bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictive Value of Plasma Long Noncoding RNA Associated With Microvascular Invasion in Hepatic Carcinoma for Preeclampsia
Authors: Li Ying , Yang Ning , Zou Xiao-yi , Li Yuan-bing , Zhang Xin , Wei Mao-ti , Li Yu-ming
Published: August 2020

Background

To investigate plasma levels of long noncoding RNA associated with microvascular invasion in hepatic carcinoma (LncRNA MVIH) in patients with preeclampsia (PE) and to explore its predictive value for PE either alone or in combination with other indicators.

Methods

Plasma samples were obtained from patients in a prospective pregnancy cohort at 7–16 weeks of gestation. Patients were divided into PE and control groups according to pregnancy outcomes. Real-time polymerase chain reaction was used to detect plasma levels of LncRNA MVIH. A univariate analysis was conducted on all indicators. Logistic regression analysis was performed on indexes with statistical differences. The receiver operating characteristic curve was used to evaluate the predict value of each independent risk factor and regression model.

Results

Before 16 weeks of pregnancy, body mass index, systolic blood pressure, diastolic blood pressure, mean arterial pressure, white blood cell (WBC), hemoglobin, alanine aminotransferase (ALT), uric acid (UA), and urine protein were positively correlated with PE while LncRNA MVIH was negatively correlated with PE. Independent markers with predictive value were LncRNA MVIH, UA, WBC, ALT, and urine protein, with the area under curve (AUC) in predicting PE of 0.763, 0.741, 0.663, 0.666, and 0.601, respectively. After combining these indexes, the AUC increased to 0.890 with sensitivity, specificity, and accuracy of 86.4%, 83.1%, and 84.7% respectively.

Conclusions

Plasma levels of LncRNA MVIH are negatively correlated with PE and have a predictive value for PE. The combination of LncRNA MVIH, UA, WBC, ALT, and urine protein has a greater predictive value.
Second hits exacerbate alcohol-related organ damage: an update
Authors: Osna Natalia A , Ganesan Murali , Seth Devanshi , Wyatt Todd A , Kidambi Srivatsan , Kharbanda Kusum K
Published: August 2020

Chronic and excessive alcohol abuse cause direct and indirect detrimental effects on a wide range of body organs and systems and accounts for ~4% of deaths worldwide. Many factors influence the harmful effects of alcohol. This concise review presents newer insights into the role of select second hits in influencing the progression of alcohol-induced organ damage by synergistically acting to generate a more dramatic downstream biological defect. This review specifically addresses on how a lifestyle factor of high fat intake exacerbates alcoholic liver injury and its progression. This review also provides the mechanistic insights into how increasing matrix stiffness during liver injury promotes alcohol-induced fibrogenesis. It also discusses how hepatotropic viral (HCV, HBV) infections as well as HIV (which is traditionally not known to be hepatotropic), are potentiated by alcohol exposure to promote hepatotoxicity and fibrosis progression. Finally, this review highlights the impact of reactive aldehydes generated during alcohol and cigarette smoke coexposure impair innate antimicrobial defense and increased susceptibility to infections. This review was inspired by the symposium held at the 17th Congress of the European Society for Biomedical research on Alcoholism in Lille, France entitled ‘Second hits in alcohol-related organ damage’.
Variation in reproductive effort, genetic diversity and mating systems across Posidonia australis seagrass meadows in Western Australia
Authors: Sinclair Elizabeth A , Edgeloe Jane M , Anthony Janet M , Statton John , Breed Martin F , Kendrick Gary A
Published: August 2020

Populations at the edges of their geographical range tend to have lower genetic diversity, smaller effective population sizes and limited connectivity relative to centre of range populations. Range edge populations are also likely to be better adapted to more extreme conditions for future survival and resilience in warming environments. However, they may also be most at risk of extinction from changing climate. We compare reproductive and genetic data of the temperate seagrass, Posidonia australis on the west coast of Australia. Measures of reproductive effort (flowering and fruit production and seed to ovule ratios) and estimates of genetic diversity and mating patterns (nuclear microsatellite DNA loci) were used to assess sexual reproduction in northern range edge (low latitude, elevated salinities, Shark Bay World Heritage Site) and centre of range (mid-latitude, oceanic salinity, Perth metropolitan waters) meadows in Western Australia. Flower and fruit production were highly variable among meadows and there was no significant relationship between seed to ovule ratio and clonal diversity. However, Shark Bay meadows were two orders of magnitude less fecund than those in Perth metropolitan waters. Shark Bay meadows were characterized by significantly lower levels of genetic diversity and a mixed mating system relative to meadows in Perth metropolitan waters, which had high genetic diversity and a completely outcrossed mating system. The combination of reproductive and genetic data showed overall lower sexual productivity in Shark Bay meadows relative to Perth metropolitan waters. The mixed mating system is likely driven by a combination of local environmental conditions and pollen limitation. These results indicate that seagrass restoration in Shark Bay may benefit from sourcing plant material from multiple reproductive meadows to increase outcrossed pollen availability and seed production for natural recruitment.
Testosterone induces plumage ornamentation followed by enhanced territoriality in a female songbird
Authors: Boersma Jordan , Enbody Erik D , Jones John Anthony , Nason Doka , Lopez-Contreras Elisa , Karubian Jordan , Schwabl Hubert
Published: August 2020

