bluuebunny/crossref_metadata_2025 huggingface dataset:
Atypical Ductal Hyperplasia on Ultrasonography-Guided Vacuum-Assisted Biopsy of the Breast
Authors: Kim Ji Hee , Han Kyunghwa , Kim Min Jung , Moon Hee Jung , Yoon Jung Hyun , Park Vivian Youngjean , Kim Eun-Kyung
Published: June 2020

The purposes of this study are to evaluate the upgrade rate of atypical ductal hyperplasia (ADH) diagnosed with ultrasonography (US)-guided vacuum-assisted biopsy (VAB) to malignancy and to identify the factors behind the underestimation. We retrospectively reviewed the pathologic results of US-guided VAB of the breast. A total of 50 ADH lesions that were surgically excised or with more than 12 months of follow-up were included. The upgrade rate of ADH was determined by dividing the number of lesions that were proven malignant on surgical excision by the total number of ADH diagnosed on VAB. Clinical, radiologic, procedural, and pathologic variables were analyzed to identify the factors behind the underestimation. The upgrade rate of ADH was found to be 16.0% (8/50 lesions). In univariable and multivariable analyses, the upgrade rates of ADH did not significantly differ among variables. In a subgroup analysis, according to history of breast cancer, the upgrade rates of ADH were significantly lower for lesions of mass than for lesions of nonmass (0% [0/23 lesions] vs 28.6% [4/14 lesions], P = 0.015), and for lesions without calcifications than for lesions with calcifications (0% [0/22 lesions] vs 26.7% [4/15 lesions], P = 0.021) in the negative history subgroup. ADH lesions in masses or without calcifications in patients without a family or personal history of breast cancer were associated with low upgrade rates. Thus, we suggest that ADH with these features can be followed rather than surgically excised after US-guided VAB.
Saline-Air Hysterosalpingo–Contrast Sonography Is Equivalent to the Modified Hysterosalpingogram Following Hysteroscopic Sterilization
Authors: Luong Emerly , Ludwin Artur , Winter Thomas , Yaklic Jerome , Maxwell Rose A. , Bhagavath Bala , Lindheim Steven R.
Published: June 2020

Purpose

To estimate the diagnostic efficacy of saline-air hysterosalpingo–contrast sonography (SA-HyCoSy) compared with the modified hysterosalpingogram (mHSG) for confirmation of both coil location and tubal occlusion following hysteroscopic sterilization.

Methods

This study included 19 women who underwent both SA-HyCoSy and mHSG where 1 test was followed by the other. Sensitivity, specificity, and positive and negative predictive values for tubal occlusion against the mHSG were calculated for each fallopian tube by 2 independent interpreters. Interrater reliability was assessed using Cohen κ statistic. Procedure time and pain level by 11-point numeric rating scale of SA-HyCoSy and mHSG were also compared.

Results

Thirty-eight fallopian tubes were evaluated. Tubal occlusion was noted in 97.3% of tubes for both interpreters with the mHSG compared with 92.1% and 94.7% with SA-HyCoSy. The positive and negative predictive values for tubal occlusion were 100%/100% and 50%/33%, respectively, with an overall agreement of 97.4% and 95.7%, κ = 0.48, P < 0.01. Saline-air HyCoSy changed interpretation of coil insert location in 50% and 44.7% for each interpreter, being downgraded from optimal to satisfactory in 42.9% (9/21) and 36% (9/25) and upgraded to optimal in 58.8% (10/17) and 61.5% (8/13), respectively. There were no statistically significant differences in procedural time (7.5 vs 9.4 minutes, P > 0.05) or maximum pain scores (2.3 vs 3.1, P > 0.05) for the mHSG compared with SA-HyCoSy.

Conclusions

Our findings revealed a high degree of diagnostic accuracy with SA-HyCoSy for tubal occlusion, although coil location changed in nearly half of cases. Avoidance of radiation and patient convenience/compliance with SA-HyCoSy may outweigh the drawbacks.
Preoperative Axillary Ultrasound Helps in the Identification of a Limited Nodal Burden in Breast Cancer Patients
Authors: Luo Haiyu , Mo Yongqian , Zhong Jieyu , Zhang Yushen , Zhu Lizhang , Shi Xiaoxin , Chen Yun
Published: June 2020

Since the Z0011 trial, the clinical evaluation of axillary status has been redirected to predicting nodal tumor burden rather than nodal metastases. Our study aimed to evaluate the value of clinicopathological factors and axillary ultrasound (US) for the prediction of a high nodal burden (≥3 metastatic lymph nodes) in breast cancer patients. A total of 532 consecutive patients who underwent preoperative axillary US and subsequent surgery for clinical T1–2 breast cancer with a final pathologic analysis were included. Clinical and pathologic variables were retrospectively evaluated. Univariate and multivariate statistical analyses were performed to identify the variables that were associated with a high nodal burden. Among the 532 patients, 110 (20.7%) had a high axillary nodal burden and 422 (79.3%) had a limited nodal burden. The multivariate analysis showed that suspicious axillary US findings (P < 0.001), clinical T2 stage (P = 0.011), the presence of lymphovascular invasion (P < 0.001), and estrogen receptor positivity (P < 0.001) were significantly associated with a high nodal burden. Patients with negative axillary US findings seldom had a high nodal burden, with a negative predictive value of 93.0% (294/316). Patients with suspicious axillary US findings, clinical T2 stage, lymphovascular invasion, and estrogen receptor positivity are more likely to have a high nodal burden, which may provide additional information for the treatment plan of breast cancer patients. Preoperative axillary US helps identify a limited nodal burden in breast cancer patients and has implications for axillary lymph node dissection and adjuvant treatment.
Lung Ultrasonography as an Accurate Diagnostic Method for the Diagnosis of Community-Acquired Pneumonia in the Elderly Population
Authors: Buda Natalia , Hajduk Adam , Jaworska Joanna , Zdrojewski Zbigniew
Published: June 2020

