bluuebunny/crossref_metadata_2025 huggingface dataset:
Nasal Reconstruction of Post-Mohs Defects >1.5 cm in a Single Cosmetic Subunit Under Local Anesthesia by a Combination of Plastic Surgeon and Mohs Surgeon Team: A Cross-sectional Study and Review of Algorithmic Nasal Defect Closures
Authors: Memar Omeed M. , Caughlin Benjamin
Published: June 2019

Introduction:

We present an algorithmic approach to the reconstruction of larger post-Mohs defects treated in a practice with both a plastic surgeon and Mohs surgeon. The aim of the study is to present post-Mohs reconstructive choices made by our team compared with closures done by solo dermatologists.

Methods:

A cross-sectional study was designed. Participants were 66 consecutive cases of nasal Mohs repairs performed under local anesthesia. For each Mohs case, data were collected on the age of the patient, smoking status, tumor type, tumor location, tumor diameter, the number of Mohs stages needed to clear the surgical margins of any remaining cancer, final defect diameter, reconstructive methods used, and postoperative complications.

Results:

Basal cell carcinoma was the most common tumor treated on the nose, and post-Mohs basal cell carcinoma defects were closed predominantly with full-thickness skin grafts (FTSGs), rotation flap (RF), or a combination of both. The sidewall was the cosmetic unit most affected by skin cancer, and defects were commonly closed by FTSG and RF. Fifty percent of the sidewall defects required more than 1 closure method, compared with 24% of the nasal tip defects. FTSG combination closure was performed on 20 cases, usually with an advancement flap.

Conclusions:

The addition of a plastic surgeon shifted the nasal reconstructive techniques when compared with dermatologists alone. Post-Mohs defect >1.5 cm in a single cosmetic subunit was reconstructed under local anesthesia with either RF or a combination of FTSG and an advancement flap, whereas dermatologists most commonly chose a primary closure.
THE EVOLUTION OF ISOLATED NEOVASCULAR TUFTS (“POPCORN”) IN RETINOPATHY OF PREMATURITY
Authors: Xue Kang , Huang Xin , Xu Sisi , Zhang Ting , Wang Xin , Zhang Meng , Ruan Lu , Ni Yingqin
Published: June 2019

Purpose:

To explore the natural evolution of isolated neovascular tufts (“popcorn”) in retinopathy of prematurity (ROP) and its significance in the progression of acute ROP.

Methods:

In this retrospective case series, 89 infants (89 eyes) in total having acute ROP were analyzed during serial retinal examinations with a RetCam III wide-angle fundus imaging system, among which 53 eyes were observed to have popcorn and 36 eyes did not. The clinical outcomes of the popcorn (+) group and the popcorn (−) group were compared.

Results:

Popcorn was located only in Zone II, Stage 2 ROP, primarily in the temporal field (65%). It appeared at a mean postmenstrual age of (37.6 ± 1.3) weeks, disappeared at (41.0 ± 2.2) weeks, and lasted for (2.8 ± 1.1) weeks. The popcorn (+) group had a significantly higher natural regression incidence than the popcorn (−) group (P < 0.05). The laser-treated eyes in the popcorn (+) group had earlier presentations (36.4 ± 0.7 vs. 38.2 ± 1.3 weeks) and shorter existences (1.5 ± 0.5 vs. 3.2 ± 0.9 weeks) of popcorn than the regressed eyes (P < 0.01, respectively).

Conclusion:

Popcorn is generally a “benign” indicator of the regression of ROP. The early presentation (<postmenstrual age 37 weeks) and short duration of popcorn require further observation.
Gynecologic Surgical Outcomes Through the Patient’s Eyes: Are Physicians Looking in the Same Direction?
Authors: Emerson Jenna , Paquet Amanda , Sangha Roopina , Robison Katina
Published: June 2019

Importance

Patient-centered care integrates the highest clinical standards with patient preferences surrounding their treatment. Increasing focus is being placed on the identification of patient-centered outcomes to optimize the impact of medical treatments on patient quality of life, as defined by patients themselves.

Objective

This article will review the central concepts of patient-centered outcomes in benign gynecologic surgery. This expert review will serve as a practical guide for surgeons to incorporate patient preferences into shared surgical decision making.

Evidence Acquisition

The current literature is examined, defining those outcomes identified by women undergoing gynecologic procedures as the most important factors in their decision making. Available literature on these patient-identified priorities is then reviewed with respect to gynecologic surgery in the preoperative, intraoperative, and postoperative periods.

Results

Each section of the article concludes with Clinical Pearls, where practical tools and key elements are summarized to assist providers with incorporating these concepts into practice.

Conclusions and Relevance

Many key outcomes have been identified by women undergoing benign gynecologic surgery in their decision-making process. Patient counseling should address clinically appropriate treatment modalities and include an exploration of patient expectations and preferences around nonclinical outcomes as well. This shared decision-making model will result in improved satisfaction with outcomes.

Target Audience

Obstetricians and gynecologists, family physicians.