We know little of the proximate mechanisms underlying the expression of signaling traits in female vertebrates. Across males, the expression of sexual and competitive traits, including ornamentation and aggressive behavior, is often mediated by testosterone. In the white-shouldered fairywren (Malurus alboscapulatus) of New Guinea, females of different subspecies differ in the presence or absence of white shoulder patches and melanic plumage, whereas males are uniformly ornamented. Previous work has shown that ornamented females circulate more testosterone and exhibit more territorial aggression than do unornamented females. We investigated the degree to which testosterone regulates the expression of ornamental plumage and territorial behavior by implanting free-living unornamented females with testosterone. Every testosterone-treated female produced a male-like cloacal protuberance, and 15 of 20 replaced experimentally plucked brown with white shoulder patch feathers but did not typically produce melanic plumage characteristic of ornamented females. Testosterone treatment did not elevate territorial behavior prior to the production of the plumage ornament or during the active life of the implant. However, females with experimentally induced ornamentation, but exhausted implants, increased the vocal components of territory defense relative to the pretreatment period and also to testosterone-implanted females that did not produce ornamentation. Our results suggest that testosterone induces partial acquisition of the ornamental female plumage phenotype and that ornament expression, rather than testosterone alone, results in elevations of some territorial behaviors.
Depositing annotated sequences in GenBank: there needs to be a better way
Authors: Smith David Roy
Published: August 2020

Submitting sequences to the National Center for Biotechnology Information (NCBI) is an integral part of research and the publication process for many disciplines within the life sciences, and it will only become more important as sequencing technologies continue to improve. Here, I argue that the available infrastructure and resources for uploading data to NCBI—especially the associated annotations of eukaryotic genomes—are inefficient, hard to use and sometimes just plain bad. This, in turn, is causing some researchers to forgo annotations entirely in their submissions. The time is overdue for the development of sophisticated, user-friendly software for depositing annotated sequences in GenBank.
Ribbon: intuitive visualization for complex genomic variation
Authors: Nattestad Maria , Aboukhalil Robert , Chin Chen-Shan , Schatz Michael C
Published: August 2020

Ribbon is an alignment visualization tool that shows how alignments are positioned within both the reference and read contexts, giving an intuitive view that enables a better understanding of structural variants and the read evidence supporting them. Ribbon was born out of a need to curate complex structural variant calls and determine whether each was well supported by long-read evidence, and it uses the same intuitive visualization method to shed light on contig alignments from genome-to-genome comparisons.

Availability and implementation

Ribbon is freely available online at http://genomeribbon.com/ and is open-source at https://github.com/marianattestad/ribbon.

Supplementary information

Supplementary data are available at Bioinformatics online.
SOAPMetaS: profiling large metagenome datasets efficiently on distributed clusters
Authors: He Shixu , Huang Zhibo , Wang Xiaohan , Fang Lin , Li Shengkang , Zhang Yong , Zhang Gengyun
Published: August 2020

Rapid increase of the data size in metagenome researches has raised the demand for new tools to process large datasets efficiently. To accelerate the metagenome profiling process in the scenario of big data, we developed SOAPMetaS, a marker gene-based multiple-sample metagenome profiling tool built on Apache Spark. SOAPMetaS demonstrates high performance and scalability to process large datasets. It can process 80 samples of FASTQ data, summing up to 416 GiB, in around half an hour; and the accuracy of species profiling results of SOAPMetaS is similar to that of MetaPhlAn2. SOAPMetaS can deal with a large volume of metagenome data more efficiently than common-used single-machine tools.

Availability and implementation

Source code is implemented in Java and freely available at https://github.com/BGI-flexlab/SOAPMetaS.

Supplementary information

Supplementary data are available at Bioinformatics online.
Evaluating recommender systems for AI-driven biomedical informatics
Authors: La Cava William , Williams Heather , Fu Weixuan , Vitale Steve , Srivatsan Durga , Moore Jason H
Published: August 2020

Motivation

Many researchers with domain expertise are unable to easily apply machine learning (ML) to their bioinformatics data due to a lack of ML and/or coding expertise. Methods that have been proposed thus far to automate ML mostly require programming experience as well as expert knowledge to tune and apply the algorithms correctly. Here, we study a method of automating biomedical data science using a web-based AI platform to recommend model choices and conduct experiments. We have two goals in mind: first, to make it easy to construct sophisticated models of biomedical processes; and second, to provide a fully automated AI agent that can choose and conduct promising experiments for the user, based on the user’s experiments as well as prior knowledge. To validate this framework, we conduct an experiment on 165 classification problems, comparing to state-of-the-art, automated approaches. Finally, we use this tool to develop predictive models of septic shock in critical care patients.

Results

We find that matrix factorization-based recommendation systems outperform metalearning methods for automating ML. This result mirrors the results of earlier recommender systems research in other domains. The proposed AI is competitive with state-of-the-art automated ML methods in terms of choosing optimal algorithm configurations for datasets. In our application to prediction of septic shock, the AI-driven analysis produces a competent ML model (AUROC 0.85±0.02) that performs on par with state-of-the-art deep learning results for this task, with much less computational effort.

Availability and implementation

PennAI is available free of charge and open-source. It is distributed under the GNU public license (GPL) version 3.

