bluuebunny/crossref_metadata_2025 huggingface dataset:
Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Authors: Angus Robert B , Sadílek David , Shaarawi Fatma , Dollimore Hayley , Liu Hsing-Che , Seidel Matthias , Sýkora Vít , Fikáček Martin
Published: August 2020

This study summarizes available data on karyotypes of water scavenger beetles (Coleoptera: Hydrophiloidea: Hydrophilidae), based on newly acquired data of 23 genera and 64 species. We combine these data with previously published data, which we review. In total, karyotypes are available for 33 genera and 95 species, covering all subfamilies and tribes. Available data indicate that most groups of the Hydrophilidae are diploid and sexually reproducing, with XY (♂) and XX (♀) sex chromosomes; the Y chromosome is always minute and does not recombine with X during meiosis. Exceptions are known in Anacaena, with parthenogenetic diploid or triploid populations in some species and sex chromosomes fused with autosomes in others. The diploid number of chromosomes is 2n = 18 in the subfamilies Acidocerinae, Chaetarthriinae, Enochrinae and Hydrophilinae. Variations are known in species of Anacaena and Berosus (both usually with 2n = 18) and in Hydrochara and Hydrophilus with an increased number of chromosomes (2n = 30). The number of chromosomes is increased in the subfamily Cylominae (2n = 24–30) and in all subclades of the subfamily Sphaeridiinae (2n = 22–32). We summarize protocols for obtaining chromosome slides used for this study and provide step-by-step guidelines to facilitate future cytogenetic studies.
What is the Molecular Basis of Nonhost Resistance?
Authors: Panstruga Ralph , Moscou Matthew J.
Published: August 2020

This article is part of the Top 10 Unanswered Questions in MPMI invited review series.

Nonhost resistance is typically considered the ability of a plant species to repel all attempts of a pathogen species to colonize it and reproduce on it. Based on this common definition, nonhost resistance is presumed to be very durable and, thus, of great interest for its potential use in agriculture. Despite considerable research efforts, the molecular basis of this type of plant immunity remains nebulous. We here stress the fact that “nonhost resistance” is a phenomenological rather than a mechanistic concept that comprises more facets than typically considered. We further argue that nonhost resistance essentially relies on the very same genes and pathways as other types of plant immunity, of which some may act as bottlenecks for particular pathogens on a given plant species or under certain conditions. Thus, in our view, the frequently used term “nonhost genes” is misleading and should be avoided. Depending on the plant–pathogen combination, nonhost resistance may involve the recognition of pathogen effectors by host immune sensor proteins, which might give rise to host shifts or host range expansions due to evolutionary-conditioned gains and losses in respective armories. Thus, the extent of nonhost resistance also defines pathogen host ranges. In some instances, immune-related genes can be transferred across plant species to boost defense, resulting in augmented disease resistance. We discuss future routes for deepening our understanding of nonhost resistance and argue that the confusing term “nonhost resistance” should be used more cautiously in the light of a holistic view of plant immunity.
From Africa to the USA: A Combined Strategy for Nursing Education
Authors: Weierbach Florence M. , Halford Sandy K.
Published: August 2020

Engaging students in class when first-hand experience is not available is challenging. Three teaching strategies, flipped classroom, a guest speaker, and technology, engaged students during a global health class. Students were given a graded preclass assignment, which was used to guide the class session when an expert physician from Zambia joined us using technology. On the day of class, students were engaged and asked questions of the physician related to global health and culture. Combining the three strategies was an innovative and effective way to engage students, with many sharing with faculty that this was their favorite class day.
Diagnostic capacity of skin tumor artificial intelligence-assisted decision-making software in real-world clinical settings
Authors: Li Cheng-Xu , Fei Wen-Min , Shen Chang-Bing , Wang Zi-Yi , Jing Yan , Meng Ru-Song , Cui Yong
Published: August 2020

Background

Youzhi artificial intelligence (AI) software is the AI-assisted decision-making system for diagnosing skin tumors. The high diagnostic accuracy of Youzhi AI software was previously validated in specific datasets. The objective of this study was to compare the performance of diagnostic capacity between Youzhi AI software and dermatologists in real-world clinical settings.

Methods

A total of 106 patients who underwent skin tumor resection in the Dermatology Department of China-Japan Friendship Hospital from July 2017 to June 2019 and were confirmed as skin tumors by pathological biopsy were selected. Dermoscopy and clinical images of 106 patients were diagnosed by Youzhi AI software and dermatologists at different dermoscopy diagnostic levels. The primary outcome was to compare the diagnostic accuracy of the Youzhi AI software with that of dermatologists and that measured in the laboratory using specific data sets. The secondary results included the sensitivity, specificity, positive predictive value, negative predictive value, F-measure, and Matthews correlation coefficient of Youzhi AI software in the real-world.

Results

The diagnostic accuracy of Youzhi AI software in real-world clinical settings was lower than that of the laboratory data (P < 0.001). The output result of Youzhi AI software has good stability after several tests. Youzhi AI software diagnosed benign and malignant diseases by recognizing dermoscopic images and diagnosed disease types with higher diagnostic accuracy than by recognizing clinical images (P = 0.008, P = 0.016, respectively). Compared with dermatologists, Youzhi AI software was more accurate in the diagnosis of skin tumor types through the recognition of dermoscopic images (P = 0.01). By evaluating the diagnostic performance of dermatologists under different modes, the diagnostic accuracy of dermatologists in diagnosing disease types by matching dermoscopic and clinical images was significantly higher than that by identifying dermoscopic and clinical images in random sequence (P = 0.022). The diagnostic accuracy of dermatologists in the diagnosis of benign and malignant diseases by recognizing dermoscopic images was significantly higher than that by recognizing clinical images (P = 0.010).