Community-acquired pneumonia (CAP) is one of the most common causes of both hospitalization and death in elderly patients. The chest x-ray (CXR) is nowadays still the imaging method of choice for patients suspected of having pneumonia. However, the sensitivity of CXR, particularly bedside chest radiography, is relatively low. Chest computed tomography, the procedure of higher precision, cannot be conducted routinely for safety, organizational, and economic reasons. Thus, lung ultrasonography (LUS) could be the most accurate diagnostic tool for CAP in the geriatric population.

This prospective observational study involving 191 elderly patients (older than 65 years), hospitalized because of suspicion of pneumonia, aimed at comparing the diagnostic accuracy of LUS and CXR to final clinical diagnosis. During the first hours of hospitalization, both CXR and LUS were conducted. At discharge, pneumonia diagnosis was confirmed in 115 patients (60.2% of the study group). Chest x-ray revealed inflammatory lesions in only 65 patients (34% of the study group, 56.5% of the patients with final pneumonia diagnosis), whereas LUS was positive in 114 patients (59.7% of the study group, 99% of the patients with final pneumonia diagnosis). Sensitivity and specificity of LUS in pneumonia diagnosis were, respectively, 99% and 98.7%, whereas CXR sensitivity and specificity were 56.5% and 100%, respectively. The positive and negative predictive values of LUS were 99% and 98.7%, whereas, for CXR, they were 100% and 60.3%, respectively.

Lung ultrasonography proved to be more effective at revealing pulmonary inflammatory lesions as compared with CXR in elderly patients suspected of pneumonia.
Evaluating the Effects of COVID-19 on Plastic Surgery Emergencies
Authors: Hassan Kareem , Prescher Hannes , Wang Frederick , Chang David W. , Reid Russell R.
Published: June 2020

Background

The COVID-19 crisis has brought many unique challenges to the health care system. Across the United States, social distancing measures have been put in place, including stay-at-home (SAH) orders, to combat the spread of this infection. This has impacted the type and volume of traumatic injuries sustained during this time. Meanwhile, steps have been taken in our health care system to assure that adequate resources are available to maintain a high standard of patient care while recognizing the importance of protecting health care providers. Using comparative data, we aim to describe the trends in traumatic injuries managed by our plastic surgery service and detail the changes in consultation policies made to minimize provider exposure.

Methods

A retrospective chart review was performed of all plastic surgery emergencies at our institution during the 3 weeks preceding the issuance of SAH orders in Chicago and the 3 weeks after. The electronic medical record was queried for patient age, type and mechanism of injury, location where injury was sustained, presence of domestic violence, length of inpatient hospital stays, and treatment rendered. The two 3-week periods were then comparatively analyzed to determine differences and trends in these variables and treatment rendered. The 2 periods were then comparatively analyzed to determine differences and trends in these variables.

Results

There was a significant decrease in trauma consults since the issuance of SAH (88 pre-SAH vs 62 post-SAH) with a marked decrease in trauma-related hand injuries. There was an increase in the percentage of assault-related injuries including those associated with domestic violence, whereas there was an overall decrease in motor vehicle collisions. There was no notable change in the location where injuries were sustained. Significantly fewer patients were seen by house staff in the emergency room, whereas those requiring surgical intervention were able to receive care without delay.

Conclusions

Stay-at-home orders in Chicago have impacted traumatic injury patterns seen by the Section of Plastic and Reconstructive Surgery at a level I Trauma Center. Safe and timely care can continue to be provided with thorough communication, vigilance, and guidance from our colleagues.
The Simplified Nasal Septal Deviation Evaluation System and Nasal Obstruction Symptom Evaluation Scale Correlation
Authors: Şahin Bayram , Çomoğlu Şenol , Aydemir Levent , Pamuk Saim , Keleş Türel Meryem Nesil
Published: June 2020