Supplementary information

Supplementary data are available at Bioinformatics online.
Social Innovation and Social Work: A Case Study of the Early Intervention Support Service
Authors: Winter Karen , Neeson Laura , Sweet Daryl , Smith Aimee , Millen Sharon , Connolly Paul
Published: August 2020

In a national and international context where there is a concern about the effectiveness of social care services for children and families to address chronic, enduring social problems and where there are finite resources available, the concept of social innovation in social work policy and practice to address need in new ways is receiving increased attention. Whilst an attractive term, social innovation in child and family services is not without its challenges in terms of conceptualisation, operationalisation, implementation and evidencing impact. This article reports on the development and evaluation of the Early Intervention Support Service (EISS), a newly designed family support service in Northern Ireland set up as part of a government-supported innovation and transformation programme that aims to deliver a voluntary, targeted, flexible and time-limited service to families experiencing emergent problems. Using the EISS as a case study, the challenges, benefits in terms of addressing policy imperatives and future direction of social innovation in social work practice are reflected upon.
Epistemology, Social Work and Substance Use
Authors: McNeil Sandra
Published: August 2020

Social work and substance use research often neglect to make epistemological perspectives explicit in their studies, inadvertently embedding numerous assumptions that remain invisible and uncontested. Consequently, the unchallenged dominance of post-positivist epistemologies in Western European countries becomes (re)produced in social work and substance use education, policies and practices, limiting space for alternative viewpoints. This narrative review examines some of the social work and substance use literature, highlighting the value of making epistemology more explicit and the importance of applying critical epistemologies to counter dominant paradigms. This article makes a unique contribution to substance use literature by examining substance use from post-positivist, social constructivist and critical paradigms and by promoting a critical social work lens. A critical paradigm is particularly useful for questioning prevailing assumptions of substance use as a medical problem requiring professional treatment and for generating greater attention to structural policies that promote a more equitable society. Social work’s commitment to human rights and social justice effectively positions the discipline to apply a critical paradigm to the field of substance use studies.
Suppressing Anterior Cingulate Cortex Modulates Default Mode Network and Behavior in Awake Rats
Authors: Tu Wenyu , Ma Zilu , Ma Yuncong , Dopfel David , Zhang Nanyin
Published: August 2020

The default mode network (DMN) is a principal brain network in the mammalian brain. Although the DMN in humans has been extensively studied with respect to network structure, function, and clinical implications, our knowledge of DMN in animals remains limited. In particular, the functional role of DMN nodes, and how DMN organization relates to DMN-relevant behavior are still elusive. Here we investigated the causal relationship of inactivating a pivotal node of DMN (i.e., dorsal anterior cingulate cortex [dACC]) on DMN function, network organization, and behavior by combining chemogenetics, resting-state functional magnetic resonance imaging (rsfMRI) and behavioral tests in awake rodents. We found that suppressing dACC activity profoundly changed the activity and connectivity of DMN, and these changes were associated with altered DMN-related behavior in animals. The chemo-rsfMRI-behavior approach opens an avenue to mechanistically dissecting the relationships between a specific node, brain network function, and behavior. Our data suggest that, like in humans, DMN in rodents is a functional network with coordinated activity that mediates behavior.
Improving in vivo human cerebral cortical surface reconstruction using data-driven super-resolution
Authors: Tian Qiyuan , Bilgic Berkin , Fan Qiuyun , Ngamsombat Chanon , Zaretskaya Natalia , Fultz Nina E , Ohringer Ned A , Chaudhari Akshay S , Hu Yuxin , Witzel Thomas , Setsompop Kawin , Polimeni Jonathan R , Huang Susie Y
Published: August 2020

Accurate and automated reconstruction of the in vivo human cerebral cortical surface from anatomical magnetic resonance (MR) images facilitates the quantitative analysis of cortical structure. Anatomical MR images with sub-millimeter isotropic spatial resolution improve the accuracy of cortical surface and thickness estimation compared to the standard 1-millimeter isotropic resolution. Nonetheless, sub-millimeter resolution acquisitions require averaging multiple repetitions to achieve sufficient signal-to-noise ratio and are therefore long and potentially vulnerable to subject motion. We address this challenge by synthesizing sub-millimeter resolution images from standard 1-millimeter isotropic resolution images using a data-driven supervised machine learning-based super-resolution approach achieved via a deep convolutional neural network. We systematically characterize our approach using a large-scale simulated dataset and demonstrate its efficacy in empirical data. The super-resolution data provide improved cortical surfaces similar to those obtained from native sub-millimeter resolution data. The whole-brain mean absolute discrepancy in cortical surface positioning and thickness estimation is below 100 μm at the single-subject level and below 50 μm at the group level for the simulated data, and below 200 μm at the single-subject level and below 100 μm at the group level for the empirical data, making the accuracy of cortical surfaces derived from super-resolution sufficient for most applications.
Frontal Cortical Monoamine Release, Attention, and Working Memory in a Perinatal Nicotine Exposure Mouse Model Following Kappa Opioid Receptor Antagonism
Authors: Zhang Lin , McCarthy Deirdre M , Eskow Jaunarajs Karen L , Biederman Joseph , Spencer Thomas J , Bhide Pradeep G
Published: August 2020

