaccines in preventing cervical cancers. However, the HPV vaccine uptake rate in Hong Kong is very low. We will develop and evaluate an innovative, theory-based multidisciplinary team-led school-based HPV vaccination health-promotion program (MDL-SHPVP), engaging female adolescents, parents/guardians, and secondary school personnel in multicomponent educational strategies and interactive discussions.

Methods and analysis:

A cluster randomized controlled trial is proposed. We will recruit 2520 female adolescents and their parents/guardians from 18 secondary day schools. The MDL-SHPVP is underpinned by the Health Belief Model and Precaution Adoption Process Model. Multicomponent interventions will be offered, including education sessions with small group dialogues with a registered nurse and trained healthcare and lay volunteers, and educational computer games. A team of volunteers will be established to raise HPV, cervical cancer, and HPV vaccine awareness. Outcomes include adolescents’ uptake of the HPV vaccine, adolescents’ intention to receive HPV vaccination, vaccine acceptance among parents/guardians, and parents’/guardians’ and adolescents’ HPV knowledge, attitudes, and beliefs. Data will be collected at baseline, 1 month, and 1 year after intervention. The generalized estimating equations analysis will be used for comparing the outcomes between the 2 groups.

Ethics and dissemination:

Ethical approval was obtained from the Joint Chinese University of Hong Kong-New Territories East Cluster Clinical Research Ethics Committee (Ref. no.: 2019.055). We will disseminate the study findings via peer-reviewed publications and presentations at relevant events and international and local conferences.

Trial registration number:

ClinicalTrials.gov NCT04438291
Nephrogenic diabetes insipidus induced by ureter obstruction due to benign prostatic hyperplasia
Authors: Lou Hanyu , Shen Yimin , Xu Yi , Zhang Wei , Ren Yuezhong
Published: September 2020

Introduction:

Diabetes insipidus can be a common cause of polyuria and hydronephrosis in the kidneys. However, there is few reported case of urinary obstruction induced nephrogenic diabetes insipidus.

Patient concerns:

A 60-year-old Chinese man came to our hospital with the complaints of polydipsia and polyuria for 1 month. His examination showed chronic kidney disease stage III with eGFR of 48.274 ml/min, and the plasma osmolality was 338.00 mOsm/(kg·H2O) with a urinary osmolality of 163.00 mOsm/(kg·H2O). Moreover, imagological examination of the urinary system showed benign prostatic hyperplasia and hydronephrosis.

Diagnosis:

He was considered with benign prostatic hyperplasia induced ureter hydronephrosis and nephrogenic diabetes insipidus.

Interventions:

He got the transurethral resection of the prostate to alleviate urinary retention.

Outcomes:

After that, the urine output gradually decreased, and the administered hydrochlorothiazide was stopped due to the improved renal function.

Conclusion:

Our study presents a case of nephrogenic diabetes insipidus caused by urinary obstruction. Differential diagnoses for diabetes insipidus as well as the relationship between nephrogenic diabetes insipidus and urinary obstruction are also considered in this study.
A comparative study for the rate of adverse outcomes in unilateral and bilateral abdominal flap breast reconstruction
Authors: Cao Zheming , Cao Jiri , Pang Xiaoyang , Du Wei , Wu Panfeng
Published: September 2020

Background:

Adverse outcomes after unilateral vs bilateral breast reconstruction involve an unknown level of risk that warrants thorough investigation.

Methods:

To address this research need, PubMed, Ovid, Medline, EMBASE, and Scopus databases were searched through systematically from January 1, 1990, to January 1, 2019 to retrieve the relevant studies on the risk of postoperative complications after unilateral vs bilateral abdominal flap breast reconstruction. According to the pre-designed inclusion criteria, available data were extracted from the relevant studies, and then analyzed comparatively in order to identify the relative risk (RR) and 95% confidence intervals (CI) applying either a random or a fixed effects model.

Results:

Eventually, 20 studies involving 8122 female subjects met the inclusion criteria. It was found that unilateral reconstruction involved a significantly higher risk of flap loss (RR: 1.56, 95% CI: 1.21–2.00; P < .05) and fat necrosis (RR: 1.60, 95% CI: 1.23–2.09; P < .05) compared to bilateral reconstruction, while bilateral reconstruction involved a greater risk of abdominal hernia/bulge (RR: 1.67, 95% CI: 1.25–2.24; P < .05). The risk was found to be higher following bilateral free transverse rectus abdominis myocutaneous (fTRAM) flaps in comparison with deep inferior epigastric perforator (DIEP) flaps (RR: 2.62, 95% CI: 1.33–5.15; P < .05).

Conclusion:

The risk of postoperative flap complications in unilateral breast reconstruction is significantly higher than that in bilateral reconstruction. Contrarily, the abdominal complications were significantly higher in the bilateral group vs the unilateral group. Meanwhile, the risk of abdominal hernia/bulge complication after bilateral breast reconstruction was significantly higher with fTRAM vs DIEP. Therefore, DIEP flaps are recommended in priority for bilateral breast reconstruction, unless specifically contraindicated.
Evaluating the efficacy and safety of bromhexine hydrochloride tablets in treating pediatric COVID-19
Authors: Wang Yuying , Zhang Yinghua , Chen Xia , Xue Kun , Zhang Tianjing , Ren Xiaohong
Published: September 2020

Background:

Bromhexine hydrochloride tablets may be effective in the treatment of Coronavirus disease 2019 (COVID-19) in children. This study will further evaluate the efficacy and safety of bromhexine hydrochloride tablets in the treatment of COVID-19 in children.