Learning Objectives

After completing this activity, the learner should be better able to support patient-centered informed decision making regarding gynecological procedures; describe the benefits of an Enhanced Recovery After Surgery protocol and the importance of preoperative pain burden; counsel patients regarding the impact of hysterectomy on sexual function; and explain incision types and their influence on cosmesis with patients.
Listeriosis in Pregnancy: A Review
Authors: Craig Amanda M. , Dotters-Katz Sarah , Kuller Jeffrey A. , Thompson Jennifer L.
Published: June 2019

Importance

Listeriosis is a rare foodborne condition that can cause serious health consequences in neonates and pregnant women. Listeria monocytogenes can be vertically transmitted to the fetus, resulting in adverse maternal, fetal, and neonatal outcomes. In this review, we summarize what is currently known about listeriosis in pregnancy and review the current management and treatment recommendations.

Objective

To summarize the clinical and relevant evidence available regarding listeriosis in pregnancy and educate providers on common clinical symptoms, sequelae, and appropriate treatment guidelines.

Evidence Acquisition

A PubMed review was conducted using search terms “pregnancy” OR “Listeria” OR “Maternal Listeriosis,” and “Neonatal Listeriosis.” The search included review articles, original research articles, and guidelines on diagnosis and management of listeriosis in pregnancy. The search was limited to the English language and publications between 1988 and July 2018.

Conclusions

Listeriosis in pregnancy can result in severe adverse maternal, fetal, and neonatal outcomes including miscarriage, preterm labor, fetal death, and neonatal meningitis and sepsis. Early treatment has been shown to improve fetal and neonatal outcomes; therefore, prevention with education and early diagnosis prompting treatment will improve overall outcomes.

Relevance

The incidence of listeriosis is expected to rise in the coming years due to changes in the US population, with increasing numbers of older Americans and Hispanic individuals, both of whom are at higher risk. Pregnant women contract listeriosis at a rate that is 16- to 18-fold greater than the general population. Given the expected increased rise in incidence and increased susceptibility of pregnant women, understanding the common clinical symptoms, maternal and fetal sequelae, and appropriate treatment guidelines is essential.

Target Audience

Obstetricians and gynecologists, family physicians.

Learning Objectives

After completing this activity, the learner should be better able to counsel patients in the preconception and antenatal period regarding listeriosis in pregnancy; identify potential risk factors and clinical signs and symptoms concerning for maternal listeriosis; and propose an antibiotic regimen for suspected exposure or confirmed diagnosis of Listeria in pregnancy.
Endometrial Scratching for Infertile Women Undergoing a First Embryo Transfer: A Systematic Review and Meta-analysis of Published and Unpublished Data From Randomized Controlled Trials
Authors: Vitagliano Amerigo , Andrisani Alessandra , Alviggi Carlo , Vitale Salvatore Giovanni , Valenti Gaetano , Sapia Fabrizio , Favilli Alessandro , Martins Wellington P. , Raine-Ferring Nick , Polanski Lukasz , Ambrosini Guido
Published: June 2019

(Abstracted from Fertil Steril 2019;111(4):734–746.e2)

Despite significant improvements in assisted reproductive technology (ART), clinical pregnancy rates (CPRs) and live-birth rates (LBRs) following in vitro fertilization and embryonic transfer (ET) remain between 30% and 40% and between 20% and 30% per ET, respectively. Endometrial scratch injury (ESI) is a technique that involves the use of common biopsy devices to damage the endometrium in order to increase its receptiveness to embryonic implantation in women undergoing ART.
Assessing Patient Opinions About Electronic Messaging for Gonorrhea and Chlamydia Result Notification and Partner Services, Durham, North Carolina
Authors: Cope Anna Barry , Seña Arlene C. , Eagle Cedar , Pol Adam , Rahman Mohammad , Peterman Thomas A.
Published: June 2019

Text or e-mail messages can provide timely notification of sexually transmitted disease results to patients. We assessed sexually transmitted disease clinic patient opinions about text/e-mail notification via a service called Chexout. Among 113 patients who opted in, the majority found results notification via texts/e-mails to be satisfactory (99.0%) and easy (92.9%).
Sexually Transmitted Infections Detected During and After Incarceration Among People with Human Immunodeficiency Virus: Prevalence and Implications for Screening and Prevention
Authors: Krieger Demi , Abe Caroline , Pottorff Alexandra , Li Xilong , Rich Josiah , Nijhawan Ank E.
Published: June 2019

Background

Incarceration and human immunodeficiency virus (HIV) are associated with sexually transmitted infections (STIs); however, little is known about STI prevalence among people living with HIV (PLWH) during and after incarceration.

Methods

Electronic medical records from the Dallas County Jail and community HIV clinics were reviewed to determine the frequency and results of testing for gonorrhea, chlamydia, syphilis, and hepatitis B virus (HBV) among PLWH incarcerated in Dallas County Jail between 2010 and 2013. HIV viral loads (VL) and evidence of STI symptoms and treatment were also collected.

Results

During 2473 incarcerations, 6 (3%) of 190 tests were positive for gonorrhea, 7 (4%) of 190 for chlamydia, 231 (21%) of 1082 for syphilis, of which 53 (23%) were new diagnoses, and 48 (5%) of 1005 for HBV surface antigen. Among 1631 releases to the community, 808 followed up in community clinics, where 21 (4%) 553 tests were positive for gonorrhea, 23 (4%) of 555 for chlamydia, 150 (19%) of 808 for syphilis, of which 31 (21%) were new diagnoses, and 24 (6%) of 421 for HBV surface antigen. The majority of new STI cases, 51 (80%) of 64 in jail and 43 (77%)of 56 in the community, had a concurrent detectable (>200 copies/mL) HIV VL.