Perinatal nicotine exposure (PNE) produces frontal cortical hypo-dopaminergic state and attention and working memory deficits consistent with neurodevelopmental disorders such as attention deficit hyperactivity disorder (ADHD). Methylphenidate alleviates ADHD symptoms by increasing extracellular dopamine and noradrenaline. Kappa opioid receptor (KOR) antagonism may be another mechanism to achieve the same results because KOR activation inhibits frontal cortical dopamine release. We administered the selective KOR antagonist norbinaltorphimine (norBNI) (20 mg/kg; intraperitoneal) or methylphenidate (0.75 mg/kg; intraperitoneal) to PNE mouse model and examined frontal cortical monoamine release, attention, and working memory. Both compounds increased dopamine and noradrenaline release but neither influenced serotonin release. Both compounds improved object-based attention and working memory in the PNE group, with norBNI’s effects evident at 2.5 h and 5.5 h but absent at 24 h. Methylphenidate’s effects were evident at 0.5 h but not at 2.5 h. norBNI’s effects temporally coincided with frontal cortical c-Jun N-terminal kinase phosphorylation. norBNI did not alter tissue dopamine content in the nucleus accumbens, offering preliminary support for lack of reinforcement.
Accuracy of a Novel Urine Test, Fujifilm SILVAMP Tuberculosis Lipoarabinomannan, for the Diagnosis of Pulmonary Tuberculosis in Children
Authors: Nicol Mark P , Schumacher Samuel G , Workman Lesley , Broger Tobias , Baard Cynthia , Prins Margaretha , Bateman Lindy , du Toit Elloise , van Heerden Judi , Szekely Rita , Zar Heather J , Denkinger Claudia M
Published: August 2020

Background

An accurate point-of-care test for tuberculosis (TB) in children remains an elusive goal. Recent evaluation of a novel point-of-care urinary lipoarabinomannan test, Fujifilm SILVAMP Tuberculosis Lipoarabinomannan (FujiLAM), in adults living with human immunodeficiency virus (HIV) showed significantly superior sensitivity than the current Alere Determine Tuberculosis Lipoarabinomannan test (AlereLAM). We therefore compared the accuracy of FujiLAM and AlereLAM in children with suspected TB.

Methods

Children hospitalized with suspected TB in Cape Town, South Africa, were enrolled (consecutive admissions plus enrichment for a group of children living with HIV and with TB), their urine was collected and biobanked, and their sputum was tested with mycobacterial culture and Xpert MTB/RIF or Xpert MTB/RIF Ultra. Biobanked urine was subsequently batch tested with FujiLAM and AlereLAM. Children were categorized as having microbiologically confirmed TB, unconfirmed TB (clinically diagnosed), or unlikely TB.

Results

A total of 204 children were enrolled and had valid results from both index tests, as well as sputum microbiological testing. Compared to a microbiological reference standard, the sensitivity of FujiLAM and AlereLAM was similar (42% and 50%, respectively), but lower than that of Xpert MTB/RIF of sputum (74%). The sensitivity of FujiLAM was higher in children living with HIV (60%) and malnourished children (62%). The specificity of FujiLAM was substantially higher than that of AlereLAM (92% vs 66%, respectively). The specificity of both tests was higher in children 2 years or older (FujiLAM, 96%; AlereLAM, 72%).

Conclusions

The high specificity of FujiLAM suggests utility as a “rule-in” test for children with a high pretest probability of TB, including hospitalized children living with HIV or with malnutrition.
Uncovering Infant Group B Streptococcal (GBS) Disease Clusters in the United Kingdom and Ireland Through Genomic Analysis: A Population-based Epidemiological Study
Authors: Collin Simon M , Groves Natalie , O’Sullivan Catherine , Jauneikaite Elita , Patel Darshana , Cunney Robert , Meehan Mary , Reynolds Arlene , Smith Andrew , Lindsay Diane , Doherty Lorraine , Davies Eleri , Chalker Victoria , Lamb Peter , Afshar Baharak , Balasegaram Sooria , Coelho Juliana , Ready Derren , Brown Colin S , Efstratiou Androulla , Le Doare Kirsty , Sriskandan Shiranee , Heath Paul T , Lamagni Theresa
Published: August 2020

Background

The true frequency of hospital outbreaks of invasive group B streptococcal (iGBS; Streptococcus agalactiae) disease in infants is unknown. We used whole genome sequencing (WGS) of iGBS isolates collected during a period of enhanced surveillance of infant iGBS disease in the UK and Ireland to determine the number of clustered cases.

Methods

Potentially linked iGBS cases from infants with early (<7 days of life) or late-onset (7–89 days) disease were identified from WGS data (HiSeq 2500 platform, Illumina) from clinical sterile site isolates collected between 04/2014 and 04/2015. We assessed time and place of cases to determine a single-nucleotide polymorphism (SNP) difference threshold for clustered cases. Case details were augmented through linkage to national hospital admission data and hospital record review by local microbiologists.

Results

Analysis of sequences indicated a cutoff of ≤5 SNP differences to define iGBS clusters. Among 410 infant iGBS isolates, we identified 7 clusters (4 genetically identical pairs with 0 SNP differences, 1 pair with 3 SNP differences, 1 cluster of 4 cases with ≤1 SNP differences) of which 4 clusters were uncovered for the first time. The clusters comprised 16 cases, of which 15 were late-onset (of 192 late-onset cases with sequenced isolates) and 1 an early-onset index case. Serial intervals between cases ranged from 0 to 59 (median 12) days.

Conclusions

Approximately 1 in 12 late-onset infant iGBS cases were part of a hospital cluster. Over half of the clusters were previously undetected, emphasizing the importance of routine submission of iGBS isolates to reference laboratories for cluster identification and genomic confirmation.
Performance of Patient-collected Specimens for Neisseria gonorrhoeae Culture
Authors: Barbee Lindley A , Golden Matthew R , Thibault Christina S , McNeil Candice J , Soge Olusegun O
Published: August 2020

Background

Neisseria gonorrhoeae culture is necessary to determine antimicrobial resistance, but typically requires specimen collection by clinicians. We sought to determine the sensitivity of patient-collected specimens for N. gonorrhoeae culture.