Methods:

The following electronic databases will be searched, with all relevant randomized controlled trials (RCTs) up to August 2020 to be included: PubMed, Embase, Web of Science, the Cochrane Library, China National Knowledge Infrastructure (CNKI), the Chongqing VIP China Science and Technology Database (VIP), Wanfang, the Technology Periodical Database, and the Chinese Biomedical Literature Database (CBM). As well as the above, Baidu, the International Clinical Trials Registry Platform (ICTRP), Google Scholar, and the Chinese Clinical Trial Registry (ChiCTR) will also be searched to obtain more comprehensive data. Besides, the references of the included literature will also be traced to supplement our search results and to obtain all relevant literature.

Results:

This systematic review will evaluate the current status of bromhexine hydrochloride in the treatment of COVID-19 in children, to evaluate its efficacy and safety.

Conclusion:

This study will provide the latest evidence for evaluating the efficacy and safety of bromhexine hydrochloride in the treatment of COVID-19 in children.

PROSPERO Registration number:

CRD42020199805.

Ethics and dissemination:

The private information of individuals will not be published. This systematic review will also not involve endangering participant rights. Ethical approval is not available. The results may be published in peer-reviewed journals or disseminated at relevant conferences.
Efficacy and safety of acupuncture for posterior circulation ischemic vertigo
Authors: Li Bo-xuan , Li Chen , Du Yu-zheng , Meng Xiang-gang
Published: September 2020

Background:

Posterior circulation ischemic vertigo (PCIV) is one of the most complaint symptoms in clinical, and is associated with high risk of recurrence. Current studies show that acupuncture has therapeutic effect on releasing symptom as well as improving the blood flow of posterior circulation. In this review, we aim to assess the efficacy and safety of acupuncture for PCIV.

Methods:

Literature of clinical randomized control trials regarding acupuncture for PCIV published before August of 2020 will be searched in databases, including 5 English databases and 4 Chinese databases. For the included studies, methodological quality will be assessed according to Cochrane Risk of Bias Tool, and evidence quality will be evaluated with Grading of Recommendations Assessment, Development and Evaluation guidelines. Data analysis will be performed using Review Manager Software.

Results:

The primary outcomes involve changes of PCIV symptoms and blood flow velocity of vertebrobasilar. The secondary outcomes include Barthel Index, National Institute of Health Stroke Scale, clinical effectiveness, and adverse reactions.

Conclusion:

Based on current clinical studies, this systematic review and meta-analysis will provide evidence-based basis for the efficacy and safety of acupuncture in treating PCIV.

Trial registration:

The protocol for this review has been registered in the INPLASY network (Registration number: INPLASY202070116).
Late outcomes of endovascular aortic stent graft therapy in patients with chronic kidney disease
Authors: Wu Chung-Cheng , Chou An-Hsun , Lin Yu-Sheng , Wu Victor Chien-Chia , Chang Shang-Hung , Chu Pao-Hsien , Cheng Yu-Ting , Ko Po-Jen , Liu Kuo-Sheng , Chen Shao-Wei
Published: September 2020

Endovascular aneurysm repair (EVAR) and thoracic endovascular aortic repair (TEVAR) are effective and minimally invasive treatment options for high-risk surgical candidates. Nevertheless, knowledge about the management of aortic stent graft therapy in chronic kidney disease (CKD) is scarce. This study aimed to examine outcomes after EVAR and TEVAR in patients with CKD.

Utilizing data from the Taiwan National Health Insurance Research Database, we retrospectively assessed patients who underwent EVAR and TEVAR therapy between January 1, 2006, and December 31, 2013. Patients were divided into CKD and non-CKD groups. Outcomes were in-hospital mortality, all-cause mortality, readmission, heart failure, and major adverse cardiac and cerebrovascular events.

There were 1019 patients in either group after matching. The CKD group had a higher in-hospital mortality rate than the non-CKD group (15.2% vs 8.3%, respectively; odds ratio, 1.92; 95% confidence interval [CI], 1.46–2.54). Patients with CKD had higher risks of all-cause mortality including in-hospital death (46.1% vs 33.1%; hazard ratio [HR], 1.61; 95% CI, 1.35–1.92), readmission rate (62.6% vs 55.0%; subdistribution HR [SHR], 1.61; 95% CI, 1.32–1.69), redo stent (7.8% vs 6.2%; SHR, 1.50; 95% CI, 1.09–2.07), and major adverse cardiac and cerebrovascular events (13.3% vs 8.8%; SHR, 1.50; 95% CI, 1.15–1.95). The subgroup analysis did not demonstrate a variation in mortality between the TEVAR and EVAR cohorts (P for interaction = .725). The dialysis group had higher risks of all-cause mortality and readmission than the CKD without dialysis and non-CKD groups.