Conclusions

Testing for gonorrhea and chlamydia was low, particularly in jail, which was attributed to testing protocols. High proportions of PLWH tested positive for syphilis and HBV infection in both settings. The majority of patients with active STIs had a detectable HIV VL. Routine, opt-out screening for STIs for PLWH during and after incarceration has the potential to identify a high proportion of STIs and improve secondary HIV prevention.
Pulmonary Granular Cell Tumors
Authors: Davis Richard , Deak Kristen , Glass Carolyn H.
Published: June 2019

Granular cell tumors are lesions of Schwannian phenotype that most frequently arise in the skin, breast, and tongue. Pulmonary granular cell tumors (pGCTs) are exceedingly rare and only a handful of cases worldwide have been reported as malignant. We report here a series of 4 pGCTs, including an extremely rare case of a malignant pGCT which underwent next-generation sequencing to identify a novel pathogenic mutation. We are the first to report any prognostic data and response to treatment. Consistent with granular cell tumors of other primary sites, the majority of pGCTs (75%) were deemed histologically and biological benign without metastasis or recurrence after resection (mean follow-up, 750 d). pGCTs occurred predominantly in women (75%) with a mean age of 57 years (range, 49 to 66 y) and variable smoking history. Notably, 2 women also developed an associated lung carcinoma (adenocarcinoma and small cell carcinoma). We also report here an exceedingly rare case of a 51-year-old nonsmoker woman diagnosed with a malignant pGCT. She presented with a 6.4×6.1×4.4 cm infrahilar left lower lobe mass with extrinsic compression and obstruction of the left mainstem on enhanced computed tomography. Pathology of the resection specimen confirmed a pGCT composed of sheets of tumor cells with pleural, pericardial, and diaphragmatic metastases. Molecular analysis by next-generation sequencing failed to yield any driver mutations common to primary lung adenocarcinomas. Only 2 previous malignant pGCTs have been reported; our case revealed a novel pathologic ATM mutation.
A Predictive Model for Identification of Children at Risk of Subsequent High-Frequency Utilization of the Emergency Department for Asthma
Authors: Samuels-Kalow Margaret E. , Bryan Matthew W. , Sommers Marilyn Sawyer , Zorc Joseph J. , Camargo Carlos A. , Mollen Cynthia
Published: June 2019

Background

Asthma is the most common chronic condition among children with high-frequency emergency department (ED) utilization. Previous research has shown in outpatients seen for asthma that acute care visits predict subsequent health care utilization. Among ED patients, however, the optimal method of predicting subsequent ED utilization remains to be described. The goal of this study was to create a predictive model to identify children in the ED who are at risk of subsequent high-frequency utilization of the ED for asthma.

Methods

We used 3 years of data, 2013–2015, drawn from the electronic health records at a tertiary care, urban, children's hospital that is a high-volume center for asthma care. Data were split into a derivation (50%) and validation/test (50%) set, and 3 models were created for testing: (1) all index patients; (2) removing patients with complex chronic conditions; and (3) subset of patients with in-network care on whom more clinical data were available. Each multivariable model was then tested in the validation set, and its performance evaluated by predicting error rate, calculation of a receiver operating characteristic (ROC) curve, and identification of the optimal cutpoint to maximize sensitivity and specificity.

Results

There were 5535 patients with index ED visits, of whom 2767 were in the derivation set and 2768 in the validation set. Of the 5535 patients, 125 patients (2.3%) had 4 or more visits for asthma in the outcome year. Significant predictors in models 1 and 2 were age and number of prior ED visits for asthma. For model 3 (additional clinical information available), the predictors were number of prior ED visits for asthma, number of primary care visits, and not having a controller medication. Areas under the ROC curve were 0.77 for model 1, 0.80 for model 2, and 0.77 for model 3.

Conclusions

Administrative data available at the time of ED triage can predict subsequent high utilization of the ED, with areas under the ROC curve of 0.77 to 0.80. The addition of clinical variables did not improve the model performance. These models provide useful tools for researchers interested in examining intervention efficacy by predicted risk group.
Paraquat Poisoning in Children
Authors: Qiu Li , Deng Ying
Published: June 2019

Objectives

Paraquat is an herbicide that is highly toxic to humans. Paraquat ingestion is a common cause of fatal poisoning in many areas of Asia. The aim of the study was to analyze the characteristics of children with acute paraquat poisoning.

Methods

This study was a retrospective analysis of case exposure to paraquat poisoning as reported to the Department of Pediatrics in The West China Second University Hospital of Sichuan University between January 2012 and December 2017. The data of these patients were extracted from the electronic health records and analyzed.

Results

A total of 123 children with paraquat poisoning were included in the study. The study showed that 67.5% of these children (83/123) were accidentally exposed to paraquat, whereas 32.5% (40/123) had intentionally ingested paraquat. The 0- to 2.9-year age group had the largest number of cases (30% of the total). One hundred (81.3%) children were discharged with a better health condition. Two children were dead at the time of hospitalization because of respiratory failure. Most children (87.8%) with paraquat poisoning were left-behind children. Paraquat poisoning did not frequently occur in the winter.

Conclusions

Left-behind children living in rural areas have a high risk of paraquat poisoning. Interventions and policies are urgently needed to prevent paraquat poisoning in children. Preventative efforts are the most important measures.
The Effect of Four-Channel Neuromuscular Electrical Stimulation on Swallowing Kinematics and Pressures
Authors: Park Donghwi , Suh Jee Hyun , Kim Hayoung , Ryu Ju Seok
Published: June 2019

Objective

The purpose of this study was to evaluate the effectiveness of the sequential four-channel neuromuscular electrical stimulation system.