Methods

We performed N. gonorrhoeae cultures on paired clinician- and patient-collected specimens from the pharynx (n = 93), rectum (n = 88), endocervix/vagina (n = 89), and urethra/urine (n = 46). We calculated the percent concordance and the kappa statistics for paired-specimen results, and determined the test sensitivity for each specimen type using positivity of either specimen in a pair as a gold standard defining the presence of true infection.

Results

At least 1 specimen was positive in 26%, 31%, 61%, and 3% of paired samples in the pharynx, rectum, urethra/urine, and endocervix/vagina, respectively. Patient- and clinician-collected results were highly concordant at the pharynx (95%; kappa = 0.85), rectum (99%; kappa = 0.97), urethra/urine (83%; kappa = 0.87), and endocervix/vagina (100%; kappa = 1.0; P ≤ .005 for all comparisons). Patient-collected pharyngeal and rectal swabs and urine were 92%, 96%, and 96% sensitive, while clinician-collected specimens at these anatomic sites were 87.5%, 100%, and 94% sensitive (P > .05 for all comparisons). Among 24 urine specimens held for 4–22 hours after collection, 100% yielded concordant N. gonorrhoeae culture results, compared to immediate processing.

Conclusions

Patient- and clinician-collected specimens are comparably sensitive for N. gonorrhoeae culture. These findings suggest that patient-collected specimens could be used to expand the availability of gonococcal antimicrobial resistance testing for both clinical and surveillance purposes.
Blastomycosis in Africa and the Middle East: A Comprehensive Review of Reported Cases and Reanalysis of Historical Isolates Based on Molecular Data
Authors: Schwartz Ilan S , Muñoz Jose F , Kenyon Chris R , Govender Nelesh P , McTaggart Lisa , Maphanga Tsidiso G , Richardson Susan , Becker Pierre , Cuomo Christina A , McEwen Juan G , Sigler Lynne
Published: August 2020

Background

Blastomycosis has been reported from countries in Africa and the Middle East, but a decades-long debate has persisted regarding whether this is the same disease known in North America and caused by Blastomyces dermatitidis and Blastomyces gilchristii.

Methods

We reviewed published cases of human and veterinary blastomycosis from Africa and the Middle East. We abstracted epidemiological and clinical features of cases, including sites of disease, diagnosis, management, outcomes, and, where available, genetic and antigenic typing of case isolates. In addition, we sequenced nucleic acids from 9 clinical isolates from Africa deposited in global collections as B. dermatitidis; for 5, we sequenced the internal transcribed spacer regions, and for the other 4 we sequenced the whole genomes.

Results

We identified 172 unique human patients with blastomycosis, including 159 patients from 25 African countries and 12 patients from 5 Middle Eastern countries, and also identified 7 reports of veterinary blastomycosis. In humans, cutaneous disease predominated (n = 100/137, 73%), followed by pulmonary (n = 73/129, 57%) and osteoarticular involvement (n = 61/128, 48%). Unusual direct microscopy/histopathological presentations included short hyphal fragments in tissues (n = 23/129, 18%). There were 34 genotyped case isolates that comprised 4 species: Blastomyces percursus (n = 22, 65%), from 8 countries throughout all regions; Blastomyces emzantsi (n = 9, 26%), from South Africa; B. dermatitidis (n = 1, 3%), from the Democratic Republic of Congo; and B. gilchristii (n = 2, 6%), from South Africa and Zimbabwe.

Conclusions

Blastomycosis occurs throughout Africa and the Middle East and is caused predominantly by B. percursus and, at least in South Africa, B. emzantsi, resulting in distinct clinical and pathological patterns of disease.
Pertussis Infections Among Pregnant Women in the United States, 2012–2017
Authors: Skoff Tami H , Faulkner Amanda E , Liang Jennifer L , Barnes Meghan , Kudish Kathy , Thomas Ebony , Kenyon Cynthia , Hoffman Marisa , Pradhan Eva , Liko Juventila , Hariri Susan
Published: August 2020

Background

Little is known about pertussis among pregnant women, a population at increased risk for severe morbidity from respiratory infections such as influenza. We used the Centers for Disease Control and Prevention’s Enhanced Pertussis Surveillance (EPS) system to describe pertussis epidemiology among pregnant and nonpregnant women of childbearing age.

Methods

Pertussis cases in women aged 18–44 years with cough onset between 1 January 2012 and 31 December 2017 were identified in 7 EPS states. Surveillance data were collected through patient and provider interviews and immunization registries. Bridged-race, intercensal population data and live birth estimates were used as denominators.

Results

We identified 1582 pertussis cases among women aged 18–44 years; 5.1% (76/1499) of patients with a known pregnancy status were pregnant at cough onset. Of the pregnant patients with complete information, 81.7% (49/60) reported onset during the second or third trimester. The median ages of pregnant and nonpregnant patients were 29.0 and 33.0 years, respectively. Most pregnant and nonpregnant patients were White (78.3% vs. 86.4%, respectively; P = .09) and non-Hispanic (72.6% vs. 77.3%, respectively; P = .35). The average annual incidence of pertussis was 7.7/100000 among pregnancy women and 7/3/100000 among nonpregnant women. Compared to nonpregnant patients, more pregnant patients reported whoop (41.9% vs. 31.3%, respectively), posttussive vomiting (58.1% vs. 47.9%, respectively), and apnea (37.3% vs. 29.0%, respectively); however, these differences were not statistically significant (P values > .05 for all). A similar proportion of pregnant and nonpregnant patients reported ever having received Tdap (tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis vaccine; 31.6% vs. 32.7%, respectively; P = .84).