Among EVAR/TEVAR recipients, CKD was independently associated with higher in-hospital mortality, postoperative complication, and all-cause mortality rates. Patients with end-stage renal disease on dialysis had worse outcomes than those in the CKD non-dialysis and non-CKD groups.
Protective effects of different doses of human milk on neonatal necrotizing enterocolitis
Authors: Zhang Baoquan , Xiu Wenlong , Dai Yue , Yang Changyi
Published: September 2020

We aim to summarize the evidence focusing on the effects of various doses of human milk on the risk of neonatal necrotizing enterocolitis (NEC). The eligible articles in the study were those investigating the association between human milk and NEC published before June 26, 2019, in the PubMed, EMBASE, the Cochrane Library, VIP database, CNKI database, and Wangfang database. The included criteria were as follows: premature infants of <37 weeks; randomly controlled trials (RCTs); those fed by mother's own milk or donor human milk; studies focused on the comparison of human milk and formula milk, involving various breast milk doses; and NEC-related studies. Compared with the exclusive formula, the incidence of NEC in the infants fed by exclusive human milk was significantly lower. The incidence of NEC in the infants fed by exclusive human milk was significantly lower than that of partial human milk [risk ratio (RR) = 0.54, 95% confidence interval (95% CI): 0.36–0.79, P < .05]. The incidence of NEC in the infants fed mainly by human milk was significantly lower than that of mainly fed by formula. Incidence of NEC in the infants fed by exclusive human milk was significantly lower than that of any formula (RR = 0.49, 95% CI: 0.34–0.71, P < .05). In summary, this meta-analysis was based on the RCTs involving the prevention of NEC using human milk. Exclusive human milk and partial human milk reduced the incidence of NEC in premature infants, especially in the those fed by high proportion of human milk. In addition, more RCTs are needed to further validate such conclusion.
The prognostic value of geriatric nutritional risk index in elderly patients with severe community-acquired pneumonia
Authors: Wei Lishuang , Xie Hailun , Li Junkang , Li Rui , Chen Weijian , Huang Lanfang , Li Xialin , Yan Ping
Published: September 2020

The geriatric nutritional risk index (GNRI) is associated with the prognosis of many diseases. However, the association between the GNRI and the prognosis of patients aged ≥65 years with severe community-acquired pneumonia (SCAP) has not been studied. We aimed to evaluate the prognostic value of GNRI in elderly SCAP patients.

This study retrospectively analyzed the clinical data of 346 patients aged ≥65 years with SCAP from December 2013 to September 2019. Patients were divided into 4 groups by the GNRI. The chi-square test or student's t test was used to compare the differences between the groups. Logistic regression analysis was used to evaluate the factors that affect prognosis. The receiver operating characteristic curve was used to compare the prognostic performance of the GNRI with other indicators. A GNRI-based nomogram was established based on the result of the multivariate analysis.

Two hundred nine (60.4%) patients had a poor prognosis. GNRI scores were significantly lower in the poor prognosis group than in the group with a good prognosis. In the multivariate analysis, gender, mean arterial pressure, neutrophil counts, and the GNRI were independently correlated with the prognosis of elderly patients. The GNRI was a significantly better predictor for poor prognosis than other indicators. The GNRI-based nomogram had excellent prediction capabilities.

GNRI is a simple and effective prognostic indicator for elderly patients with SCAP, and a GNRI-based nomogram can aid in developing individualized treatment plans for elderly patients with SCAP.
Endoscopic Pancreatic Function Testing (ePFT) in Children
Authors: Patel Nishant , Sellers Zachary M. , Grover Amit , Liu Quin Y. , Maqbool Asim , Morinville Veronique D. , Abu‐El‐Haija Maisam , Husain Sohail Z.
Published: September 2020

Endoscopic pancreatic function testing (ePFT) is one of the few ways to directly diagnose exocrine pancreatic insufficiency, and considerable confusion regarding indications, utility, and interpretation of the test remains. This position paper of the Pancreas Committee of the North American Society of Pediatric Gastroenterology, Hepatology and Nutrition reviews the history and indications for ePFT in children. We compare various methods in current practice and determine their strengths and limitations, and based on data from children and adults we provide guidance on a protocol on how to perform ePFT in children. Lastly, we pose areas in need of further research relating to ePFT in children.
Unusual Clinical Course for Untreated Malformative Biliary Atresia Infant
Authors: Di Dato Fabiola , Ranucci Giulia , de Ville de Goyet Jean , Alberti Daniele , Iorio Raffaele
Published: September 2020

In biliary atresia, infants left untreated, and in those with unsuccessful porto‐enterostomy, hepatic condition and function worsen rapidly towards cirrhosis, malnutrition, portal hypertension with ascites, and variceal haemorrhage; many die within the first 3 years of life unless they benefit from liver replacement. We describe a girl with biliary atresia splenic malformation syndrome, who had portal vein cavernoma and microsplenia; she did not undergo porto‐enterostomy. She survived with her native liver over the age of 3 years. Remarkably, she remained in satisfactory condition in absence of ascites or severe hepatic dysfunction, when 4 other similar patients—managed during the same period of time—all had the usual clinical deterioration and ascites, with the need for liver replacement. To our knowledge, there is no similar report in literature. Possible pathogenetic mechanisms and the role of portal hypertension as important factors are discussed.
Clinical Performance of the BD CTGCTV2 Assay for the BD MAX System for Detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis Infections
Authors: Van Der Pol Barbara , Torres-Chavolla Edith , Kodsi Salma , Cooper Charles K. , Davis Thomas E. , Fife Kenneth H. , Taylor Stephanie N. , Augenbraun Michael H. , Gaydos Charlotte A.
Published: September 2020

Background

Diagnostic options to combat the increasing rates of sexually transmitted infections recorded throughout the world increasingly include multiplex assays. Here we describe the estimated sensitivity and specificity of a triplex molecular assay that simultaneously detects Chlamydia trachomatis (CT), Neisseria gonorrhoeae (or gonococci [GC]), and Trichomonas vaginalis (TV).