Nasal septal deviation (NSD) is a common condition in otorhinolaryngology practice. The aim of this study was to investigate the possible relationship between localization and severity of NSD, and related complaints as well as to suggest a simplified assessment method for NSD. Seventy-five patients who complaint nasal obstruction were enrolled this study. The affected nasal cavity was divided into 4 separate sections as follows: antero-superior (AS), antero-inferior (AI), postero-superior (PS), and postero-inferior (PI). Each section was determined according to its relationship to the both superior edge and head of the inferior turbinate. The NSD score was calculated separately for each section according to its relationship with lateral nasal wall. The NSD-related complaints were assessed via the Nasal Obstruction Symptom Evaluation (NOSE) scale. There were 42 male and 33 female patients, with an age range of 18 to 44 years. The mean NSD score was 2.18 ± 0.63 for AS section, 1.92 ± 0.67 for AI section, 1.54 ± 0.70 for PS section, and 1.18 ± 0.60 for PI section. The mean total NSD score was 6.84 ± 1.97 while the mean NOSE score was 12.5 ± 5.11. There was a strong positive correlation between total NSD and NOSE scores when the NSD score was 6 or more (r = 0.9556). This correlation was also present when each section was evaluated separately. The strongest correlation was detected for AS section deviations. Our septal classification system provides a simple and effective evaluation of NSDs. The NSDs which affect internal valve are more related with nasal obstruction and patients’ discomfort.
Quantification of Nasal Septal Deviation With Computed Tomography Data
Authors: Denour Erika , Roussel Lauren O. , Woo Albert S. , Boyajian Michael , Crozier Joseph
Published: June 2020

Background:

Despite extensive literature on the classification and management of nasal septal deviation (NSD) for preoperative planning, standardized objective measures to evaluate the NSD severity remains challenging. In this study, we quantitatively analyzed NSD to determine the most predictive two-dimensional (2D) computed tomography (CT)-landmark for overall three-dimensional (3D) septal morphology derived from nasal airway segmentation.

Methods:

A retrospective study was conducted at a large academic center. One hundred four patients who underwent CT scans of the face were selected from a computer imaging database. Demographic variables were screened to ensure an equal number of men and women in different age groups. Digital Imaging and Communications in Medicine files were imported for 3D nasal cavity segmentation using 3D Slicer software. A volumetric analysis was performed to determine 3D NSD ratios. These values were compared to previously reported methods of obtaining objective 2D NSD measures using OsiriX and MATLAB software. Maximum deviation values were calculated using OsiriX, while the root mean square values were retrieved using MATLAB. Deviation area and curve to line ratios were both quantified using OsiriX and MATLAB.

Results:

The data set consisted of 52 men and 52 women patients aged 20 to 100 years (mean = 58 years, standard deviation = 23 years). There was a strong correlation between 3D NSD ratio and maximum deviation (r = 0.789, P < 0.001) and deviation area (r = 0.775, P < 0.001). Deviation area (r = 0.563, P < 0.001), root mean square (r = 0.594, P < 0.001), and curve to line ratio (r = 0.470, P < 0.001) had a positive correlation of moderate strength. The curve to line ratio was not significant (r = 0.019, P = 0.85).

Conclusions:

The 2D CT-based NSD landmarks maximum deviation and deviation area were the most predictive of the severity of NSD from 3D nasal cavity segmentation. We present a robust open-source method that may be useful in predicting the severity of NSD in CT images.
Evaluation of the Nasopharyngeal Cannula Use After Orthognathic Surgery: Permeability of the Nasal Airways and Discomfort of the Patient With Cleft Lip and Palate
Authors: Jordão Maycon Rafael Zanoni , Valente Ana Carolina Boneti , Mello Marina de Almeida Barbosa , Silveira Juliana Specian Zabotini da , Moura Junior Hélcio José de , Yamashita Renata Paciello , Yaedú Renato Yassutaka Faria
Published: June 2020

It is believed that the use of the nasopharyngeal cannula can maintain the patent upper airway in the immediate post-operative period of orthognathic surgery. The present study is a randomized clinical trial with the objective of evaluating the difference in the use of the nasopharyngeal cannula in the post-operative period of orthognathic surgery with respect to permeability and discomfort. The sample was composed of 26 individuals with repaired cleft lip and palate randomly distributed in 2 groups with and without nasopharyngeal cannula. The evaluation was composed by Visual Analogue Scale (VAS), test with Altman mirror in 4 pre-operative periods, 6, 24, 30 hours after the operation. Rhinomanometry was also performed, a flow- pressure technique in 2 distinct moments, 6 and 24 hours after surgery. As a result, greater discomfort, greater obstruction as well as a reduction in the area of bilateral minimum nasal cross-section (ASTM) and increased resistance in the group with nasopharyngeal cannula are observed. In the intra-group comparison with the lowest ASTM values, the test group showed a significant difference between the first and the second moments (P = 0.001). It can be concluded that the nasopharyngeal cannula contributes to increase discomfort, worsens airway permeability by decreasing ASTM and increasing nasal resistance. Regarding the length of stay of the nasopharyngeal cannula, it can be said that from 6 hours onwards it does not contribute to the reduction of discomfort, airway permeability and assist in hemostasis.
How to Produce Cheap and Easy Custom-Made Sterilizable Filtering Facepiece 2/3 Masks for Healthcare Providers During Pandemic COVID-19 Emergency
Authors: Vellone Valentino , Marianetti Tito M. , Di Renzo Luca , Ricci Alessandro , Bocciolesi Federico , Ramieri Valerio
Published: June 2020

On January 8, 2020, a novel coronavirus was officially announced as the causative pathogen of coronavirus disease (COVID-19) by the Chinese Center for Disease Control and Prevention.

On February 26, COVID-19 has been recognized in 34 countries, with a total of 80,239 laboratory-confirmed patients and 2700 deaths.