Conclusions

Our analysis suggests that incidence of pertussis and clinical characteristics of disease are similar among pregnant and nonpregnant women. Continued monitoring is important to further define pertussis epidemiology in pregnant women.
Investigating the Meat Pathway as a Source of Human Nontyphoidal Salmonella Bloodstream Infections and Diarrhea in East Africa
Authors: Crump John A , Thomas Kate M , Benschop Jackie , Knox Matthew A , Wilkinson David A , Midwinter Anne C , Munyua Peninah , Ochieng John B , Bigogo Godfrey M , Verani Jennifer R , Widdowson Marc-Alain , Prinsen Gerard , Cleaveland Sarah , Karimuribo Esron D , Kazwala Rudovick R , Mmbaga Blandina T , Swai Emanuel S , French Nigel P , Zadoks Ruth N
Published: August 2020

Background

Salmonella Enteritidis and Salmonella Typhimurium are major causes of bloodstream infection and diarrheal disease in East Africa. Sources of human infection, including the role of the meat pathway, are poorly understood.

Methods

We collected cattle, goat, and poultry meat pathway samples from December 2015 through August 2017 in Tanzania and isolated Salmonella using standard methods. Meat pathway isolates were compared with nontyphoidal serovars of Salmonella enterica (NTS) isolated from persons with bloodstream infections and diarrheal disease from 2007 through 2017 from Kenya by core genome multi-locus sequence typing (cgMLST). Isolates were characterized for antimicrobial resistance, virulence genes, and diversity.

Results

We isolated NTS from 164 meat pathway samples. Of 172 human NTS isolates, 90 (52.3%) from stool and 82 (47.7%) from blood, 53 (30.8%) were Salmonella Enteritidis sequence type (ST) 11 and 62 (36.0%) were Salmonella Typhimurium ST313. We identified cgMLST clusters within Salmonella Enteritidis ST11, Salmonella Heidelberg ST15, Salmonella Typhimurium ST19, and Salmonella II 42:r:- ST1208 that included both human and meat pathway isolates. Salmonella Typhimurium ST313 was isolated exclusively from human samples. Human and poultry isolates bore more antimicrobial resistance and virulence genes and were less diverse than isolates from other sources.

Conclusions

Our findings suggest that the meat pathway may be an important source of human infection with some clades of Salmonella Enteritidis ST11 in East Africa, but not of human infection by Salmonella Typhimurium ST313. Research is needed to systematically examine the contributions of other types of meat, animal products, produce, water, and the environment to nontyphoidal Salmonella disease in East Africa.
Identification of a Cluster of Extended-spectrum Beta-Lactamase–Producing Klebsiella pneumoniae Sequence Type 101 Isolated From Food and Humans
Authors: Aguilar-Bultet Lisandra , Bagutti Claudia , Egli Adrian , Alt Monica , Maurer Pekerman Laura , Schindler Ruth , Furger Reto , Eichenberger Lucas , Roloff Tim , Steffen Ingrid , Huebner Philipp , Stadler Tanja , Tschudin-Sutter Sarah
Published: August 2020

We report a cluster of extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae sequence type 101, derived from 1 poultry and 2 clinical samples collected within the setting of a prospective study designed to determine the diversity and migration of ESBL-producing Enterobacterales between humans, foodstuffs, and wastewater.
Impact of the Centers for Medicare and Medicaid Services Sepsis Core Measure on Antibiotic Use
Authors: Pakyz Amy L , Orndahl Christine M , Johns Alicia , Harless David W , Morgan Daniel J , Bearman Gonzalo , Hohmann Samuel F , Stevens Michael P
Published: August 2020

Background

The Centers for Medicare and Medicaid Services (CMS) implemented a core measure sepsis (SEP-1) bundle in 2015. One element was initiation of broad-spectrum antibiotics within 3 hours of diagnosis. The policy has the potential to increase antibiotic use and Clostridioides difficile infection (CDI). We evaluated the impact of SEP-1 implementation on broad-spectrum antibiotic use and CDI occurrence rates.

Methods

Monthly adult antibiotic data for 4 antibiotic categories (surgical prophylaxis, broad-spectrum for community-acquired infections, broad-spectrum for hospital-onset/multidrug-resistant [MDR] organisms, and anti–methicillin-resistant Staphylococcus aureus [MRSA]) from 111 hospitals participating in the Clinical Data Base Resource Manager were evaluated in periods before (October 2014–September 2015) and after (October 2015–June 2017) policy implementation. Interrupted time series analyses, using negative binomial regression, evaluated changes in antibiotic category use and CDI rates.

Results

At the hospital level, there was an immediate increase in the level of broad-spectrum agents for hospital-onset/MDR organisms (+2.3%, P = .0375) as well as a long-term increase in trend (+0.4% per month, P = .0273). There was also an immediate increase in level of overall antibiotic use (+1.4%, P = .0293). CDI rates unexpectedly decreased at the time of SEP-1 implementation. When analyses were limited to patients with sepsis, there was a significant level increase in use of all antibiotic categories at the time of SEP-1 implementation.