Methods

Participants (2547 women and 1159 men) were recruited from 12 clinics in the United States. BD CTGCTV2 for BD MAX System assay (CTGCTV2) results were obtained from vaginal and endocervical swabs, endocervical samples in cytology medium, and female and male urine. Results were compared with infection standards that were sample type and pathogen dependent.

Results

Female specimen sensitivity estimates ranged from 92.7% to 98.4%, 92.9% to 100%, and 86.6% to 100% for CT, GC and TV, respectively. Male urine sensitivity estimates were 96.7%, 99.2%, and 97.9% for CT, GC, and TV, respectively. Specificity estimates were >98.7% for all sample types.

Conclusions

BD CTGCTV2 performed well using a variety of sample types. As a true triplex assay, performed using a benchtop instrument, BD CTGCTV2 may be useful in settings where no testing is currently performed and in settings, such as reference laboratories, where testing turnaround time may be several days. Use of this assay at local laboratories may result in greater access to testing and a shorter time to result, which are important steps for improving our ability to combat sexually transmitted infections.
Self-reported Symptoms of Anxiety Predict Positive Suicide Risk Screening in Adolescents Presenting to the Emergency Department
Authors: Powell Daniel S. , Lanzillo Elizabeth C. , Jay Samantha Y. , Tanenbaum Mira , Bridge Jeffrey A. , Wharff Elizabeth A. , Ballard Elizabeth , Pao Maryland , Horowitz Lisa M.
Published: September 2020

Objective

The objective of this study was to assess whether patient-reported anxiety symptoms are associated with suicide risk in pediatric emergency department (ED) patients. An additional objective was to examine differences between patients presenting for medical/surgical or psychiatric complaints.

Methods

Pediatric patients aged 10 to 21 years were recruited from 3 pediatric EDs. Participants completed self-report questionnaires assessing for suicidal ideation and behavior, in addition to questions of interest about recent feelings of unbearable anxiety and depression. Adjusted odds ratios were calculated to assess the relationship between endorsement of recent anxiety and screening positive for suicide risk.

Results

Data were analyzed from 522 participants, including 344 presenting with medical/surgical chief complaints and 178 presenting with psychiatric complaints. Overall, 28.9% of participants screened positive for suicide risk, 29.9% endorsed recent feelings of anxiety, and 24.3% endorsed recent feelings of depression. Patients who self-reported recent anxiety symptoms were 5 times more likely to screen positive for suicide risk (adjusted odds ratios = 5.18, 95% confidence interval = 3.06–8.76). Analysis of the 344 medical/surgical patients revealed that this subsample was also 5 times more likely to screen positive for suicide risk if they endorsed recent anxiety (adjusted odds ratios = 4.87, 95% confidence interval = 2.09–11.36).

Conclusions

Self-reported suicidal ideation and feelings of unbearable anxiety are prevalent among patients presenting to pediatric EDs. Patients who self-report recent feelings of unbearable anxiety are significantly more likely to screen positive for suicide risk, regardless of whether their presenting complaint is medical/surgical or psychiatric in nature.
Persistent Racial and Sex Disparities in Outcomes After Coronary Artery Bypass Surgery
Authors: Enumah Zachary Obinna , Canner Joseph K. , Alejo Diane , Warren Daniel S. , Zhou Xun , Yenokyan Gayane , Matthew Thomas , Lawton Jennifer S. , Higgins Robert S. D.
Published: September 2020

Objective:

The purpose of this study was to assess the temporal trends in 30-day mortality by race group for patients undergoing coronary artery bypass grafting (CABG) between 2011 and 2018 and to investigate the effect of race and sex on postoperative outcomes after CABG.

Summary Background Data:

Cardiovascular diseases remain a leading cause of death in the United States with studies demonstrating increased morbidity and mortality for black and female patients undergoing surgery. In the post drug-eluting stent era, studies of racial disparities CABG are outdated.

Methods:

We performed a retrospective analysis of the Society for Thoracic Surgeons database for patients undergoing CABG between 2011 and 2018. Primary outcome was 30-day mortality. Secondary outcomes included postoperative length of stay, surgical site infection, sepsis, pneumonia, stroke, reoperation, reintervention, early extubation, and readmission.

Results:

The study population was comprised of 1,042,506 patients who underwent isolated CABG between 2011 and 2018. Among all races, Black patients had higher rates of preoperative comorbidities. Compared with White patients, Black patients had higher overall mortality (2.76% vs 2.19%, P < 0.001). On univariable regression, Black patients had higher rates of death, infection, pneumonia, and postoperative stroke compared to White patients. On multivariable regression, Black patients had higher odds of 30-day mortality compared to white patients [odds ratio (OR) = 1.11, 95% confidence interval (CI) 1.05–1.18]. Similarly, female patients had higher odds of death compared to males (OR = 1.26, 95% CI 1.21–1.30).