Conclusion

The diagnostic accuracy of Youzhi AI software for skin tumors in real-world clinical settings was not as high as that of using special data sets in the laboratory. However, there was no significant difference between the diagnostic capacity of Youzhi AI software and the average diagnostic capacity of dermatologists. It can provide assistant diagnostic decisions for dermatologists in the current state.
Factors associated with the incidence of ectopic pregnancy in women undergoing assisted reproductive treatment
Authors: Jin Xiao-Ying , Li Chao , Xu Wen , Liu Liu , Wei Min-Ling , Fei Hai-Yi , Li Jing , Zhou Feng , Zhang Song-Ying
Published: August 2020

Background

Ectopic pregnancy (EP) is a common complication in women undergoing assisted reproductive treatment, but the underlying causes for this remain unclear. This study aimed to explore factors affecting the incidence of EP in in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI).

Methods

This was a retrospective study on the incidence of EP in IVF/ICSI cycles between January 1, 2013 and December 31, 2017. Patient age, infertility diagnosis (tubal factor or not), primary or secondary infertility, type of cycle (frozen-thawed or fresh), type of embryo(s) transferred (cleavage embryo or blastocyst), number of embryos transferred (one, two, or three), previous history of EP, and endometrial combined thickness were analyzed to explore their relationships with the incidence of EP. Based on clinical typing results, the patients were divided into an EP group or a non-EP group. Categorical variables were analyzed using Chi-squared test or Fisher exact test. Logistic regression analysis was performed to explore their associations with the incidence of EP.

Results

The percentage of patients with primary infertility in EP group was significantly lower than that in non-EP group (31.3% vs. 46.7%, χ
2 = 26.032, P < 0.001). The percentage of patients with tubal infertility in EP group was also significantly higher than that in non-EP group (89.2% vs. 63.6%, χ
2 = 77.410, P < 0.001). The percentages of patients with transfer of cleavage-stage embryo or blastocyst (91.4% vs. 84.4%, χ
2 = 10.132, P = 0.001) and different endometrial combined thickness (ECT) (χ
2 = 18.373, P < 0.001) differed significantly between EP and non-EP groups. For patients who had a previous history of one to four EPs, the percentage of patients undergoing transfer of a cleavage-stage embryo was significantly higher in EP group than that in non-EP group (92.2% vs. 77.6%, χ
2 = 13.737, P < 0.001). In multivariate logistic regression analysis, tubal infertility was strongly associated with EP (adjusted odds ratio: 3.995, 95% confidence interval: 2.706–5.897, P < 0.001).

Conclusions

In IVF/ICSI cycles, transfer of a blastocyst-stage embryo, especially for patients with a previous history of EP, reduced the rate of EP. Tubal infertility was strongly associated with EP.
Cochlear Implant Therapy Improves the Quality of Life in Older Patients—A Prospective Evaluation Study
Authors: Issing Christian , Baumann Uwe , Pantel Johannes , Stöver Timo
Published: August 2020

Objective:

To determine the effects of cochlear implant (CI) hearing rehabilitation on quality of life in older patients (≥65 yr).

Study design:

Prospective observational study.

Setting:

Department of Oto-Rhino-Laryngology, Medical University Frankfurt/Main.

Patients:

Patients aged between 65 and 86 years who received unilateral CI therapy for the first time.

Intervention:

Unilateral cochlear implantation.

Main Outcome Measures:

In addition to audiological parameters, the World Health Organization Quality-of-Life Scale – old (WHOQL-OLD) was used to assess quality of life prior to surgery, at the time of first fitting of the audio processor (approx. 1 mo after surgery) and 6 months afterward. Dementia and depression were excluded using dementia detection test (DemTect) and geriatric depression scale.

Results:

Speech recognition improved significantly during the study period. Furthermore, the total WHOQL-OLD score showed a significant improvement of quality of life comparing the preoperative and the 6 months data (60.0 ± 15.7 to 66.8 ± 12.2 points) (p = 0.001). Only 6 months after surgery, comparable quality of life values were achieved compared to the corresponding population average of the same age group (67.96 ± 14.74 points). No statistically significant difference remained between the study group and the age-adjusted population average (p = 0.37).

Conclusion:

To achieve auditory rehabilitation, CI treatment in older patients can be strongly recommended, not only hearing rehabilitation, but also to improve quality of life.
Aligning Hearing Aid and Cochlear Implant Improves Hearing Outcome in Bimodal Cochlear Implant Users
Authors: Holtmann Laura Christine , Janosi Anna , Bagus Heike , Scholz Tim , Lang Stephan , Arweiler-Harbeck Diana , Hans Stefan
Published: August 2020

Objective:

Patients with unilateral deafness and residual hearing on the contralateral ear can benefit from a cochlear implant (CI) on one side and a hearing aid (HA) on the other. However, hearing improvement among these patients is heterogenous. Interindividual differences in bimodal benefit may be caused by a mismatch of CI and HA. The aim of this study was to clinically apply a HA fitting strategy and to evaluate hearing outcome with and without a dedicated bimodal fitting formula.