Conclusions

SEP-1 implementation was associated with immediate and long-term increases in broad-spectrum hospital-onset/MDR organism antibiotics. Antimicrobial stewardship programs should evaluate sepsis treatment for opportunities to de-escalate broad therapy as indicated.
A content-based dataset recommendation system for researchers—a case study on Gene Expression Omnibus (GEO) repository
Authors: Patra Braja Gopal , Roberts Kirk , Wu Hulin
Published: August 2020

It is a growing trend among researchers to make their data publicly available for experimental reproducibility and data reusability. Sharing data with fellow researchers helps in increasing the visibility of the work. On the other hand, there are researchers who are inhibited by the lack of data resources. To overcome this challenge, many repositories and knowledge bases have been established to date to ease data sharing. Further, in the past two decades, there has been an exponential increase in the number of datasets added to these dataset repositories. However, most of these repositories are domain-specific, and none of them can recommend datasets to researchers/users. Naturally, it is challenging for a researcher to keep track of all the relevant repositories for potential use. Thus, a dataset recommender system that recommends datasets to a researcher based on previous publications can enhance their productivity and expedite further research. This work adopts an information retrieval (IR) paradigm for dataset recommendation. We hypothesize that two fundamental differences exist between dataset recommendation and PubMed-style biomedical IR beyond the corpus. First, instead of keywords, the query is the researcher, embodied by his or her publications. Second, to filter the relevant datasets from non-relevant ones, researchers are better represented by a set of interests, as opposed to the entire body of their research. This second approach is implemented using a non-parametric clustering technique. These clusters are used to recommend datasets for each researcher using the cosine similarity between the vector representations of publication clusters and datasets. The maximum normalized discounted cumulative gain at 10 (NDCG@10), precision at 10 (p@10) partial and p@10 strict of 0.89, 0.78 and 0.61, respectively, were obtained using the proposed method after manual evaluation by five researchers. As per the best of our knowledge, this is the first study of its kind on content-based dataset recommendation. We hope that this system will further promote data sharing, offset the researchers’ workload in identifying the right dataset and increase the reusability of biomedical datasets.

Database URL: http://genestudy.org/recommends/#/
PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins
Authors: Kondo Hiroko X , Kanematsu Yusuke , Masumoto Gen , Takano Yu
Published: August 2020

Heme participates in a wide range of biological functions such as oxygen transport, electron transport, oxygen reduction, transcriptional regulation and so on. While the mechanism of each function has been investigated for many heme proteins, the origin of the diversity of the heme functions is still unclear and a crucial scientific issue. We have constructed a database of heme proteins, named Python-based database and analyzer for DIStortion of Heme porphyrin (PyDISH), which also contains some analysis tools. The aim of PyDISH is to integrate the information on the structures of hemes and heme proteins and the functions of heme proteins. This database will provide the structure–function relationships focusing on heme porphyrin distortion and lead to the elucidation of the origin of the functional diversity of heme proteins. In addition, the insights obtained from the database can be used for the design of protein function. PyDISH contains the structural data of more than 13 000 hemes extracted from the Protein Data Bank, including heme porphyrin distortion, axial ligands coordinating to the heme and the orientation of the propionate sidechains of heme. PyDISH also has information about the protein domains, including Uniprot ID, protein fold by CATH ID, organism, coordination distance and so on. The analytical tools implemented in PyDISH allow users to not only browse and download the data but also analyze the structures of heme porphyrin by using the analytical tools implemented in PyDISH. PyDISH users will be able to utilize the obtained results for the design of protein function.

Database URL: http://pydish.bio.info.hiroshima-cu.ac.jp/
ThRSDB: a database of Thai rice starch composition, molecular structure and functionality
Authors: Wanichthanarak Kwanjeera , Thitisaksakul Maysaya
Published: August 2020

As starch properties can affect end product quality in many ways, rice starch from Thai domesticated cultivars and landraces has been the focus of increasing research interest. Increasing knowledge in this area creates a high demand from the research community for better organized information. The Thai Rice Starch Database (ThRSDB) is an online database containing data extensively curated from original research articles on Thai rice starch composition, molecular structure and functionality. The key aim of the ThRSDB is to facilitate accessibility to dispersed rice starch information for, but not limited to, both research and industrial users. Currently, 373 samples from 191 different Thai rice cultivars have been collected from 39 published articles. The ThRSDB includes the search functions necessary for accessing data together with a user-friendly web interface and interactive visualization tools. We have also demonstrated how the collected data can be efficiently used to observe the relationships between starch parameters and rice cultivars through correlation analysis and Partial Least Squares Discriminant Analysis.

Database URL: http://thairicestarch.kku.ac.th
Reclassification of prosthesis–patient mismatch after transcatheter aortic valve replacement using predicted vs. measured indexed effective orifice area
Authors: Ternacle Julien , Guimaraes Leonardo , Vincent Flavien , Côté Nancy , Côté Mélanie , Lachance Dominique , Clavel Marie-Annick , Abbas Amr E , Pibarot Philippe , Rodés-Cabau Josep
Published: August 2020

Aims

The objective was to compare the incidence and impact on outcomes of measured (PPMM) vs. predicted (PPMP) prosthesis–patient mismatch following transcatheter aortic valve replacement (TAVR).