Design

As a prospective case-control study, ten healthy subjects and ten patients with dysphagia were prospectively enrolled. Swallowing with and without sequential four-channel neuromuscular electrical stimulation (suprahyoid, infrahyoid muscles) was evaluated via videofluoroscopic swallowing study and high-resolution manometry.

Results

Results showed that the sequential four-channel neuromuscular electrical stimulation significantly improved the videofluoroscopic dysphagia scale during thick-fluid swallowing in patients with dysphagia. Furthermore, the kinematic analysis of videofluoroscopic swallowing study showed a tendency that neuromuscular electrical stimulation reduced duration of hyoid bone movement during thin- or thick-fluid swallowing. The high-resolution manometry parameters—maximal pressure of velopharynx, tongue base, cricopharyngeal pressure, minimal upper esophageal sphincter pressure, area of velopharynx, upper esophageal sphincter activity time, and duration of nadir upper esophageal sphincter—during thin-fluid swallowing were significantly improve in both groups compared with the high-resolution manometry parameters without neuromuscular electrical stimulation.

Conclusion

The sequential four-channel neuromuscular electrical stimulation may help improve the parameters of videofluoroscopic swallowing study, kinematic analysis of the hyoid bone movement, and high-resolution manometry during swallowing. Further investigations are needed to better examine the effects of neuromuscular electrical stimulation in patients with dysphagia.
The Effect of the Breast Cancer Provider Discussion Law on Breast Reconstruction Rates in New York State
Authors: Fu Rose H. , Baser Onur , Li Lu , Kurlansky Paul , Means Jessica , Rohde Christine H.
Published: June 2019

Background:

New York State passed the Breast Cancer Provider Discussion Law in 2010, mandating discussion of insurance coverage for reconstruction and expedient plastic surgical referral, two significant factors found to affect reconstruction rates. This study examines the impact of this law.

Methods:

A retrospective cohort study of the New York State Planning and Research Cooperative System database to examine breast reconstruction rates 3 years before and 3 years after law enactment was performed. Difference-interrupted time series models were used to compare trends in the reconstruction rates by sociodemographic factors and provider types.

Results:

The study included 32,452 patients. The number of mastectomies decreased from 6479 in 2008 to 5235 in 2013; the rate of reconstruction increased from 49 percent in 2008 to 62 percent in 2013. This rise was seen across all median income brackets, races, and age groups. When comparing before to after law enactment, the increase in risk-adjusted reconstruction rates was significantly higher for African Americans and elderly patients, but the disparity in reconstruction rates did not change for other races, different income levels, or insurance types. Reconstruction rates were also not significantly different between those treated in various hospital settings.

Conclusions:

The aim of the Breast Cancer Provider Discussion Law is to improve reconstruction rates through provider-driven patient education. The authors’ data show significant change following law passage in African American and elderly populations, suggesting effectiveness of the law. The New York State Provider Discussion Law may provide a template for other states to model legislation geared toward patient-centered improvement of health outcomes.
Adipose-Derived Stem Cells and Ceiling Culture-Derived Preadipocytes Cultured from Subcutaneous Fat Tissue Differ in Their Epigenetic Characteristics and Osteogenic Potential
Authors: Sasahara Yoshitaro , Kubota Yoshitaka , Kosaka Kentaro , Adachi Naoki , Yamaji Yoshihisa , Nagano Hidekazu , Akita Shinsuke , Kuroda Masayuki , Tanaka Tomoaki , Bujo Hideaki , Mitsukawa Nobuyuki
Published: June 2019

Background:

Adipose-derived stem cells and ceiling culture-derived preadipocytes can be harvested from subcutaneous adipose tissue. Little is known about the epigenetic differences, which may contribute to differences in osteogenic potential, between these cell types. The purpose of this study was to address the osteogenic potential and underlying epigenetic status of adipose-derived stem cells and ceiling culture-derived preadipocytes.

Methods:

Adipose-derived stem cells and ceiling culture-derived preadipocytes were cultured from abdominal subcutaneous fat tissues of four metabolically healthy, lean female patients. After 7 weeks of culture, cellular responses to osteogenic differentiation media were examined. To evaluate the osteogenic potentials of undifferentiated adipose-derived stem cells and ceiling culture-derived preadipocytes, two types of epigenetic assessment were performed using next-generation sequencing: DNA methylation assays with the Human Methylation 450K BeadChip, and chromatin immunoprecipitation assays for trimethylation of histone H3 at lysine 4.

Results:

Human ceiling culture-derived preadipocytes showed greater osteogenic differentiation ability than did adipose-derived stem cells. In an epigenetic survey of the promoters of four osteogenic regulator genes (RUNX2, SP7, ATF4, and BGLAP), the authors found a general trend toward decreased CpG methylation and increased trimethylation of histone H3 at lysine 4 levels in ceiling culture-derived preadipocytes as compared to adipose-derived stem cells, indicating that these genes were more likely to be highly expressed in ceiling culture-derived preadipocytes.