Study Design:

Prospective non-randomized study.

Setting:

Tertiary referral center.

Patients:

Twelve patients using a CI processor and a conventional HA were enrolled. Before and after the new HA had been adjusted to the patient and linked to the CI, pure-tone audiometry and localization tests were performed. Speech perception was determined in quiet and noise. Tests were repeated after 6 and 12 weeks. To evaluate the subjective listening comfort two questionnaires (Oldenburg Inventory and HISQUI19) were assessed.

Intervention:

Therapeutic.

Results Main outcome measure:

Word recognition in quiet, sentence recognition in noise. Speech perception in noise improved significantly: directed suppression of noise helped to segregate the target speech signal from a mixture of sounds or competing speakers. Evaluation of the questionnaires revealed a positive subjective hearing experience compared with patients’ initial settings of the devices.

Conclusion:

By linking CI and HA hearing and speech perception can be improved. However, good counselling at the outset is essential to obtain enhanced outcome.
Posttraumatic Cranial Suture Diastasis in Pediatric Temporal Bone Fractures
Authors: Reeve Nathaniel H. , Kahane Jacob B. , Miller Jordan , Cross Chad , Young Allen , Ng Matthew
Published: August 2020

Objective:

Only a handful of case reports exist describing posttraumatic sutural diastasis in the calvarium and none report concurrent temporal bone involvement. We aim to describe diastasis along the temporal bone suture lines in the setting of temporal bone trauma and to identify clinical sequelae.

Study Design:

Retrospective case review.

Setting:

Tertiary Level 1 trauma center.

Patients:

Forty-four patients aged 18 and younger who suffered a temporal bone fracture from 2013 to 2018 were identified. Diastasis and diastasis with displacement at the occipitomastoid, lambdoid, sphenosquamosal and petro-occipital sutures, and synchondroses were determined.

Main Outcome Measures:

The presence of temporal bone suture and synchondrosal diastasis following temporal bone trauma. Diastasis was defined as sutural separation of a distance greater than 1 mm in comparison to the contralateral side.

Results:

Using our diastasis diagnostic criteria, diastasis occurred in 41.5% of temporal bone fractures. Transverse fracture types were significantly associated with diastasis (p ≤ 0.001). Lower Glasgow Coma Scale (GCS) and loss of consciousness (LOC) were associated with the presence of diastasis with displacement and diastasis (p = 0.034 and p = 0.042, respectively). Otic capsule violation was more common in fractures with diastasis but did not reach statistical significance. There were two cases of cerebrospinal fluid otorrhea and three deaths in cases that featured diastasis.

Conclusion:

Our findings indicate that diastasis is a positive predictor for higher disruptive force injuries and more severe outcomes and complications. Posttraumatic temporal bone suture diastasis may represent a separate clinico-pathologic entity in addition to the usual temporal bone fracture classification types.
Outcomes and Safety of Blenderized Tube Feedings in Pediatric Patients
Authors: Kernizan Daphney , Mintz Daria , Colin Michele , Lee Melanie , Yoakam Lindsay , Chen Yen Ping , Iofel Elizaveta , Koniaris Soula , Weidner Melissa
Published: August 2020

Introduction:

Recently, significant interest from families and healthcare providers has arisen to use blenderized tube feedings (BTF). Although many institutions are providing this nutritional option, literature documenting outcomes and safety is lacking.

Methods:

A retrospective chart review was performed on pediatric patients receiving BTF at Rutgers‐Robert Wood Johnson University Hospital between January 2013 and April 2017. Demographic data and dietary information before and after BTF were collected. Reasons for diet initiation, symptoms, and anthropometrics were recorded. Adverse events and outcomes were assessed through physician documentation and relevant medication changes.

Results:

Thirty‐five patients (24 boys) received BTF. Age at initiation of BTF ranged from 1 to 19 years (mean 8.3 +/− 5.8 [SD] years). Length of follow‐up ranged from 1 to 45 months (mean 15 +/− 12.2 months). The most common reason for starting BTF was gastroesophageal reflux disease (GERD) (N = 32). Almost all patients were on medications for GERD, constipation, or gastrointestinal dysmotility before starting BTF (N = 33). Majority of patients had improvement in relevant symptoms (N = 20); 13 of 33 patients on gastrointestinal medications were able to wean or stop medication(s). BMI z scores did not differ before and after BTF initiation (P = 0.558). No serious life‐threatening adverse events were found.

Conclusions:

Our data suggest that BTF is a safe dietary intervention that may improve gastrointestinal symptoms in pediatric patients. Further prospective studies are needed to compare safety and efficacy of BTF and commercial formulas in pediatric patients.
Feasibility Study of a New Magnetic Resonance Imaging Mini-capsule Device to Measure Whole Gut Transit Time in Paediatric Constipation
Authors: Sharif Hayfa , Abrehart Nichola , Hoad Caroline L. , Murray Kathryn , Perkins Alan C. , Smith Murray , Gowland Penny A. , Spiller Robin C. , Harris Roy , Kirkham Sian , Loganathan Sabarinathan , Papadopoulos Michalis , Frost Kate , Devadason David , Marciani Luca
Published: August 2020

Objective:

In England, 27,500 children are referred annually to hospital with constipation. An objective measure of whole gut transit time (WGTT) could aid management. The current standard WGTT assessment, the x-ray radiopaque marker (ROM) test, gives poor definition of colonic anatomy and the radiation dose required is undesirable in children. Our objective was to develop an alternative magnetic resonance imaging (MRI) WGTT measure to the x-ray ROM test and to demonstrate its initial feasibility in paediatric constipation.