Protecting healthcare workers from infectious hazards is paramount to ensuring their safety in delivering health care.

In addition, being able to protect healthcare workers, constituting the front-line response against high-threat respiratory pathogens, such as severe acute respiratory syndrome coronavirus 2, is important for reducing secondary transmission in healthcare-associated outbreaks.

Authors present a simple, reliable, and cheap protocol to produce a custom-made sterilizable filtering facepiece 2/3 masks for healthcare providers during pandemic COVID-19 emergency.
Nonomuraea typhae sp. nov., an endophytic actinomycete isolated from the root of cattail pollen (Typha angustifolia L.)
Authors: Peng Chenghui , Zhuang Xiaoxin , Wang Zhiyan , Gao Congting , Zhao Junwei , Song Jia , Liu Chongxi , Shen Yue
Published: June 2020

A novel endophytic actinomycete, designated strain p1410T, was isolated from the root of cattail pollen (Typha angustifolia L.) and characterized using a polyphasic approach. The strain had morphological characteristics and chemotaxonomic properties identical to those of members of the genus

Nonomuraea

. It produced spiral chains of spores on aerial mycelium as well as forming a pseudosporangium. Whole-cell hydrolysates contained meso-diaminopimelic acid, glucose, ribose and madurose. The menaquinones detected were MK-9(H2), MK-9(H4) and MK-9(H0). The major fatty acids were 10-methyl C17 : 0, iso-C16 : 0 and C17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol mannoside and an unknown glycolipid. The DNA G+C content of the draft genome sequence, consisting of 11.4 Mbp, was 70.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain p1410T belongs to the genus

Nonomuraea

with the highest sequence similarity to

Nonomuraea candida

HMC10T (98.6 %), but phylogenetically clustered with

Nonomuraea endophytica

YIM 65601T (98.4 %) and

Nonomuraea longicatena

NRRL 15532T (98.3 %). Based on its phenotypic characteristics, DNA–DNA relatedness and average nucleotide identity, the strain is considered to represent a novel species of the genus

Nonomuraea

, for which the name Nonomuraea typhae sp. nov. is proposed. The type strain is p1410T (=CCTCC AA 2019044T=JCM 33461T).
Sphingomonas segetis sp. nov., isolated from spinach farming field soil
Authors: Lee Jae-Chan , Whang Kyung-Sook
Published: June 2020

A Gram-stain-negative bacterium, designated strain YJ09T, was isolated from spinach farming field soil at Shinan in the Republic of Korea. Cells of strain YJ09T were found to be strictly aerobic, non-motile, non-spore-forming creamy-yellow rods which can grow at 20–37 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–0.5 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain YJ09T belongs to the genus

Sphingomonas

with high sequence similarities to

Sphingomonas parvus

GP20-2 T (98.0 %),

Sphingomonas agri

HKS-06T (97.7 %) and

Sphingomonas lutea

JS5T (97.4 %). The results of phylogenetic analysis indicated that strain YJ09T formed a distinct phyletic line in the genus

Sphingomonas

and the results of DNA–DNA relatedness studies demonstrated that strain YJ09T could be separated from its closest relatives in the genus

Sphingomonas

. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, an unidentified phospholipid and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18:1
 ω7c, C16 
: 0 and C16:1
 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of this novel isolate was 65.9 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ09T is considered to represent a novel species in the genus

Sphingomonas

, for which the name Sphingomonas segetis sp. nov. is proposed. The type strain is YJ09T (=KACC 19551T=NBRC 113247T).
COVID-19: A model correlating BCG vaccination to protection from mortality implicates trained immunity
Authors: Green Cameron M. , Fanucchi Stephanie , Dominguez-Andres Jorge , Fok Ezio T. , Moorlag Simone J.C.F.M. , Negishi Yutaka , Joosten Leo A. B. , Netea Mihai G. , Mhlanga Musa M.
Published: June 2020

We use a data quality model to demonstrate that BCG vaccination is correlated with protection from death from COVID19

From a mechanistic perspective, BCG is well described to elicit its protective non-specific effects through the process of trained immunity.

Therapeutically enhancing trained immunity may therefore be an important mechanism in protection from the lethal effects of COVID19
Covid-19 Epidemiological Factor Analysis: Identifying Principal Factors with Machine Learning
Authors: Dolgikh Serge
Published: June 2020

Based on a subset of Covid-19 Wave 1 cases at a time point near TZ+3m (April, 2020), we perform an analysis of the influencing factors for the epidemics impacts with several different statistical methods. The consistent conclusion of the analysis with the available data is that apart from the policy and management quality, being the dominant factor, the most influential factors among the considered were current or recent universal BCG immunization and the prevalence of smoking.
The attitudes, perceptions and experiences of medical school applicants following the closure of schools and cancellation of public examinations in 2020 due to the COVID-19 pandemic
Authors: Woolf Katherine , Harrison Dave , McManus I C
Published: June 2020

Objective

To describe medical applicants’ experiences of education and their views on changes to medical school admissions, including the awarding of calculated grades, following the 2020 closure of schools and universities, and the cancellation of public examinations in the United Kingdom due to the COVID-19/coronavirus pandemic. To understand how applicants from diverse social backgrounds might differ in these regards.