Conclusions:

In the modern era, racial and sex disparities in mortality and postoperative morbidity after coronary bypass surgery persist with Black patients and female patients consistently experiencing worse outcomes than White male patients. Although there may be unknown or underappreciated biological mechanisms at play, future research should focus on socioeconomic, cultural, and multilevel factors.
A New Screening Method for COVID-19 based on Ocular Feature Recognition by Machine Learning Tools
Authors: Fu Yanwei , Li Feng , Wang Wenxuan , Tang Haicheng , Qian Xuelin , Gu Mengwei , Xue Xiangyang
Published: September 2020

The Coronavirus disease 2019 (COVID-19) has affected several million people. With the outbreak of the epidemic, many researchers are devoting themselves to the COVID-19 screening system. The standard practices for rapid risk screening of COVID-19 are the CT imaging or RT-PCR (real-time polymerase chain reaction). However, these methods demand professional efforts of the acquisition of CT images and saliva samples, a certain amount of waiting time, and most importantly prohibitive examination fee in some countries. Recently, some literatures have shown that the COVID-19 patients usually accompanied by ocular manifestations consistent with the conjunctivitis, including conjunctival hyperemia, chemosis, epiphora, or increased secretions. After more than four months study, we found that the confirmed cases of COVID-19 present the consistent ocular pathological symbols; and we propose a new screening method of analyzing the eye-region images, captured by common CCD and CMOS cameras, could reliably make a rapid risk screening of COVID-19 with very high accuracy. We believe a system implementing such an algorithm should assist the triage management or the clinical diagnosis. To further evaluate our algorithm and approved by the Ethics Committee of Shanghai public health clinic center of Fudan University, we conduct a study of analyzing the eye-region images of 303 patients (104 COVID-19, 131 pulmonary, and 68 ocular patients), as well as 136 healthy people. Remarkably, our results of COVID-19 patients in testing set consistently present similar ocular pathological symbols; and very high testing results have been achieved in terms of sensitivity and specificity. We hope this study can be inspiring and helpful for encouraging more researches in this topic.
Generalizable cursor click control using grasp-related neural transients
Authors: Dekleva Brian M , Weiss Jeffrey M , Boninger Michael L , Collinger Jennifer L
Published: September 2020

Intracortical brain-computer interfaces (iBCI) have the potential to restore independence for individuals with significant motor or communication impairments. One of the most realistic avenues for clinical translation of iBCI technology is to enable control of a computer cursor—i.e. movement-related neural activity is interpreted (decoded) and used to drive cursor function. Both nonhuman primate and human studies have demonstrated high-level cursor translation control using attempted upper limb reaching movements. However, cursor click control—based on identifying attempted grasp—has only been successful in providing discrete click functionality; the ability to maintain click during translation does not yet exist. Here we present a novel decoding approach for cursor click based on identifying transient neural responses that emerge at the onset and offset of intended hand grasp. We demonstrate in a human participant, who used the BCI system independently in his home, that this transient-based approach provides high-functioning, generalized click control that can be used for both point-and-click and click-and-drag applications.
A machine-learning approach to human footprint index estimation with applications to sustainable development
Authors: Keys Patrick W. , Barnes Elizabeth A. , Carter Neil H.
Published: September 2020

The human footprint index is an extensively used tool for interpreting the accelerating pressure of humanity on Earth. Up to now, the process of creating the human footprint index has required significant data and modeling, and updated versions of the index often lag the present day by many years. Here we introduce a near-present, global-scale machine learning-based human footprint index (ml-HFI) which is capable of routine update using satellite imagery alone. We present the most up-to-date map of the human footprint index, and document changes in human pressure during the past 20 years (2000 to 2019). Moreover, we demonstrate its utility as a monitoring tool for the United Nations Sustainable Development Goal 15 (SDG15), “Life on Land”, which aims to foster sustainable development while conserving biodiversity. We identify 43 countries that are making progress toward SDG15 while also experiencing increases in their ml-HFI. We examine a subset of these in the context of conservation policies that may or may not enable continued progress toward SDG15. This has immediate policy relevance, since the majority of countries globally are not on track to achieve Goal 15 by the declared deadline of 2030. Moving forward, the ml-HFI may be used for ongoing monitoring and evaluation support toward the twin goals of fostering a thriving society and global Earth system.
Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers
Authors: Yao Jun , Xu Hengyi , Ferrick-Kiddie Elizabeth A. , Nottingham Ryan M. , Wu Douglas C. , Ares Manuel , Lambowitz Alan M.
Published: September 2020