Methods:

With the Nottingham Young Person's Advisory Group we developed a small (8 × 4 mm), inert polypropylene capsule shell filled with MRI-visible fat emulsion. The capsule can be imaged using MRI fat and water in-phase and out-of-phase imaging. Sixteen patients with constipation and 19 healthy participants aged 7 to 18 years old were recruited. Following a common ROM protocol, the participants swallowed 24 mini-capsules each day for 3 days and were imaged on days 4 and 7 using MRI. The number of successful studies (feasibility) and WGTT were assessed. Participants’ EuroQoL Visual Analogue Scale were also collected and compared between the day before the taking the first set of mini-capsules to the day after the last MRI study day.

Results:

The mini-capsules were imaged successfully in the colon of all participants. The WGTT was 78 ± 35 hours (mean ± standard deviation) for patients, and 36 ± 16 hours, P < 0.0001 for healthy controls. Carrying out the procedures did not change the EuroQoL Visual Analogue Scale scores before and after the procedures.

Conclusions:

Magnetic Resonance Imaging in Paediatric Constipation was a first-in-child feasibility study of a new medical device to measure WGTT in paediatric constipation using MRI. The study showed that the new method is feasible and is well tolerated.
Clinical Criteria Can Identify Children With Osteopenia in Newly Diagnosed Crohn Disease
Authors: Ronel Naama , Tzion Raffi Lev , Orlanski‐Meyer Esther , Shteyer Eyal , Guz‐Mark Anat , Assa Amit , Strich David , Turner Dan , Ledder Oren
Published: August 2020

Objectives:

Chronic inflammation of Crohn disease (CD) is associated with reduced bone mineral density (BMD). As bone mass is almost exclusively accrued during childhood, early recognition of osteopenia is especially important in pediatric CD. We aimed to identify variables associated with osteopenia to guide dual‐energy X‐ray absorptiometry (DXA) scan screening to those who most need it.

Methods:

This was a retrospective inception cohort study of children newly diagnosed with CD, and routinely referred to DXA scans. Demographic and explicit clinical data were recorded along with whole‐body less head BMD, adjusted for age, sex, and height by z‐scores.

Results:

Of the 116 included children (mean age 13 ± 3.1 years, 67 [58%] boys, mean body mass index [BMI] 16.7 ± 2.6), 63 (54%) had normal BMD (z‐score > −1) or borderline osteopenia (−1 ≥ z‐score > −2) and 53 (46%) had osteopenia (z‐score ≤ −2). Osteopenia was associated with lower BMI z‐score (−0.8 ± 1.2 vs −1.8 ± 1.1, P < 0.001) and higher PCDAI (33.7 ± 15.2 vs 25.7 ± 16.5; P = 0.009) than those with BMD z‐score >−2. In total, 59% of children with BMI z‐score <−0.5 had moderate‐severe osteopenia and only 18% of those with higher z‐scores. Multivariate logistic regression identified BMI z‐score as the sole risk factor (OR 1.28 [95% CI 1.08–1.52], P = 0.005). BMI z‐score ≥−0.5 excludes osteopenia with a sensitivity 87%, specificity 49%, NPV 82%, and PPV 59%.

Conclusions:

Osteopenia was found in nearly half of children with newly onset CD. BMI z‐score <−0.5 should prompt referral to DXA screening.
Autoantibodies and Donor-specific Antibodies are Associated With Graft Dysfunction in Pediatric Liver Transplantation
Authors: Saelens Emma Monique , Van Biervliet Stephanie , Vande Velde Saskia , Van Winckel Myriam , Rogiers Xavier , Vanlander Aude , Daniëls Liesbeth , Bonroy Carolien , De Bruyne Ruth M.L.
Published: August 2020

Objectives:

Autoantibodies (AAb) and donor-specific HLA antibodies (DSA) are frequently present in pediatric liver transplant (LT) recipients. Their clinical significance remains incompletely understood. We aimed to investigate the prevalence of serum AAb and DSA in pediatric LT recipients and its correlation with patient characteristics and histological and biochemical parameters.

Methods:

We retrospectively reviewed the data from 62 pediatric LT patients in follow-up at Ghent University Hospital between January 2007 and February 2018. Blood samples with AAb measurement were taken systematically, liver biopsies (LB) were performed on clinical indication.

Results:

AAb were detected in 27 (43.3%) patients, with antinuclear antibodies (ANA) being the most frequently (24%) encountered AAb. There was an association between AAb positivity and female gender (P = 0,032) and deceased donor LT (P = 0,006). Patients with positive AAb underwent a higher number of LB during their follow-up (P < 0,001), and an association was found with the presence of nonspecific histologic alterations (P = 0,032) in the absence of de novo autoimmune hepatitis. Positive AAb were also associated with higher alkaline phosphatase (P < 0,001), ALT (P < 0,001), AST (P < 0,001), γ-GT (P = 0,001), IgG (P = 0,011) and lower albumin (P = 0,029). Fourteen out of 50 (28%) patients were DSA-positive, mostly anti-HLA class II. DSA positivity was associated with T-cell-mediated rejection (P = 0,019), higher total (P = 0,033), and direct (P = 0,012) bilirubin and γ-GT (P < 0,001).