Design

Cross-sectional questionnaire study forming part of the longitudinal United Kingdom Medical Applicant Cohort Study (UKMACS).

Setting

United Kingdom medical school admissions.

Participants

2887 participants (68% female; 64% with at least one degree-educated parent; 63% with at least one parent in the highest socioeconomic group) completed an online questionnaire between 8thand 22ndApril 2020. To be invited to complete the questionnaire, participants had to have registered to take the University Clinical Admissions Test (UCAT) in 2019 and to have agreed to be invited to take part in the study, or they needed to have completed one or more previous UKMACS questionnaires. They also need to have been seriously considering applying to study medicine in the UK for entry in 2020 between May and October 2019, and be resident in the UK or Islands/Crown Dependencies.

Main outcome measures

Views on calculated grades, views on potential changes to medical school admissions and teaching in 2020 and 2021, reported experiences of education following the closure of educational institutions in March 2020.

Results

Respondents had concerns about the calculated grades that will replace A-level examinations, especially female applicants and applicants from Black Asian and Minority Ethnic (BAME) backgrounds who felt teachers would find it difficult to grade and rank students accurately, as well as those from non-selective state schools and those living in deprived areas who had some concerns about the grade standardisation process. Calculated grades were not considered fair enough by a majority to use in the acceptance or rejection of medical offer-holders, but several measures - including interview and aptitude test scores - were considered fair enough to use in combination. Respondents from non-selective state (public) schools reported less use of and less access to educational resources compared to their counterparts at private/selective schools. In particular they reported less online teaching in real time, and reported spending less time studying during the lockdown.

Conclusions

The coronavirus pandemic will have significant and long term impacts on the selection, education and performance of our future medical workforce. It is important that the views and experiences of medical applicants from diverse backgrounds are taken into consideration in decisions affecting their futures and the future of the profession.
Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia
Authors: Navapurkar Vilas , Scott Josefin Bartholdson , Maes Mailis , Hellyer Thomas P , Higginson Ellen , Forrest Sally , Pereira-Dias Joana , Parmar Surendra , Heasman-Hunt Emma , Polgarova Petra , Brown Jo , Titti Lissamma , Smith William PW , Scott Jonathan , Rostron Anthony , Routledge Matthew , Sapsford David , Török M.Estée , McMullan Ronan , Enoch David A , Wong Vanessa ,   The VAPrapid investigators, Curran Martin D , Brown Nicholas M , Simpson A John , Herre Jurgen , Dougan Gordon , Morris Andrew Conway
Published: June 2020

Background

Microbial cultures for the diagnosis of pneumonia take several days to return a result, and are frequently negative, compromising antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing.

Methods

The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable.

Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group.

Results

128 stored samples were tested, with sensitivity of 97% (95% CI 88-100%). Prospectively 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (IQR 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (OR 2.9 (95%1.5-5.5).

Conclusions

Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.

Trial registration

The prospective study was registered with clinicaltrials.govNCT03996330
A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection
Authors: Huang Weiren , Yu Lei , Wen Donghua , Wei Dong , Sun Yangyang , Zhao Huailong , Ye Yu , Chen Wei , Zhu Yongqiang , Wang Lijun , Wang Li , Wu Wenjuan , Zhao Qianqian , Xu Yong , Gu Dayong , Nie Guohui , Zhu Dongyi , Guo Zhongliang , Ma Xiaoling , Niu Liman , Huang Yikun , Liu Yuchen , Peng Bo , Zhang Renli , Zhang Xiuming , Li Dechang , Liu Yang , Yang Guoliang , Liu Lanzheng , Zhou Yunying , Wang Yunshan , Hou Tieying , Gao Qiuping , Li Wujiao , Chen Shuo , Hu Xuejiao , Han Mei , Zheng Huajun , Weng Jianping , Cai Zhiming , Zhang Xinxin , Song Fei , Zhao Guoping , Wang Jin
Published: June 2020

High Ct-values falling in the grey zone are frequently encountered in SARS-CoV-2 detection by real-time reverse transcription PCR (rRT-PCR) and have brought urgent challenges in diagnosis of samples with low viral load. Based on the single-stranded DNA reporter trans-cleavage activity by Cas12a upon target DNA recognition, we create a Specific Enhancer for detection of PCR-amplified Nucleic Acids (SENA) to confirm SARS-CoV-2 detection through specifically targeting its rRT-PCR amplicons. SENA is highly sensitive, with its limit of detection being at least 2 copies/reaction lower than that of the corresponding rRT-PCR, and highly specific, which identifies both false-negative and false-positive cases in clinic applications. SENA provides effective confirmation for nucleic acid amplification-based molecular diagnosis, and may immediately eliminate the uncertainty problems of rRT-PCR in SARS-CoV-2 clinic detection.