Methods and results

All consecutives patients who underwent TAVR between 2007 and 2018 were included. Effective orifice area (EOA) was measured by Doppler-echocardiography using the continuity equation and predicted according to the normal reference for each model and size of valve. PPM was defined using EOA indexed (EOAi) to body surface area as moderate if ≤0.85 cm2/m2 and severe if ≤ 0.65 cm2/m2 (respectively, ≤ 0.70 and ≤ 0.55 cm2/m2 if body mass index ≥ 30 kg/m2). The outcome endpoints were high residual gradient (≥20 mmHg) and the composite of cardiovascular mortality and hospital readmission for heart failure at 1 year. Overall, 1088 patients underwent a TAVR (55% male, age 79.1 ± 8.4 years, and STS score 6.6 ± 4.7%); balloon-expandable device was used in 83%. Incidence of moderate (10% vs. 27%) and severe (1% vs. 17%) PPM was markedly lower when defined by predicted vs. measured EOAi (P < 0.001). Balloon-expandable device implantation (OR: 1.90, P = 0.029) and valve-in-valve procedure (n = 118; OR: 3.21, P < 0.001) were the main factors associated with PPM occurrence. Compared with measured PPM, predicted PPM showed stronger association with high residual gradient. Severe measured or predicted PPM was not associated with clinical outcomes.

Conclusion

The utilization of the predicted EOAi reclassifies the majority of patients with PPM to no PPM following TAVR. Compared with measured PPM, predicted PPM had stronger association with haemodynamic outcomes, while both methods were not associated with clinical outcomes.
A case series on inflammatory cardiomyopathy and suspected cardiac sarcoidosis: role of cardiac PET in management
Authors: Kennel Peter J , Raza Farhan , Kim Jiwon , Singh Parmanand , Borczuk Alain , Krishnan Udhay , Karas Maria , Sobol Irina
Published: August 2020

Background

Presentation of life-threatening arrhythmias concomitantly with a new-onset non-ischaemic cardiomyopathy raises concern for an inflammatory cardiomyopathy such as cardiac sarcoidosis or cardiac manifestations of connective tissue disease. Comprehensive workup for specific aetiologies may be unrevealing except for signs of myocardial inflammation identified on cardiac positron emission tomography (PET). Here, we present five cases of such subjects and their clinical course.

Case summary

We collected clinical, imaging, pathological, and follow-up data of five subjects presenting with arrhythmias and unexplained new-onset cardiomyopathy. Mean age was 56.2 ± 5.8 years. Three subjects presented with ventricular tachycardia and two with atrial arrhythmias. Echocardiography showed a mean left ventricular ejection fraction of 37 ± 9%. Significant coronary artery disease was ruled out in all cases as the cause of the cardiomyopathy. All patients underwent cardiac magnetic resonance imaging (MRI) and PET scan at presentation and follow-up. In all patients, cardiac MRI revealed hyperenhancement in epicardial and mid-myocardial pattern in a non-coronary distribution, while PET scan revealed fluorodeoxyglucose (FDG) mismatch defects in multiple foci in a non-coronary distribution. Right ventricular biopsy was obtained in all patients and revealed interstitial fibrosis and cardiomyocyte hypertrophy. On median follow-up of 210 days, all subjects had improvement in both heart failure symptoms and arrhythmias and repeat PET in four out of five patients showed decreased inflammation.

Discussion

A high level of suspicion for inflammatory cardiomyopathy is needed in patients presenting with new unexplained cardiomyopathy and arrhythmias. A cardiac FDG-PET should be considered for diagnosis if cardiac inflammation is in the differential. This can inform further decisions regarding targeted immunomodulation therapy that may be helpful in this cohort.
Massive pulmonary embolism with intra-hospital cardiac arrest and full recovery of right ventricular function after veno-arterial extracorporeal membrane oxygenation therapy: a case report
Authors: Camen Stephan , Söffker Gerold , Kluge Stefan , Zengin Elvin
Published: August 2020

Background

Massive pulmonary embolism (PE) with shock constitutes a life-threatening disease, challenging physicians with the need for fast decision-making in an emergency situation. While thrombolytic treatment or thrombectomy are considered the treatment of choice in high-risk PE, these strategies might not be able to unload the right ventricle (RV) fast enough in some patients with severe cardiogenic shock.

Case summary

We present a case of a patient with massive bilateral central PE who presented in cardiogenic shock, rapidly deteriorating to cardiac arrest. After successful re-establishing spontaneous circulation, the patient remained highly unstable, necessitating a treatment strategy ensuring a quick stabilization of the circulation. Therefore, we decided to use veno-arterial extracorporeal membrane oxygenation (vaECMO) as a supportive strategy allowing for autolysis of the lung to dissolve the thrombi (bridge to recovery). We were able to wean the patient from vaECMO support within 4 days and documented a complete recovery of right ventricular in echocardiography before hospital discharge.

Discussion

The concept of vaECMO treatment alone might be a valuable alternative in selected patients with massive PE and cardiogenic shock, in whom thrombolytic therapy might not unload the RV fast enough.
One-stage off pump combined transapical aortic valve replacement and ascending aorta endografting
Authors: Gerosa Gino , Cibin Giorgia , Antonello Michele , D’Onofrio Augusto
Published: August 2020

An 84-year-old patient was referred for severe symptomatic aortic valve stenosis and focal chronic dissection of the ascending aorta. After multidisciplinary discussion, the patient was scheduled for combined transapical transcatheter aortic valve replacement and ascending aorta stent-grafting. The procedure was performed with a balloon aortic valvuloplasty followed by a custom-made stent graft implantation into the ascending aorta and then by balloon-expandable transapical transcatheter aortic valve replacement. The patient had an uneventful hospital stay. In conclusion, in selected high-risk patients, transapical combined ascending aorta stent-grafting and transcatheter aortic valve replacement are feasible and safe.