Conclusions:

The presence of AAb and DSA is associated with histological and biochemical parameters of graft dysfunction. Larger prospective studies are warranted to investigate the causal relationships between AAb and DSA development and outcome parameters post pediatric LT.
Optimizing Nurse Engagement
Authors: Holskey Michele Price , Rivera Reynaldo R.
Published: August 2020

Nurse leaders seek effective strategies to engage nurses in decision-making when striving for clinical excellence. When leaders cultivate safe environments, nurses are encouraged to discover new knowledge and innovations. In our institution, nurse leaders designed a systematic guide using Liberating Structures to empower nurses to develop a professional practice model.
Airinemes: thin cellular protrusions mediate long-distance signalling guided by macrophages
Authors: Eom Dae Seok
Published: August 2020

Understanding the mechanisms of cell-to-cell communication is one of the fundamental questions in biology and medicine. In particular, long-range signalling where cells communicate over several cell diameters is vital during development and homeostasis. The major morphogens, their receptors and intracellular signalling cascades have largely been identified; however, there is a gap in our knowledge of how such signalling factors are propagated over a long distance. In addition to the diffusion-based propagation model, new modalities of disseminating signalling molecules have been identified. It has been shown that cells can communicate with direct contact through long, thin cellular protrusions between signal sending and receiving cells at a distance. Recent studies have revealed a type of cellular protrusion termed ‘airinemes’ in zebrafish pigment cell types. They share similarities with previously reported cellular protrusions; however, they also exhibit distinct morphology and features. Airinemes are indispensable for pigment pattern development by mediating long-distance Delta-Notch signalling between different pigment cell types. Notably, airineme-mediated signalling is dependent on skin-resident macrophages. Key findings of airineme-mediated intercellular signalling in pattern development, their interplay with macrophages and their implications for the understanding of cellular protrusion-mediated intercellular communication will be discussed.
Natural barriers: waterfall transit by small flying animals
Authors: Ortega-Jimenez Victor M. , Herbst Eva C. , Leung Michelle S. , Dudley Robert
Published: August 2020

Waterfalls are conspicuous geomorphological features with heterogeneous structure, complex dynamics and multiphase flows. Swifts, dippers and starlings are well-known to nest behind waterfalls, and have been reported to fly through them. For smaller fliers, by contrast, waterfalls seem to represent impenetrable barriers, but associated physical constraints and the kinematic responses of volant animals during transit are unknown. Here, we describe the flight behaviour of hummingbirds (the sister group to the swifts) and of various insect taxa as they fly through an artificial sheet waterfall. We additionally launched plastic balls at different speeds at the waterfall so as to assess the inertial dependence of sheet penetration. Hummingbirds were able to penetrate the waterfall with reductions in both their translational speed, and stroke amplitude. The body tilted more vertically and exhibited greater rotations in roll, pitch and yaw, along with increases in tail spread and pitch. The much smaller plastic balls and some flies moving at speeds greater than 2.3 m s−1and 1.6 m s−1, respectively, also overcame effects of surface tension and water momentum and passed through the waterfall; objects with lower momentum, by contrast, entered the sheet but then fell along with the moving water. Waterfalls can thus represent impenetrable physical barriers for small and slow animal fliers, and may also serve to exclude both predators and parasites from nests of some avian taxa.
Colorimetric Test for Fast Detection of SARS-CoV-2 in Nasal and Throat Swabs
Authors: Della Ventura Bartolomeo , Cennamo Michele , Minopoli Antonio , Campanile Raffaele , Bolletti Censi Sergio , Terracciano Daniela , Portella Giuseppe , Velotta Raffaele
Published: August 2020

Mass testing is fundamental to face the pandemic caused by the coronavirus SARS-CoV-2 discovered at the end of 2019. To this aim, it is necessary to establish reliable, fast and cheap tools to detect viral particles in biological material so to identify the people capable to spread the infection. We demonstrate that a colorimetric biosensor based on gold nanoparticle (AuNP) interaction induced by SARS-CoV-2 lends itself as an outstanding tool for detecting viral particles in nasal and throat swabs. The extinction spectrum of a colloidal solution of multiple viral-target gold nanoparticles – AuNPs functionalized with antibodies targeting three surface proteins of SARS-CoV-2 (spike, envelope and membrane) – is redshifted in few minutes when mixed to a solution containing the viral particle. The optical density of the mixed solution measured at 560 nm was compared to the threshold cycle (Ct) of a Real Time-PCR (gold standard for detecting the presence of viruses) finding that the colorimetric method is able to detect very low viral load with a detection limit approaching that of RT-PCR. Since the method is sensitive to the infecting viral particle rather than to its RNA, the achievements reported here open new perspective not only in the context of the current and possible future pandemics, but also in microbiology as the biosensor proves itself to be a powerful though simple tool for measuring the viral particle concentration.
Mycobacterium tuberculosis whole genome sequence data support repurposing antileprosy antibiotic as antituberculosis
Authors: Saad Jamal , Gallou Jenny , Brieu Nathalie , Drancourt Michel , Baron Sophie Alexandra
Published: August 2020

Background

We implanted WGS as the routine method to profile the antibiotic susceptibility of M. tuberculosis isolates focusing on in silico resistance to antileprosy drugs that we recently proposed to reposition for the treatment of pulmonary tuberculosis.