One Sentence Summary

CRISPR-Cas12a-based COVID-19 diagnosis.
Overview on COVID-19 outbreak indicators across Brazilian federative units
Authors: Guerra-Shinohara Elvira Maria , Weber Simone Schneider , Paniz Clóvis , Gomes Guilherme Wataru , Shinohara Eduardo Jun , Gandra Tiago Borges Ribeiro , Pereira Indiara Correia , Jarcem Karine Gomes , de Almeida Zanre Renato Ferreira , Barreto Acácia Gimenez , De Carli Alessandro Diogo
Published: June 2020

Background

The 2019 coronavirus disease pandemic (COVID-19) spread rapidly across Brazil. The country has 27 federative units, with wide regional differences related to climate, lifestyle habits, socioeconomic characteristics and population density. Therefore, we aimed to document and monitor the increase in COVID-19 cases across each federative unit in Brazil, by tracking its progression from inception to 15 May 2020.

Methods

Observational study.

Results

The first confirmed COVID-19 case in the country was notified in São Paulo on 26 February, while the first death occurred on 17 March, in Rio de Janeiro. Since then, there has been a dramatic increase in both confirmed cases and deaths from the disease. São Paulo, in the Southeast region, was initially considered the COVID-19 epidemic epicentre in Brazil. However, 10 states in the North and Northeast regions were ranked among the 14 highest incidences (over 100 cases per 100,000 people) observed on 15 May. Higher incidence rates (>100 cases per 100,000) were associated to higher rates of inadequate water supply and sewerage (OR, 5.83 (95% CI, 1.08–29.37, P=0.041)). North and Northeast states with the highest social vulnerability index scores had higher increases in the incidence rate between 14 April and 15 May. States with medium human development index (HDI) showed higher incidence increases from 14 April to 15 May, being seven of them with ratios in the range from 27.49 to 63.73 times.

Conclusion

Spreading of COVID-19 in Brazil differs across both regions and federative units, being influenced by different socioeconomic contexts.
Obesity and Race Alter Gene Expression in Skin
Authors: Walker Jeanne M. , Garcet Sandra , Aleman Jose O. , Mason Christopher E. , Danko David , Zuffa Simone , Swann Jonathan R. , Krueger James , Breslow Jan L. , Holt Peter R.
Published: June 2020

Obesity is accompanied by dysfunction of many organs, but effects on the skin have received little attention. We studied differences in epithelial thickness by histology and gene expression by Affymetrix gene arrays and PCR in the skin of 10 obese (BMI 35-50) and 10 normal weight (BMI 18.5-26.9) postmenopausal women paired by age and race. Epidermal thickness did not differ with obesity but the expression of genes encoding proteins associated with skin blood supply and wound healing were altered. In the obese, many gene expression pathways were broadly downregulated and subdermal fat showed pronounced inflammation. There were no changes in skin microbiota or metabolites. African American subjects differed from Caucasians with a trend to increased epidermal thickening. In obese African Americans, compared to obese Caucasians, we observed altered gene expression that may explain known differences in water content and stress response. African Americans showed markedly lower expression of the gene encoding the cystic fibrosis transmembrane regulator characteristic of the disease cystic fibrosis. The results from this preliminary study may explain the functional changes found in the skin of obese subjects and African Americans.
Instantaneous amplitude and shape of postrhinal theta oscillations differentially encode running speed
Authors: Ghosh Megha , Shanahan Benjamin E. , Furtak Sharon C. , Mashour George A. , Burwell Rebecca D. , Ahmed Omar J.
Published: June 2020

Hippocampal theta oscillations have a temporally asymmetric waveform shape, but it is not known if this theta asymmetry extends to all other cortical regions involved in spatial navigation and memory. Here, using both established and improved cycle-by-cycle analysis methods, we show that theta waveforms in the postrhinal cortex are also temporally asymmetric. On average, the falling phase of postrhinal theta cycles lasts longer than the subsequent rising phase. There are, however, rapid changes in both the instantaneous amplitude and instantaneous temporal asymmetry of postrhinal theta cycles. These rapid changes in amplitude and asymmetry are very poorly correlated, indicative of a mechanistic disconnect between these theta cycle features. We show that the instantaneous amplitude and asymmetry of postrhinal theta cycles differentially encode running speed. Although theta amplitude continues to increase at the fastest running speeds, temporal asymmetry of the theta waveform shape plateaus after medium speeds. Our results suggest that the amplitude and waveform shape of individual postrhinal theta cycles may be governed by partially independent mechanisms and emphasize the importance of employing a single cycle approach to understanding the genesis and behavioral correlates of cortical theta rhythms.
Improved Monoisotopic Mass Estimation for Deeper Proteome Coverage
Authors: Rad Ramin , Li Jiaming , Mintseris Julian , O’Connell Jeremy , Gygi Steven P. , Schweppe Devin K
Published: June 2020

Accurate assignment of monoisotopic peaks is essential for the identification of peptides in bottom-up proteomics. Misassignment or inaccurate attribution of peptidic ions leads to lower sensitivity and fewer total peptide identifications. In the present work we present a performant, open-source, cross-platform algorithm, Monocle, for the rapid reassignment of instrument assigned precursor peaks to monoisotopic peptide assignments. We demonstrate that the present algorithm can be integrated into many common proteomics pipelines and provides rapid conversion from multiple data source types. Finally, we show that our monoisotopic peak assignment results in up to a two-fold increase in total peptide identifications compared to analyses lacking monoisotopic correction and a 44% improvement over previous monoisotopic peak correction algorithms.
RoboCOP: Jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data
Authors: Mitra Sneha , Zhong Jianling , MacAlpine David M. , Hartemink Alexander J.
Published: June 2020