Conclusions:

The surveyed epigenetic differences between adipose-derived stem cells and ceiling culture-derived preadipocytes were consistent with the observed differences in osteogenic potential. These results enhance the authors’ understanding of these cells and will facilitate their further application in regenerative medicine.
Brief Report: Markers of Spontaneous Preterm Delivery in Women Living With HIV: Relationship With Protease Inhibitors and Vitamin D
Authors: Weinberg Adriana , Huo Yanling , Kacanek Deborah , Patel Kunjal , Watts D. Heather , Wara Diane , Hoffman Risa M. , Klawitter Jelena , Christians Uwe ,   for IMPAACT P1025 Team
Published: June 2019

Background:

Women living with HIV (WLHIV) have increased risk of spontaneous preterm delivery (SPTD). We sought to identify plasma predictors of SPTD and their correlations with factors that increase the risk of SPTD, such as vitamin D deficiency and use of protease inhibitors.

Design:

Plasma was obtained from 103 WLHIV with SPTD (≤35 weeks gestation) and 205 controls with term deliveries (TDs; ≥37 weeds) matched to cases 2:1 by race and gestational age at blood draw. TNFα, IFNγ, IL6, IL8, IL1β, IL18, IL17, granulocyte colony stimulating factor (GCSF), MCP1, IP10, sIL2Rα, sCD14, vascular endothelial factor a, monocyte colony stimulation factor, GROα, MMP9, IL10, TGFβ, sCTLA4, and eicosanoids were compared between cases adjusting for known SPTD risk factors.

Results:

Participants had similar demographic characteristics, but cases had higher plasma HIV RNA, lower CD4 cells, and more advanced HIV disease compared with controls. High sIL2Rα was associated with increased risk of SPTD. High sCD14, GCSF, PGF2α, and 5-HEPE were marginally associated with increased risk of SPTD. Women who initiated protease inhibitors-containing antiretroviral treatment before or during the first trimester had higher levels of GCSF and 5-HEPE compared with women without such exposure before plasma collection. Vitamin D insufficiency was associated with higher inflammatory sCD14 and PGF2α, and lower anti-inflammatory 5-HEPE.

Conclusions:

The best plasma predictor of SPTD in WLHIV was sIL2Rα, a marker of T-cell activation. Markers of monocyte activation and eicosanoids were marginally increased in WLHIV and SPTD, suggesting that they may also play a role in the pathogenesis of this disorder.
Modelling bacterial twitching in fluid flows: a CFD-DEM approach
Authors: Jayathilake Pahala Gedara , Li Bowen , Zuliani Paolo , Curtis Tom , Chen Jinju
Published: June 2019

Bacterial habitats are often associated with fluid flow environments. There is a lack of models of the twitching motility of bacteria in shear flows. In this work, a three-dimensional modelling approach of Computational Fluid Dynamics (CFD) coupled with the Discrete Element Method (DEM) is proposed to study bacterial twitching on flat and groove surfaces under shear flow conditions. Rod-shaped bacteria are modelled as groups of spherical particles and Type IV pili attached to bacteria are modelled as dynamic springs which can elongate, retract, attach and detach. The CFD-DEM model of rod-shape bacteria is validated against orbiting of immotile bacteria in shear flows. The effects of fluid flow rate and surface topography on twitching motility are studied. The model can successfully predict upstream twitching motility of rod-shaped bacteria in shear flows. Our model can predict that there would be an optimal range of wall shear stress in which bacterial upstream twitching is most efficient. The results also indicate that when bacteria twitch on groove surfaces, they are likely to accumulate around the downstream side of the groove walls.
Predicting Synthetic Lethal Interactions using Heterogeneous Data Sources
Authors: Liany Herty , Jeyasekharan Anand , Rajan Vaibhav
Published: June 2019

Motivation

A synthetic lethal (SL) interaction is a relationship between two functional entities where the loss of either one of the entities is viable but the loss of both entities is lethal to the cell. Such pairs can be used as drug targets in targeted anticancer therapies, and so, many methods have been developed to identify potential candidate SL pairs. However, these methods use only a subset of available data from multiple platforms, at genomic, epigenomic and transcriptomic levels; and hence are limited in their ability to learn from complex associations in heterogeneous data sources.

Results

In this paper we develop techniques that can seamlessly integrate multiple heterogeneous data sources to predict SL interactions. Our approach obtains latent representations by collective matrix factorization based techniques, which in turn are used for prediction through matrix completion. Our experiments, on a variety of biological datasets, illustrate the efficacy and versatility of our approach, that outperforms state-of-the-art methods for predicting SL interactions and can be used with heterogeneous data sources with minimal feature engineering.

Availability

Software available athttps://github.com/lianyh

Contact

vaibhav.rajan@nus.edu.sg
The Dreem Headband as an Alternative to Polysomnography for EEG Signal Acquisition and Sleep Staging
Authors: Arnal Pierrick J. , Thorey Valentin , Ballard Michael E. , Hernandez Albert Bou , Guillot Antoine , Jourde Hugo , Harris Mason , Guillard Mathias , Van Beers Pascal , Chennaoui Mounir , Sauvet Fabien
Published: June 2019