Methods

We prospectively performed WGS of 112 M. tuberculosis isolates recovered from respiratory tract samples of 106 patients diagnosed with pulmonary tuberculosis between 2017 and 2019 and defined their antibiotic susceptibility profile to 17 antibiotics including antileprotics drugs.

Results

We incidentally observed 08 sequence variations in 07 genes, specific to seven sublineages. Altogether, we observed 09 (8%) rifampicin-resistant, 05 (4.4%) multidrug-resistant and 02 (1.7%) extensively-drug resistant isolates; whereas only one isolate exhibited in silico resistance to clofazimine.

Conclusion

These results support repurposing of antileprosis antibiotics as antituberculosis; and offer new targets for genotyping M. tuberculosis.
Study of Coronavirus Impact on Parisian Population from April to June using Twitter and Text Mining Approach
Authors: Chire Saire Josimar E. , Cruz Jimy Frank Oblitas
Published: August 2020

The fast spreading of coronavirus name covid19, generated the actual pandemic forcing to change daily activities. Health Councils of each country promote health policies, close borders and start a partial or total lockdown. One of the first countries in Europe with high impact was Italy. Besides at the end of April, one country with a shared border was on the top of 10 countries with more total cases, then France started with its own battle to beat coronavirus. This paper studies the impact of coronavirus in the poopulation of Paris, France from April 23 to June 18, using Text Mining approach, processing data collected from Social Network and using trends related of searching. First finding is a decreasing pattern of publications/interest, and second is related to health crisis and economical impact generated by coronavirus.
Invasion performance-similarity found among multiple cell systems
Authors: Prakash Om
Published: August 2020

Understanding of inter-system behavior develops biologically relevant intuition for drug repositioning as well as other biological research. But combining all the possible genes interactions into a system, and furthermore comparisons of multiple systems are a challenge on time ground with feasible experiments. In present study, 64 cell lines from 11 different organs were compared for their invasion performance. RNA expressions of 23 genes were used to create systems artificial neural network (ANN) models. ANN models were prepared for all 64 cell lines and observed for their invasion performance through network mapping. The resulted cell line clusters bear feasible capacity to perform experiments for biologically relevant research motivations as drug repositioning and selective targeting etc.; and can be used for analysis of invasion related aspects.
Abnormal Upregulation of Cardiovascular Disease Biomarker PLA2G7 Induced by Proinflammatory Macrophages in COVID-19 patients
Authors: Li Yang , Jiang Yongzhong , Zhang Yi , Li Naizhe , Yin Qiangling , Liu Linlin , Lv Xin , Liu Yan , Li Aqian , Fang Bin , Li Jiajia , Ye Hengping , Yang Gang , Cui Xiaoxian , Liu Yang , Qu Yuanyuan , Li Chuan , Li Jiandong , Li Dexin , Wang Shiwen , Gai Zhongtao , Zhan Faxian , Liang Mifang
Published: August 2020

BACKGROUND

Coronavirus disease 2019 (COVID-19) triggers distinct patterns of pneumonia progression with multiorgan disease, calling for cell- and/or tissue-type specific host injury markers.

METHODS

An integrated hypothesis-free single biomarker analysis framework was performed on nasal swabs (n = 484) from patients with COVID-19 in GSE152075. The origin of candidate biomarker was assessed in single-cell RNA data (GSE145926). The candidate biomarker was validated in a cross-sectional cohort (n = 564) at both nucleotide and protein levels.

RESULTS

Phospholipase A2 group VII (PLA2G7) was identified as a candidate biomarker in COVID-19. PLA2G7 was predominantly expressed by proinflammatory macrophages in lungs emerging with progression of COVID-19. In the validation stage, PLA2G7 was found in patients with COVID-19 and pneumonia, especially in severe pneumonia, rather than patients suffered mild H1N1 influenza infection. Up to 100% positive rates of PLA2G7 were positively correlated with not only viral loads in patients with COVID-19 but also severity of pneumonia in non-COVID-19 patients. Although Ct values of PLA2G7 in severe pneumonia was significantly lower than that in moderate pneumonia (P = 7.2e-11), no differences were observed in moderate pneumonia with COVID-19 between severe pneumonia without COVID-19 (P = 0.81). Serum protein levels of PLA2G7, also known as lipoprotein-associated phospholipase A2 (Lp-PLA2), were further found to be elevated and beyond the upper limit of normal in patients with COVID-19, especially among the re-positive patients.

CONCLUSIONS

We firstly identified and validated PLA2G7, a biomarker for cardiovascular diseases (CVDs), was abnormally enhanced in COVID-19 patients at both nucleotide and protein aspects. These findings provided indications into the prevalence of cardiovascular involvements seen in COVID-19 patients. PLA2G7 could be a hallmark of COVID-19 for monitoring disease progress and therapeutic response.