Previous Thermostable Group II Intron Reverse Transcriptase sequencing (TGIRT-seq) found that human plasma contains short (≤300 nt) structured full-length excised linear intron RNAs (FLEXIs) with potential utility as blood-based biomarkers. Here, TGIRT-seq identified >9,000 different FLEXIs in human cells, including relatively abundant FLEXIs with cell-type-specific expression patterns. Analysis of published CLIP-seq datasets identified 126 RNA-binding proteins (RBPs) that bind different FLEXIs, including 53 RBPs that bind ≥30 FLEXIs. These RBPs included splicing factors, transcription factors, a chromatin remodeling protein, cellular growth regulators, and proteins with cytoplasmic functions. Analysis of published datasets identified subsets of these RBPs that bind at FLEXI splice sites and impact alternative splicing or FLEXI host gene mRNA levels. Hierarchical clustering identified 6 subsets of RBPs whose binding sites were co-enriched in different subsets of FLEXIs: AGO1-4 and DICER, including but not limited to annotated agotrons and mirtron pre-miRNAs; DKC1, NOLC1, SMNDC1, and AATF (Apoptosis Antagonizing Transcription Factor), including but not limited to FLEXIs encoding snoRNAs; two sets of alternative splicing factors; and two sets that included RBPs with cytoplasmic functions (e.g., LARP4, PABPC4, METAP2, and ZNF622) together with nuclear regulatory proteins. The subsets of host genes encoding FLEXIs that bind these RBPs were enriched with non-FLEXI other short and long introns that bind the same RBPs, and TGIRT-seq of nuclear and cytoplasmic fractions from 4 cell lines showed cytoplasmic enrichment of FLEXIs with binding sites for RBPs that function in the cytoplasm. Collectively, our findings suggest that different subsets of RBPs bind FLEXIs and other introns to coordinately regulate the expression of functionally related host genes and then co-localize with stably bound FLEXIs to different intracellular locations. The cell-type specific expression of relatively abundant FLEXIs suggests utility as cellular as well as blood-based RNA biomarkers.
Automated detection of Hainan gibbon calls for passive acoustic monitoring
Authors: Dufourq Emmanuel , Durbach Ian , Hansford James P. , Hoepfner Amanda , Ma Heidi , Bryant Jessica V. , Stender Christina S. , Li Wenyong , Liu Zhiwei , Chen Qing , Zhou Zhaoli , Turvey Samuel T.
Published: September 2020

1

Extracting species calls from passive acoustic recordings is a common preliminary step to ecological analysis. For many species, particularly those occupying noisy, acoustically variable habitats, the call extraction process continues to be largely manual, a time-consuming and increasingly unsustainable process. Deep neural networks have been shown to offer excellent performance across a range of acoustic classification applications, but are relatively underused in ecology.

We describe the steps involved in developing an automated classifier for a passive acoustic monitoring project, using the identification of calls of the Hainan gibbon(Nomascus hainanus), one of the world’s rarest mammal species, as a case study. This includes preprocessing - selecting a temporal resolution, windowing and annotation; data augmentation; processing - choosing and fitting appropriate neural network models; and postprocessing - linking model predictions to replace, or more likely facilitate, manual labelling.

Our best model converted acoustic recordings into spectrogram images on the mel frequency scale, using these to train a convolutional neural network. Model predictions were highly accurate, with per-second false positive and false negative rates of 1.5% and 22.3%. Nearly all false negatives were at the fringes of calls, adjacent to segments where the call was correctly identified, so that very few calls were missed altogether. A postprocessing step identifying intervals of repeated calling reduced an eight-hour recording to, on average, 22 minutes for manual processing, and did not miss any calling bouts over 72 hours of test recordings. Gibbon calling bouts were detected regularly in multi-month recordings from all selected survey points within Bawangling National Nature Reserve, Hainan.

We demonstrate that passive acoustic monitoring incorporating an automated classifier represents an effective tool for remote detection of one of the world’s rarest and most threatened species. Our study highlights the viability of using neural networks to automate or greatly assist the manual labelling of data collected by passive acoustic monitoring projects. We emphasise that model development and implementation be informed and guided by ecological objectives, and increase accessibility of these tools with a series of notebooks that allow users to build and deploy their own acoustic classifiers.
Nicotine and Opioid Polysubstance Abuse: Enhancement of opioid self-administration by systemic nicotine and modulation of opioid-associated memories by insular nicotine
Authors: Loney Gregory C , King Christopher P , Meyer Paul J
Published: September 2020

Concurrent nicotine use is associated with increased liability for the development and exacerbation of opioid-use disorders. Habitual use of nicotine containing products increases propensity to misuse prescription opioids and its prevalence is substantially increased in individuals currently involved in opioid-treatment programs. Nicotine enhances self-administration of many classes of drugs in rodents, though evidence for direct effects on opioids is lacking. We sought to measure the effects of nicotine pretreatment on the reinforcing efficacy of opioids in both self-administration and contextual conditioning paradigms. First, we measured the effect of systemic nicotine pretreatment on self-administration of two opioids. Additionally, we measured the degree to which systemic nicotine pretreatment impacts the formation of morphine-associated contextual memories in conditioned taste avoidance and place preference paradigms. Given the involvement of the insula in the maintenance of substance abuse, its importance in nicotine addiction, and findings that insular inactivation impairs contextual drug conditioning, we examined whether nicotine administered directly to the insula could recapitulate the effects of systemic nicotine. We demonstrate that systemic nicotine pretreatment significantly enhances opioid self-administration and alters contextual conditioning. Furthermore, intra-insula nicotine similarly altered morphine contextual conditioning by blocking the formation of taste avoidance at all three morphine doses tested (5.0, 10, & 20 mg/kg), while shifting the dose-response curve of morphine in the place preference paradigm rightward. In conclusion, these data demonstrate that nicotine facilitates opioid intake and is partly acting within the insular cortex to obfuscate aversive opiate memories while potentiating approach to morphine-associated stimuli at higher doses.
Visual QC Protocol for FreeSurfer Cortical Parcellations from Anatomical MRI
Authors: Raamana Pradeep Reddy , Theyers Athena , Selliah Tharushan , Bhati Piali , Arnott Stephen R. , Hassel Stefanie , Nanayakkara Nuwan D. , Scott Christopher J. M. , Harris Jacqueline , Zamyadi Mojdeh , Lam Raymond W. , Milev Roumen , Müller Daniel J. , Rotzinger Susan , Frey Benicio N. , Kennedy Sidney H , Black Sandra E. , Lang Anthony , Masellis Mario , Symons Sean , Bartha Robert , MacQueen Glenda M ,   The CAN-BIND Investigator Team,   The ONDRI Investigators, Strother Stephen C.
Published: September 2020