Despite the central role of sleep in our lives and the high prevalence of sleep disorders, sleep is still poorly understood. The development of ambulatory technologies capable of monitoring brain activity during sleep longitudinally is critical to advancing sleep science and facilitating the diagnosis of sleep disorders. We introduced the Dreem headband (DH) as an affordable, comfortable, and user-friendly alternative to polysomnography (PSG). The purpose of this study was to assess the signal acquisition of the DH and the performance of its embedded automatic sleep staging algorithms compared to the gold-standard clinical PSG scored by 5 sleep experts. Thirty-one subjects completed an over-night sleep study at a sleep center while wearing both a PSG and the DH simultaneously. We assessed 1) the EEG signal quality between the DH and the PSG, 2) the heart rate, breathing frequency, and respiration rate variability (RRV) agreement between the DH and the PSG, and 3) the performance of the DH’s automatic sleep staging according to AASM guidelines vs. PSG sleep experts manual scoring. Results demonstrate a strong correlation between the EEG signals acquired by the DH and those from the PSG, and the signals acquired by the DH enable monitoring of alpha (r= 0.71 ± 0.13), beta (r= 0.71 ± 0.18), delta (r = 0.76 ± 0.14), and theta (r = 0.61 ± 0.12) frequencies during sleep. The mean absolute error for heart rate, breathing frequency and RRV was 1.2 ± 0.5 bpm, 0.3 ± 0.2 cpm and 3.2 ± 0.6 %, respectively. Automatic Sleep Staging reached an overall accuracy of 83.5 ± 6.4% (F1 score : 83.8 ± 6.3) for the DH to be compared with an average of 86.4 ± 8.0% (F1 score: 86.3 ± 7.4) for the five sleep experts. These results demonstrate the capacity of the DH to both precisely monitor sleep-related physiological signals and process them accurately into sleep stages. This device paves the way for high-quality, large-scale, longitudinal sleep studies.
Targeted Clinical Metabolomics Platform for the Stratification of Diabetic Patients
Authors: Ahonen Linda , Jäntti Sirkku , Suvitaival Tommi , Theilade Simone , Risz Claudia , Kostiainen Risto , Rossing Peter , Orešič Matej , Hyötyläinen Tuulia
Published: June 2019

Background

Several small molecule biomarkers have been reported in the literature for prediction and diagnosis of (pre)diabetes, its co-morbidities and complications. Here, we report the development and validation of a novel, quantitative, analytical method for use in the diabetes clinic. This method enables the determination of a selected panel of 36 metabolite biomarkers from human plasma.

Methods

Based on a review of the literature and our own data, we selected a panel of metabolites indicative of various clinically-relevant pathogenic stages of diabetes. We combined these candidate biomarkers into a single ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method and optimized it, prioritizing simplicity of sample preparation and time needed for analysis, enabling high-throughput analysis in clinical laboratory settings.

Results

We validated the method in terms of limit of (a) detection (LOD), (b) limit of quantitation (LOQ), (c) linearity (R2), (d) linear range, and (e) intra- and inter-day repeatability of each metabolite. The method’s performance was demonstrated in the analysis of selected samples from a diabetes cohort study. Metabolite levels were associated with clinical measurements and kidney complications in type 1 diabetes (T1D) patients. Specifically, both amino acids and amino acid-related analytes were associated with macro-albuminuria. Additionally, specific bile acids were associated with kidney function, anti-hypertensive medication, statin medication and clinical lipid measurements.

Conclusions

The developed analytical method is suitable for robust determination of selected plasma metabolites in the diabetes clinic.
Improved control of Septoria tritici blotch in durum wheat using cultivar mixtures
Authors: Ben M’Barek S. , Karisto P. , Abdedayem W. , Laribi M. , Fakhfakh M. , Kouki H. , Mikaberidze A. , Yahyaoui A.
Published: June 2019

Mixtures of cultivars with contrasting levels of resistance can suppress infectious diseases in wheat, as demonstrated in numerous field experiments. Most studies focused on airborne pathogens in bread wheat, while splash-dispersed pathogens have received less attention, and no studies have been conducted in durum wheat. We conducted a two-year field experiment in Tunisia, to evaluate the performance of cultivar mixtures with varying proportions of resistance (0–100%) in controlling the polycyclic, splash-dispersed disease Septoria tritici blotch (STB) in durum wheat. To measure STB severity, we used a high-throughput method based on digital image analysis of 3074 infected leaves collected from 42 and 40 experimental plots during the first and second years, respectively. This allowed us to quantify pathogen reproduction on wheat leaves and to acquire a large dataset that exceeds previous studies with respect to accuracy and precision. Our analyses show that introducing only 25% of a disease-resistant cultivar into a pure stand of a susceptible cultivar provides a substantial reduction of almost 50% in disease severity compared to the susceptible pure stand. However, comprising the resistant component of two cultivars instead of one did not further improve disease control, contrary to predictions of epidemiological theory. Susceptible cultivars can be agronomically superior to resistant cultivars or be better accepted by growers for other reasons. Hence, if mixtures with only a moderate proportion of the resistant cultivar provide a similar degree of disease control as resistant pure stands, as our analysis indicates, such mixtures are more likely to be accepted by growers.
High and asymmetric somato-dendritic coupling of V1 layer 5 neurons independent of visual stimulation and locomotion
Authors: Francioni Valerio , Padamsey Zahid , Rochefort Nathalie L.
Published: June 2019