FUNDING

This study was supported by grants from China Mega-Projects for Infectious Disease (2018ZX10711001), National Natural Science Foundation of China (82041023).
Quantifying the efficiency of non-pharmaceutical interventions against SARS-COV-2 transmission in Europe
Authors: garchitorena Andres , Gruson Hugo , Cazelles Bernard , Roche Benjamin
Published: August 2020

Since the emergence of SARS-CoV-2, governments around the World have implemented a combination of public health responses based on non-pharmaceutical interventions (NPIs), with significant social and economic consequences. Though most European countries have overcome the first epidemic wave, it remains of high priority to quantify the efficiency of different NPIs to inform preparedness for an impending second wave. In this study, combining capture-recapture methods with Bayesian inference in an age-structured mathematical model, we use a unique European dataset compiled by the European Centre for Disease Control (ECDC) to quantify the efficiency of 24 NPIs and their combinations (referred to as public health responses, PHR) in reducing SARS-Cov-2 transmission rates in 32 European countries. Of 166 unique PHR tested, we found that median decrease in viral transmission was 74%, which is enough to suppress the epidemic. PHR efficiency was positively associated with the number of NPIs implemented. We found that bans on mass gatherings had the largest effect among NPIs, followed by school closures, teleworking, and stay home orders. Partial implementation of most NPIs resulted in lower than average response efficiency. This first large-scale estimation of NPI and PHR efficiency against SARS-COV-2 transmission in Europe suggests that a combination of NPIs targeting different population groups should be favored to control future epidemic waves.
Evolving Virulence? Decreasing COVID-19 Complications among Massachusetts Healthcare Workers: A Cohort Study
Authors: Lan Fan-Yun , Filler Robert , Mathew Soni , Iliaki Eirini , Osgood Rebecca , Bruno-Murtha Lou Ann , Kales Stefanos N.
Published: August 2020

The hypothesis of attenuating SARS-CoV-2 virulence has been raised. We examined the temporal distribution of COVID-19 complications (ER visits, hospitalization, intubation/code, and/or death) among healthcare workers in one system that applied uniform screening criteria throughout the research period, and found the complication rate significantly decreased after April 15, 2020.
MORPHIOUS: A Machine Learning Workflow to Naively Detect the Activation of Microglia and Astrocytes
Authors: Silburt Joseph , Aubert Isabelle
Published: August 2020

In cases of brain injury, degeneration and repair, defining microglia and astrocytic activation using cellular markers alone remains a challenging task. We developed MORPHIOUS, an unsupervised machine learning workflow that utilizes a one-class support vector machine to segment clusters of activated glia by only referencing examples of non-activated glia. Here, glial activation was triggered using focused ultrasound to permeabilize the hippocampal blood-brain barrier. Analyzing the hippocampal sections seven days later, MORPHIOUS identified two classes of microglia which showed characteristic activation features, including increases in ionized calcium-binding adapter molecule 1 expression, soma size, and de-ramification. MORPHIOUS was further used to identify clusters of activated astrocytes, which showed increased expression of glial fibrillary acidic protein and branching. Thus, by only referencing untreated glia morphologies, MORPHIOUS can identify diverse and novel manifestations of glial activation. This provides significant improvements for characterizing glial activation in cases of injury, neurodegeneration, and regeneration.
Learning can be detrimental for a parasitic wasp
Authors: Bertoldi Valeria , Rondoni Gabriele , Peri Ezio , Conti Eric , Brodeur Jacques
Published: August 2020

Animals have evolved the capacity to learn, and the conventional view is that learning allows individuals to improve foraging decisions. We describe a first case of maladaptive learning where a parasitoid learns to associate chemical cues from an unsuitable host, thereby re-enforcing a reproductive cul-de-sac (evolutionary trap).Telenomus podisiparasitizes eggs of the exotic stink bugHalyomorpha halysat the same rate as eggs of its coevolved host,Podisus maculiventris, but the parasitoid cannot complete its development in the exotic species. We hypothesized thatT. podisilearns to exploit cues from this non-coevolved species, thereby increasing unsuccessful parasitism rates. We conducted bioassays to compare the responses of naïvevs. experienced parasitoids on chemical footprints left by one of the two host species. Both naïve and experienced females showed a higher response to footprints ofP. maculiventristhan ofH. halys. Furthermore, parasitoids that gained an experience onH. halyssignificantly increased their residence time within the arena and the frequency of re-encounter with the area contaminated by chemical cues. Maladaptive learning in theT. podisi-H. halysassociation is expected to further decrease parasitoid reproductive success and have consequences for population dynamics of sympatric native and exotic host species.
Consequences of the divergence of Methionine AdenosylTransferase
Authors: Chouhan Bhanupratap Singh , Gade Madhuri H. , Martinez Desirae , Toledo-Patino Saacnicteh , Laurino Paola
Published: August 2020

Methionine adenosyltransferase (MAT), which catalyzes the biosynthesis of S-adenosylmethionine from L-methionine and ATP, is an ancient, highly conserved enzyme present in all three domains of life. Although the MAT enzymes of each domain are believed to share a common ancestor, the sequences of archaeal MATs show a high degree of divergence from the sequences of bacterial and eukaryotic MATs. However, the structural and functional consequences of this sequence divergence are not well understood. Here, we use structural bioinformatics analysis and ancestral sequence reconstruction to highlight the consequences of archaeal MAT divergence. We show that the dimer interface containing the active site, which would be expected to be well conserved across all three domains, diverged considerably between the bacterial/eukaryotic MATs and archaeal MATs. Furthermore, the characterization of reconstructed ancestral archaeal MATs showed that they probably had low substrate specificity which expanded during their evolutionary trajectory hinting towards the observation that all the modern day MAT enzymes from the three-kingdom probably originated from a common specific ancestor and then archaea MATs diverged in sequence, structure and substrate specificity. Altogether, our results show that the archaea MAT is an ideal system for studying an enzyme family which evolved to display high degrees of divergence at the sequence/structural levels and yet are capable of performing the same catalytic reactions as their orthologous counterparts.
In vivo Restricted-Diffusion Imaging (RDI) is sensitive to differences in axonal density in typical children and adults
Authors: Garic Dea , Yeh Fang-Cheng , Graziano Paulo , Dick Anthony Steven
Published: August 2020