Quality control of morphometric neuroimaging data is essential to improve reproducibility. Owing to the complexity of neuroimaging data and subsequently the interpretation of their results, visual inspection by trained raters is the most reliable way to perform quality control. Here, we present a protocol for visual quality control of the anatomical accuracy of FreeSurfer parcellations, based on an easy-to-use open source tool called VisualQC. We comprehensively evaluate its utility in terms of error detection rate and inter-rater reliability on two large multi-site datasets, and discuss site differences in error patterns. This evaluation shows that VisualQC is a practically viable protocol for community adoption.
Bioinformatical analysis identified significant genes in the PI3K-Akt signaling pathway relating with poor prognosis of skin cutaneous melanoma
Authors: Zhang Yingzi , Zhang Yunlan , Hu Xuyun
Published: September 2020

Skin cutaneous melanoma (SKCM) is the most serious form of skin cancer and the reliable genetic prognostic biomarkers are not clear. The purpose of the present academic work was to identify reliable prognostic biomarkers and understand the underlying mechanism. Gene expression profiles of GSE31909, GSE104849 and GSE111766 were available from Gene Expression Omnibus (GEO). DEGs were collected from 13 melanoma samples and 12 melanocyte samples which were in the three profile datasets by GEO2R analysis. Gene ontology (GO) analysis and KEGG analysis were performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID).We further established protein-protein interaction (PPI) and identify core genes with Search Tool for the Retrieval of Interacting Genes (STRING) and Molecular Complex Detection (MCODE) app in Cytoscape software. There were total of 63 consistently expressed genes in the three datasets, including eight up-regulated genes enriched in biological processes like osteoblast differentiation and extracellular matrix organization, and cell component like extracellular space, while 55 down-regulated genes enriched in positive regulation of gene expression, intracellular signal transduction, cell adhesion and apoptotic process. With prognostic information and expression data from UALCAN and Gene Expression Profiling Interactive Analysis (GEPIA), we identified three significant genes (TNC, SPP1 and KIT). After Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, all three genes were located in the PI3K-Akt Signaling Pathway. Our results provide additional genetic biomarkers for SKCM patients.
Assessing the influence of climate on future wintertime SARS-CoV-2 outbreaks
Authors: Baker Rachel E. , Yang Wenchang , Vecchi Gabriel A. , Jessica E. Metcalf C. , Grenfell Bryan T.
Published: September 2020

High susceptibility has limited the role of the climate in the SARS-CoV-2 pandemic to date. However, understanding a possible future effect of climate, as susceptibility declines and the northern-hemisphere winter approaches, is an important open question. Here we use an epidemiological model, constrained by observations, to assess the sensitivity of future SARS-CoV-2 disease trajectories to local climate conditions. We find this sensitivity depends on both the susceptibility of the population and the efficacy of non-pharmaceutical controls (NPIs) in reducing transmission. Assuming high susceptibility, more stringent NPIs may be required to minimize outbreak risk in the winter months. Our results imply a role for meteorological forecasts in projecting outbreak severity, however, reducing uncertainty in epidemiological parameters will likely have a greater impact on generating accurate predictions and reflects the strong leverage of NPIs on future outbreak severity.
Hopeful monsters: Unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense-antisense pairs
Authors: Warren Jessica M. , Sloan Daniel B.
Published: September 2020

Although tRNA structure is one of the most conserved and recognizable shapes in molecular biology, aberrant tRNAs are frequently found in the mitochondrial genomes of metazoans. The structure of several mitochondrial tRNAs is so degenerate that doubts have been raised about their expression and function. Mites from the arachnid superorder Acariformes are predicted to have some of the shortest mitochondrial tRNAs, with apparent base mismatches in acceptor stems and a complete loss of cloverleaf-life shape. While performing mitochondrial isolations and recently developed RNA-seq methods to capture mature, CCA-tailed tRNAs in plant tissue, we inadvertently sequenced the mitochondrial tRNAs from a common plant pest, the acariform miteTetranychus urticae,to a high enough coverage to detect all previously annotatedT. urticaetRNA regions. The results not only confirm expression, CCA-tailing and post-transcriptional base modification of these highly divergent tRNAs, but also revealed widespread sense and antisense expression of tRNA genes in theT. urticaemitochondrial genome. Mirrored expression of mitochondrial tRNA genes has been previously hypothesized but not demonstrated to be extensive in any system. We discuss the functional roles that these divergent tRNAs could have as both decoding molecules in translation and processing signals in transcript maturation pathways for other genes, as well as how the surprising finding of sense-antisense tRNA pairs adds another dimension to the bizarre tRNA biology of mitochondrial genomes.
Synaptic plasticity in the orbitofrontal cortex explains how risk attitude adapts to the range of risk prospects
Authors: Brochard Jules , Daunizeau Jean
Published: September 2020