Chromatin is the tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and level of occupancy of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. On the other hand, epigenomic accessibility data like ATAC-seq, DNase-seq, and MNase-seq provide insight into the chromatin landscape of all factors bound along the genome, but with minimal insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin information from epigenomic accessibility data with nucleotide sequence to compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors at once. We apply RoboCOP to MNase-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome. Using available protein-binding datasets from the literature, we show that our model predicts the binding of these factors genome-wide more accurately than existing methods.
Detection dogs as a help in the detection of COVID-19 Can the dog alert on COVID-19 positive persons by sniffing axillary sweat samples ? Proof-of-concept study
Authors: Grandjean Dominique , Sarkis Riad , Tourtier Jean-Pierre , Julien-Lecocq Clothilde , Benard Aymeric , Roger Vinciane , Levesque Eric , Bernes-Luciani Eric , Maestracci Bruno , Morvan Pascal , Gully Eric , Berceau-Falancourt David , Pesce Jean-Luc , Lecomte Bernard , Haufstater Pierre , Herin Gregory , Cabrera Joaquin , Muzzin Quentin , Gallet Capucine , Bacqué Hélène , Broc Jean-Marie , Thomas Leo , Lichaa Anthony , Moujaes Georges , Saliba Michele , Kuhn Aurore , Galey Mathilde , Berthail Benoit , Lapeyre Lucien , Méreau Olivier , Matteï Marie-Nicolas , Foata Audrey , Bey Louisa , Philippe Anne-Sophie , Abassi Paul , Pisani Ferri , Delarbre Marlène , Orsini Jean-Marc , Capelli Anthoni , Renault Steevens , Bachir Karim , Kovinger Anthony , Comas Eric , Stainmesse Aymeric , Etienne Erwan , Voeltzel Sébastien , Mansouri Sofiane , Berceau-Falancourt Marlène , Leva Brice , Faure Frederic , Dami Aimé , Costa Marc Antoine , Tafanelli Jean-Jacques , Luciani Jean-Benoit , Casalot Jean-Jacques , Charlet Lary , Ruau Eric , Issa Mario , Grenet Carine , Billy Christophe , Desquilbet Loic
Published: June 2020

The aim of this study is to evaluate if the sweat produced by COVID-19 persons (SARS-CoV-2 PCR positive) has a different odour for trained detection dogs than the sweat produced by non COVID-19 persons. The study was conducted on 3 sites, following the same protocol procedures, and involved a total of 18 dogs. A total of 198 armpits sweat samples were obtained from different hospitals. For each involved dog, the acquisition of the specific odour of COVID-19 sweat samples required from one to four hours, with an amount of positive samples sniffing ranging from four to ten. For this proof of concept, we kept 8 dogs of the initial group (explosive detection dogs and colon cancer detection dogs), who performed a total of 368 trials, and will include the other dogs in our future studies as their adaptation to samples scenting takes more time.

The percentages of success of the dogs to find the positive sample in a line containing several other negative samples or mocks (2 to 6) were 100p100 for 4 dogs, and respectively 83p100, 84p100, 90p100 and 94p100 for the others, all significantly different from the percentage of success that would be obtained by chance alone.

We conclude that there is a very high evidence that the armpits sweat odour of COVID-19+ persons is different, and that dogs can detect a person infected by the SARS-CoV-2 virus.
Automated Detection of Ripple Oscillations in Long-Term Scalp EEG from Patients with Infantile Spasms
Authors: McCrimmon Colin M. , Riba Aliza , Garner Cristal , Maser Amy L. , Shrey Daniel W. , Lopour Beth A.
Published: June 2020

Objective

Scalp high frequency oscillations (HFOs) are a promising biomarker of epileptogenicity in infantile spasms (IS) and many other epilepsy syndromes, but prior studies have relied on visual analysis of short segments of data due to the prevalence of artifacts in EEG. Therefore, we set out to develop a fully automated method of HFO detection that can be applied to large datasets, and we sought to robustly characterize the rate and spatial distribution of HFOs in IS.

Methods

We prospectively collected long-term scalp EEG data from 13 subjects with IS and 18 healthy controls. For patients with IS, recording began prior to diagnosis and continued through initiation of treatment with adenocorticotropic hormone (ACTH). The median analyzable EEG duration was 18.2 hours for controls and 83.9 hours for IS subjects (∼1300 hours total). Ripples (80-250 Hz) were detected in all EEG data using an automated algorithm.

Results

HFO rates were substantially higher in patients with IS compared to controls. In IS patients, HFO rates were higher during sleep compared to wakefulness (median 5.5/min and 2.9/min, respectively;p=0.002); controls did not exhibit a difference in HFO rate between sleep and wakefulness (median 0.98/min and 0.82/min, respectively). Spatially, the difference between IS patients and controls was most salient in the central/posterior parasaggital region, where very few HFOs were detected in controls. In IS subjects, ACTH therapy significantly decreased the rate of HFOs.