Active dendrites impact sensory processing and behaviour. However, it remains unclear how active dendritic integration relates to somatic output in vivo. We imaged semi-simultaneously GCaMP6s signals in the soma, trunk and distal tuft dendrites of layer 5 pyramidal neurons in the awake mouse primary visual cortex. We found that apical tuft signals were dominated by widespread, highly correlated calcium transients throughout the tuft. While these signals were highly coupled to trunk and somatic transients, the frequency of calcium transients was found to decrease in a distance-dependent manner from soma to tuft. Ex vivo recordings suggest that low-frequency back-propagating action potentials underlie the distance-dependent loss of signals, while coupled somato-dendritic signals can be triggered by high-frequency somatic bursts or strong apical tuft depolarization. Visual stimulation and locomotion increased neuronal activity without affecting somato-dendritic coupling. High, asymmetric somato-dendritic coupling is therefore a widespread feature of layer 5 neurons activity in vivo.
Absence of Replication fork associated factor CTF4 and F-box motif Encoding Gene SAF1 leads to reduction in Cell Size and Stress Tolerance Phenotype inS. cerevisiae
Authors: Sharma Meenu , Singh Samar , Verma V. , Bairwa Narendra K
Published: June 2019

Chromosome transmission fidelity factor, Ctf4 inS. cerevisiaeassociates with replication fork and helps in the sister chromatid cohesion. At the replication fork, Ctf4 links DNA helicase with the DNA polymerase. The absence of Ctf4 invokes replication checkpoint in the cells. The Saf1 ofS.cerevisiaeinteracts with Skp1 of SCF-E3 ligase though F box-motif and ubiquitinates the adenine deaminase Aah1 during phase transition due to nutrient stress. The genetic interaction between the CTF4 and SAF1 has not been studied. Here we report genetic interaction between CTF4 and SAF1 which impacts the growth fitness and response to stress. The single and double gene deletions of SAF1 and CTF4 were constructed in the BY4741 genetic background. The strains were tested for growth on rich media and media containing stress causing agents. Thesaf1Δctf4Δ cells with reduced cell size showed the fastest growth phenotype on YPD medium when compared with thesaf1Δ,ctf4Δ,and WT. Thesaf1Δctf4Δ cells also showed the tolerance to MMS, NaCl, Glycerol, SDS, Calcofluor white, H2O2, DMSO, Benomyl, and Nocodazole when compared with the saf1Δ,ctf4Δ, and WT cells. However,saf1Δctf4Δ cells showed the sensitivity to HU when compared with WT andsaf1Δ. Based on these observations we suggest that SAF1 and CTF4 interact genetically to regulate the cell size, growth and stress response.
Revealing microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation
Authors: Hosoda Shion , Nishijima Suguru , Fukunaga Tsukasa , Hattori Masahira , Hamada Michiaki
Published: June 2019

Recent research has revealed that there are various microbial species in the human gut microbiome. To clarify the structure of the human gut microbiome, many data mining methods have been applied to microbial composition data. Cluster analysis, one of the key data mining methods that have been used in human gut microbiome research, can classify the human gut microbiome into three clusters, called enterotypes. The human gut microbiome has been suggested to be composed of the microbial assemblages or groups of co-occurring microbes, and one human gut microbiome can contain several microbial assemblages. However, cluster analysis can cluster samples into groups without capturing minor assemblages. In addition, a reliable method of assemblage detection has not been established, and little is known about the distributions of microbial assemblages at a population-level scale. Accordingly, the purpose of this study was to clarify the microbial assemblages in the human gut microbiome. In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method, which was first proposed for the classification of documents in natural language processing. We applied LDA to a large-scale human gut metagenome dataset and found that a four-assemblage LDA model can represent relationships between enterotypes and assemblages with high interpretability. This model indicates that each individual tends to have several assemblages, and each of three assemblages corresponded to each enterotype. However, the C-assemblage can exist in all enterotypes. Interestingly, the dominant genera of the C-assemblage (Clostridium, Eubacterium, Faecalibacterium, Roseburia, Coprococcus, and Butyrivibrio) included butyrate-producing species such as Faecalibacterium prausnitzii. Finally, we revealed that genera mainly appearing in the same assemblage were correlated to each other. We conducted an assemblage analysis on a large-scale human gut metagenome dataset using LDA, a powerful method for detection of microbial assemblages. This approach has the potential to reveal the structure of the human gut microbiome.
The mechanical stability of the world’s tallest broadleaf trees
Authors: Jackson T. , Shenkin A. , Majalap N. , bin Jami J. , bin Sailim A. , Reynolds G. , Coomes D.A. , Chandler C.J. , Boyd D.S. , Burt A. , Wilkes Phil , Disney M. , Malhi Y.
Published: June 2019

The factors that limit the maximum height of trees, whether ecophysiological or mechanical, are the subject of longstanding debate. Here we examine the role of mechanical stability in limiting tree height and focus on trees from the tallest tropical forests on Earth, in Sabah, Malaysian Borneo, including the recently discovered tallest tropical tree, a 100.8 mShorea faguetiana. We use terrestrial laser scans,in situstrain gauge data and finite-element simulations to map the architecture of tall broadleaf trees and monitor their response to wind loading. We demonstrate that a tree’s risk of breaking due to gravity or self-weight decreases with tree height and is much more strongly affected by tree architecture than by material properties. In contrast, wind damage risk increases with tree height despite the larger diameters of tall trees, resulting in a U-shaped curve of mechanical risk with tree height. The relative rarity of extreme wind speeds in north Borneo may be the reason it is home to the tallest trees in the tropics.
Illuminating the functional rare biosphere of the Greenland Ice Sheet’s Dark Zone
Authors: Gokul Jarishma K. , Cameron Karen A. , Irvine-Fynn Tristram D.L. , Cook Joseph M. , Hubbard Alun , Stibal Marek , Hegarty Matt , Mur Luis A.J. , Edwards Arwyn
Published: June 2019