Many deleterious behaviors, such as procrastinating on urgent matters or sustaining a toxic relationship, are irrational. But is irrational behavior the incidental outcome of biological constraints imposed on neural information processing? In particular, can those constraints alter decisions, even when people know the consequences of alternative actions? Recent studies indicate that orbitofrontal neurons encode decision value in relative terms, i.e. value signals in OFC neurons are normalized with respect to the context. Value-based decisions may thus exhibit irrational context-dependence effects. A candidate explanation is “efficient coding”: OFC neurons may mitigate information loss by adapting their (bounded) output firing properties to the recent value range. This is seducing, because it suggests that relative value coding is the brain’s best attempt to produce rational behavior, given its own hard-wired biological constraints. However, whether the behavioral implications of this scenario are met, how it generalizes to realistic situations in which OFC neurons construct value from multiple decision-relevant attributes, and what its neurophysiological bases are, is unclear. Here, we address these issues by re-analyzing two open fMRI datasets from theOpenNeuro.orginitiative, where people have to integrate prospective gains and losses to decide whether to gamble or not. First, we show that peoples’ risk attitudes critically depend on the range of gain prospects they are exposed to. Importantly, counter to simple efficient coding scenarios, differences in gain ranges induce progressive changes in peoples’ sensitivity to both gains and losses. Second, we use artificial neural network models to show that hebbian rewiring processes between attribute-specific and attribute-integration neurons predict (out-of-sample) both context-dependence effects in peoples’ risk attitude and multivariate patterns of fMRI activity in the OFC. Under mild conditions on distributed population codes for decision attributes, hebbian plasticity eventually translates the distribution of reweighted attribute signals towards the responsive range of integration neurons. In turn, integration units exhibit the known features of range adaptation, including (but not limited to), relative value coding. Our results demonstrate how hebbian plasticity within brain networks may result in range adaptation, eventually yielding complex though predictable irrational behavior.
The erosion of biodiversity and biomass in the Atlantic Forest biodiversity hotspot
Authors: Lima Renato A. F. , Oliveira Alexandre A. , Pitta Gregory R. , de Gasper André L. , Vibrans Alexander C. , Chave Jérôme , ter Steege Hans , Prado Paulo I.
Published: September 2020

Tropical forests are being deforested worldwide, and the remaining fragments are suffering from biomass and biodiversity erosion. Quantifying this erosion is challenging because ground data on tropical biodiversity and biomass are often sparse. Here, we use an unprecedented dataset of 1,819 field surveys covering the entire Atlantic Forest biodiversity hotspot. We show that 83–85% of the surveys presented losses in forest biomass and tree species richness, functional traits and conservation value. On average, forest fragments had 25–32% less biomass, 23–31% fewer species, and 33%, 36% and 42% fewer individuals of late-successional, large-seeded and endemic species, respectively. Biodiversity and biomass erosion were both lower inside strictly protected conservation units, particularly in large ones. We estimate that biomass erosion across the Atlantic Forest remnants was equivalent to the loss of 55-70 thousand km2of forests or US$2.3-2.6 billion in carbon credits. These figures have direct implications on mechanisms of climate change mitigation.
Peripheral blood mononuclear cells preferentially activate 11-oxygenated androgens
Authors: Schiffer Lina , Bossey Alicia , Taylor Angela E , Akerman Ildem , Scheel-Toellner Dagmar , Storbeck Karl-Heinz , Arlt Wiebke
Published: September 2020

Context

Androgens are important modulators of immune cell function impacting proliferation, differentiation and cytokine production. The local generation of active androgens from circulating androgen precursors is an important mediator of androgen action in peripheral androgen target cells or tissue.

Objective

To characterize the activation of classic and 11-oxygenated androgens in human peripheral blood mononuclear cells (PBMCs).

Methods

PBMCs were isolated from healthy male donors and incubated ex vivo with precursors and active androgens of the classic and 11-oxygenated androgen pathways. Steroids were quantified by liquid chromatography-tandem mass spectrometry. The expression of genes encoding steroid-metabolizing enzymes was assessed by quantitative PCR.

Results

PBMCs generated 8-fold higher amounts of the active 11-oxygenated androgen 11-ketotestosterone than the classic androgen testosterone from their respective precursors. We identified the enzyme AKR1C3 as the major reductive 17β-hydroxysteroid dehydrogenase in PBMCs responsible for both conversions and found that within the PBMC compartment natural killer cells are the major site of AKRC13 expression and activity. Steroid 5α-reductase type 1 catalyzed the 5α-reduction of classic but not 11-oxygenated androgens in PBMCs. Lag time prior to the separation of cellular components from whole blood increased 11KT serum concentrations in a time-dependent fashion, with significant increases detected from two hours after blood collection.

Conclusions

11-oxygenated androgens are the preferred substrates for androgen activation by AKR1C3 in PBMCs, primarily conveyed by natural killer cell AKR1C3 activity, yielding 11KT the major active androgen in PBMCs. Androgen metabolism by PBMCs can affect the measurement results of serum 11-ketotestosterone concentrations, if samples are not separated in a timely fashion.