Discussion

Here we show for the first time that a fully automated algorithm can be used to detect HFOs in long-term scalp EEG, and the results are accurate enough to clearly discriminate healthy subjects from those with IS. We also provide a detailed characterization of the spatial distribution and rates of HFOs associated with infantile spasms, which may have relevance for diagnosis and assessment of treatment response.
A mathematical modelling approach to uncover factors influencing the spread ofCampylobacterin a flock of chickens
Authors: Rawson Thomas , Paton Robert , Colles Frances M. , Maiden Martin C.J. , Dawkins Marian Stamp , Bonsall Michael B.
Published: June 2020

Despite continued efforts into improving biosecurity protocol,Campylobactercontinues to be detected in the majority of commercial chicken flocks across Europe. Using an extensive data set ofCampylobacterprevalence within a chicken breeder flock for over a year, multiple Bayesian models are presented to explore the dynamics of the spread ofCampylobacterin response to seasonal variation, species-specificity, bird health and total infection prevalence. It was found that birds within the flock varied greatly in their response to bacterial challenge, and that this phenomena had a large impact in the overall prevalence of different species ofCampylobacter. Campylobacter jejuniappeared more frequently in the summer, whileCampylobacter colipersisted for a longer duration, amplified by the most susceptible birds in the flock. Our study suggests that strains ofCampylobacterthat appear most frequently likely possess no demographic advantage, but are instead amplified due to the health of the birds that ingest it.
A Genomics Resource for Genetics, Physiology, and Breeding of West African Sorghum
Authors: Faye Jacques M. , Maina Fanna , Akata Eyanawa A. , Sine Bassirou , Diatta Cyril , Mamadou Aissata , Marla Sandeep , Bouchet Sophie , Teme Niaba , Rami Jean-Francois , Fonceka Daniel , Cisse Ndiaga , Morris Geoffrey P.
Published: June 2020

Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolorL. Moench) in West Africa has diversified across a mosaic of cultures and end-uses, and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing was used to generate 159,101 high-quality biallelic SNPs, with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP (π = 0.00045), only slightly less than in a global diversity panel (π = 0.00055). Linkage disequilibrium decayed to background level (r2< 0.1) by ~50 kb in the WASAP. Genome-wide diversity was structured both by botanical type, and by populations within botanical type, with eight ancestral populations identified. Most populations were distributed across multiple countries, suggesting several potential common gene pools across the national programs. Genome-wide association studies of days to flowering and plant height revealed eight and three significant quantitative trait loci (QTL), respectively, with major height QTL at canonical height lociDw3andSbHT7.1. Colocalization of two of eight major flowering time QTL with flowering genes previously described in US germplasm (Ma6andSbCN8) suggests that photoperiodic flowering in WA sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics-enabled breeding of climate-resilient varieties in West Africa.
Annotating high-impact 5’untranslated region variants with the UTRannotator
Authors: Zhang Xiaolei , Wakeling Matthew , Ware James , Whiffin Nicola
Published: June 2020

Current tools to annotate the predicted effect of genetic variants are heavily biased towards protein-coding sequence. Variants outside of these regions may have a large impact on protein expression and/or structure and can lead to disease, but this effect can be challenging to predict. Consequently, these variants are poorly annotated using standard tools. We have developed a plugin to the Ensembl Variant Effect Predictor, the UTRannotator, that annotates variants in 5’untranslated regions (5’UTR) that create or disrupt upstream open reading frames (uORFs). We investigate the utility of this tool using the ClinVar database, providing an annotation for 30.8% of all 5’UTR (likely) pathogenic variants, and highlighting 31 variants of uncertain significance as candidates for further follow-up. We will continue to update the UTR annotator as we gain new knowledge on the impact of variants in UTRs.

Availability and implementation

UTRannotator is freely available on Github:https://github.com/ImperialCardioGenetics/UTRannotator

Supplementary information

Supplementary data are available at bioRxiv.
Local adaptation can cause both peaks and troughs in nucleotide diversity within populations
Authors: Jasper Russ J. , Yeaman Sam
Published: June 2020

Local adaptation is expected to cause high FSTat sites linked to a causal locus, however this pattern can also be driven by background or positive selection. Within-population nucleotide diversity could provide a means to differentiate these scenarios, as both background and positive selection deplete diversity, whereas some theoretical studies have shown that local adaptation increases it. However, it is unclear whether such theoretical predictions generalize to more complicated models. Here, we explore how local adaptation shapes genome-wide patterns in nucleotide diversity and FST, extending previous work to study the effect of variable degrees of polygenicity and genotypic redundancy in an adaptive trait, and different levels of population structure. We show that local adaptation produces two very different patterns depending on the relative strengths of migration and selection, either markedly decreasing or increasing within-population diversity at linked sites at equilibrium. When migration is low, regions of depleted diversity can extend large distances from the causal locus, with substantially more diversity eroded than expected with background selection. With higher migration, peaks occur over much smaller genomic distances but with much larger magnitude changes in diversity. In spatially extended clinal environments both patterns can be found within a single species, with increases in diversity at the center of the range and decreases towards the periphery. Our results demonstrate that there is no universal diagnostic signature of local adaptation based on nucleotide diversity, however, given that neither background nor positive selection inflate diversity, when peaks are found they strongly suggest local adaptation.