The Dark Zone of the western Greenland Ice Sheet is the most expansive region of contiguous bare terrestrial ice in the Northern Hemisphere. Microbial processes within the Dark Zone play an important role in driving extensive albedo reduction and amplified melting, yet the composition and function of those consortia have not been fully identified. Here we present the first results from joint 16S rRNA gene and 16S rRNA (cDNA) analysis for the comparison of input (snow), storage (cryoconite), and output (supraglacial stream water) habitats across the Dark Zone over the melt season. Our analysis reveals that all three Dark Zone communities are characterized by a preponderance of rare taxa exhibiting high protein synthesis potential (PSP). Furthermore, taxa with high PSP represent highly connected “bottlenecks” within community structure, consistent with roles as metabolic hubs within their communities. Finally, the detection of low abundance-high PSP taxa affiliated withMethylobacteriumwithin snow and stream water indicates a potential role forMethylobacteriumin the carbon cycle of Greenlandic snowpacks, and importantly, the export of potentially active methylotrophs to the bed of the Greenland Ice Sheet. By comparing the dynamics of bulk and potentially active microbial communities in the Dark Zone of the Greenland Ice Sheet our study provides insight into the mechanisms and impacts of the microbial colonization of this critical region of our melting planet.
A case for a reverse-frame coding sequence in a group of positive-sense RNA viruses
Authors: Dinan Adam M. , Lukhovitskaya Nina I. , Olendraite Ingrida , Firth Andrew E.
Published: June 2019

Positive-sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-sense RNA viruses are generally accepted to encode proteins solely on the positive strand. However, we previously identified a surprisingly long (~1000 codons) open reading frame (ORF) on the negative strand of some members of the familyNarnaviridaewhich, together with RNA bacteriophages of the familyLeviviridae, form a sister group to all other positive-sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungi and plant transcriptomic datasets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95% of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution andde novoorigin of genes.
HAT1 drives a gene-metabolite circuit that links nutrient metabolism to histone production
Authors: Gruber Joshua J. , Geller Benjamin , Lipchik Andrew M. , Chen Justin , Salahudeen Ameen A. , Ram Ashwin N. , Ford James M. , Kuo Calvin J. , Snyder Michael P.
Published: June 2019

The energetic costs of duplicating chromatin along with DNA replication are large and therefore likely depend on nutrient sensing checkpoints and metabolic inputs. By studying chromatin modifiers regulated by epithelial growth factor, we identify histone acetyltransferase 1 (HAT1) as an induced gene that enhances cell proliferation by coordinating histone production with glucose metabolism. In addition to its canonical role as a cytoplasmic free histone H4 acetyltransferase, a HAT1-containing complex binds specifically at promoters of H4 genes. HAT1 stimulated acetate delivery and consumption at H4 promoters to drive S-phase H4 transcription. This required the presence of a histone H4-specific promoter element in the region of HAT1 chromatin binding. These data describe a feed-forward circuit whereby HAT1-dependent capture of acetyl-groups drives further H4 production to support growth-factor dependent proliferation. These findings also extend to human disease and animal models, as high HAT1 levels associate with poor outcomes across multiple cancer types.
Frataxin deficiency induces lipid accumulation and affects thermogenesis in brown adipose tissue
Authors: Turchi Riccardo , Tortolici Flavia , Guidobaldi Giulio , Iacovelli Federico , Falconi Mattia , Rufini Stefano , Faraonio Raffaella , Casagrande Viviana , De Angelis Lorenzo , Federici Massimo , Carotti Simone , Francesconi Maria , Zingariello Maria , Morini Sergio , Bernardini Roberta , Maurizio Mattei , Lettieri-Barbato Daniele , Aquilano Katia
Published: June 2019

Decreased expression of the mitochondrial protein frataxin (FXN) causes Friedreich’s ataxia (FRDA). FRDA is a neurodegenerative disease also characterized by systemic metabolic alterations that increase the risk of developing type 2 diabetes thus aggravating FRDA prognosis. Brown adipose tissue (BAT) is a mitochondria-enriched and anti-diabetic tissue that, in addition to its thermoregulatory role, turns excess energy into heat to maintain energy balance. Here we report that the FXN knock-in/knock-out (KIKO) mouse shows reduced energy expenditure and VO2, hyperlipidemia, decreased insulin sensitivity and enhanced circulating levels of leptin, recapitulating diabetes-like signatures. FXN deficiency leads to alteration of mitochondrial structure and oxygen consumption, decreased lipolysis and lipid accumulation in BAT. Transcriptomic data highlighted a blunted thermogenesis response, as several biological processes related to thermogenesis (e.g. response to temperature stimuli, mitochondrial gene transcription, triglyceride metabolism, adipogenesis) resulted affected in BAT of KIKO mice upon cold exposure. Decreased adaptation to cool temperature in association with limited PKA-mediated lipolysis and downregulation of the expression of the genes controlling mitochondrial metabolism and lipid catabolism were observed in KIKO mice. T37i brown adipocytes and primary adipocytes with FXN deficiency showed reduced thermogenesis and adipogenesis markers respectively recapitulating the molecular signatures detected in KIKO mice.

Collectively our data point to BAT dysfunction in FRDA and suggest BAT as a promising target to overcome metabolic complications in FRDA.