Background

The ability to dissociate axonal densityin vivofrom other microstructural properties of white matter is important for the diagnosis and treatment of neurologic disease, and new methods to do so are being developed. We investigated one such method–restricted diffusion imaging (RDI)–to see whether it can more accurately replicate histological axonal density patterns in the corpus callosum (CC) of adults and children compared to diffusion tensor imaging (DTI), neurite orientation dispersion and density imaging (NODDI), and generalized q-sampling imaging (GQI) methods. To do so, we compared known axonal density patterns defined by histology to to diffusion-weighted imaging (DWI) scans of 840 healthy 20- to 40-year-old adults, and, in a replication and extension, to DWI scans of 129 typically developing 7-month-old to 18-year-old children and adolescents. Contrast analyses were used to to compare pattern similarities between thein-vivometric and previously-published histological density models. We found that RDI was effective at mapping axonal density of small (Cohen’sd= 2.60) and large fiber sizes (Cohen’sd= 2.84) in adults. The same pattern was observed in the developing sample (Cohen’sd= 3.09 and 3.78, respectively). Other metrics, notably NODDI’s intracellular volume fraction (ICVF), were also sensitive to differences in axonal density across the longitudinal axis of the CC. In conclusion, the study showed that RDI is effective at measuring axonal density of small and large axons in adults and children, with both single- and multi-shell acquisition DWI data. Its effectiveness and availability to be used on standard as well as advanced DWI acquisitions makes it a promising method in clinical settings.
The Temporal Statistics of Musical Rhythm across Western Genres: An Amplitude Modulation Phase Hierarchy Model
Authors: Daikoku Tatsuya , Goswami Usha
Published: August 2020

Statistical learning by the human brain plays a core role in the development of cognitive systems like language and music. Both music and speech have structured inherent rhythms, however the acoustic sources of these rhythms are debated. Theoretically, rhythm structures in both systems may be related to a novel set of acoustic statistics embedded in the amplitude envelope, statistics originally revealed by modelling children’s nursery rhymes. Here we apply similar modelling to explore whether the amplitude modulation (AM) timescales underlying rhythm in music match those in child-directed speech (CDS). Utilising AM-driven phase hierarchy modelling previously applied to infant-directed speech (IDS), adult-directed speech (ADS) and CDS, we test whether the physical stimulus characteristics that yield speech rhythm in IDS and CDS describe rhythm in music. Two models were applied. One utilized a low-dimensional representation of the auditory signal adjusted for known mechanisms of the human cochlear, and the second utilized probabilistic amplitude demodulation, estimating the modulator (envelope) and carriers using Bayesian inference. Both models revealed a similar hierarchically-nested temporal modulation structure across Western musical genres and instruments. Core bands of AM and spectral patterning matched prior analyses of IDS and CDS, and music showed strong phase dependence between slower bands of AMs, again matching IDS and CDS. This phase dependence is critical to the perception of rhythm. Control analyses modelling other natural sounds (wind, rain, storms, rivers) did not show similar temporal modulation structures and phase dependencies. We conclude that acoustic rhythm in language and music has a shared statistical basis.
Automated improvement of stickleback reference genome assemblies with Lep-Anchor software
Authors: Kivikoski Mikko , Rastas Pasi , Löytynoja Ari , Merilä Juha
Published: August 2020

We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.7 Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.
PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction
Authors: Liu Yuanlong , Teng Chong , Xia Rui , Meyers Blake C.
Published: August 2020

Phased secondary small interfering RNAs (phasiRNAs) constitute a major category of small RNAs in plants, but most of their functions are still poorly defined. Some phasiRNAs, known as trans-acting siRNAs, are known to target complementary mRNAs for degradation and to function in development. However, the targets or biological roles of other phasiRNAs remain speculative. New insights into phasiRNA biogenesis, their conservation, and their variation across the flowering plants continue to emerge due to the increased availability of plant genomic sequences, deeper and more sophisticated sequencing approaches, and improvements in computational biology and biochemical/molecular/genetic analyses. In this review, we survey recent progress in phasiRNA biology, with a particular focus on two classes associated with male reproduction: 21-nucleotide (accumulate early in anther ontogeny) and 24-nucloetide (produced in somatic cells during meiosis) phasiRNAs. We describe phasiRNA biogenesis, function, and evolution and define the unanswered questions that represent topics for future research.
Synthesis, crystal structure and Hirshfeld surface analysis of 1,7-dimethyl-5a,6,11a,12-tetrahydrobenzo[b]benzo[5,6][1,4]oxazino[2,3-e][1,4]oxazine
Authors: Çınar Emine Berrin , Yeşilbağ Semanur , Doğan Onur Erman , Ağar Erbil , Dege Necmi , Saif Eiad
Published: August 2020

Molecules of the title compound, C16H16N2O2, occupy special positions on the twofold rotation axes. The heterocyclic ring adopts a slightly twisted envelope conformation with one of the two junction carbon atoms as the flap. The mean planes through the two halves of the molecule form a dihedral angle of 72.01 (2)°. In the crystal, molecules are linked by pairs of C—H...O and N—H...C contacts into layers parallel to (100). H...H contacts make the largest contribution to the Hirshfeld surface (58.9%).