bluuebunny/crossref_metadata_2025 huggingface dataset:
Technical Overview of the Kansas Mesonet
Authors: Patrignani Andres , Knapp Mary , Redmond Christopher , Santos Eduardo
Published: September 2020

The Kansas Mesonet is a multipurpose network consisting of 62 automated environmental monitoring stations (as of 2019) covering the state of Kansas. Each station is equipped with research-grade instrumentation and measures precipitation, air temperature, air relative humidity, barometric pressure, wind speed and direction, solar radiation, soil temperature, and soil moisture. Observations are transferred to dedicated computer servers every 5 min via cellular modems. Data are archived and subjected to periodic quality control tests and are disseminated in near–real time through a dedicated web portal. The observations collected by the Kansas Mesonet are widely used for irrigation water management, crop modeling, pest management, wildland fire management, drought monitoring, wind energy production, environmental research, and animal management. This paper provides a technical overview of the Kansas Mesonet and includes a complete description of the instrumentation, siting criteria, instrument verification procedures, and value-added products.
Systematic Evaluation of the Impact of Assimilating a Network of Ground-Based Remote Sensing Profilers for Forecasts of Nocturnal Convection Initiation during PECAN
Authors: Degelia Samuel K. , Wang Xuguang , Stensrud David J. , Turner David D.
Published: September 2020

Nocturnal convection is often initiated by mechanisms that cannot be easily observed within the large gaps between rawinsondes or by conventional surface networks. To improve forecasts of such events, we evaluate the systematic impact of assimilating a collocated network of high-frequency, ground-based thermodynamic and kinematic profilers collected as part of the 2015 Plains Elevated Convection At Night (PECAN) experiment. For 13 nocturnal convection initiation (CI) events, we find small but consistent improvements when assimilating thermodynamic observations collected by Atmospheric Emitted Radiance Interferometers (AERIs). Through midlevel cooling and moistening, assimilating the AERIs increases the fractions skill score (FSS) for both nocturnal CI and precipitation forecasts. The AERIs also improve various contingency metrics for CI forecasts. Assimilating composite kinematic datasets collected by Doppler lidars and radar wind profilers (RWPs) results in slight degradations to the forecast quality, including decreases in the FSS and traditional contingency metrics. The impacts from assimilating thermodynamic and kinematic profilers often counteract each other, such that we find little impact on the detection of CI when both are assimilated. However, assimilating both datasets improves various properties of the CI events that are successfully detected (timing, distance, shape, etc.). We also find large variability in the impact of assimilating these remote sensing profilers, likely due to the number of observing sites and the strength of the synoptic forcing for each case. We hypothesize that the lack of flow-dependent methods to diagnose observation errors likely contributes to degradations in forecast skill for many cases, especially when assimilating kinematic profilers.
Neuroleptic Malignant Syndrome: A Potential Etiology of Multisystem Organ Failure in a Burn Patient
Authors: Ficarino Hannah M. , Caposole Michael Z. , Noelle Davis S. , N. Krebsbach Mackenzie , McGowin Emily F. , Alexander Kaitlin M. , Kinnard Christopher M. , Simmons Jon D.
Published: September 2020

Neuroleptic malignant syndrome (NMS) is described in the medical literature but rarely seen among acutely ill trauma patients. A 44-year-old man with burns to the hands and back after a chemical explosion was transported to an outside facility where he received treatment for presumed acute coronary syndrome after developing ventricular tachycardia and elevated serum troponins after the exposure. His cardiac catheterization was unremarkable, but an echocardiogram revealed severe cardiomyopathy, and he was also in multisystem organ failure. He was transferred to our facility after hospital day 2 for treatment of his multisystem organ failure and 2% total body surface area burns. His laboratory results were remarkable for a creatine kinase of >100 000 units/L, and he required 14 g of intravenous calcium. Upon further investigation, the patient reported taking ziprasidone for his bipolar disorder, and he had a core temperature of 103.5 °F on his initial presentation to the outside facility. As he convalesced, the unifying diagnosis was NMS. NMS is a side effect of antipsychotic therapy and is manifested by hyperpyrexia, rigidity, autonomic instability, and altered consciousness. An elevated creatine kinase >100 000 units/L is almost pathognomonic for NMS. Patients can also present with leukocytosis, organ failure, and electrolyte disturbances including hypocalcemia. We hypothesized that dehydration, the warm environmental conditions at our patient’s job, and immense stress resulting in a catecholamine surge following his trauma were inciting triggers to this event. This case highlights the importance of considering alternate diagnoses in patients whose clinical presentation does not fit the most “obvious cause.”
Prevalence of Tinnitus in an Aging Population and Its Relation to Age and Hearing Loss
Authors: Oosterloo Berthe C. , Croll Pauline H. , Baatenburg de Jong Robert J. , Ikram M. Kamran , Goedegebure André
Published: September 2020

Objectives

Tinnitus is a common hearing‐related disorder, which may have a large impact on daily life. With aging populations worldwide, it is important to gain insight in the occurrence of tinnitus at older ages and to understand its relationship with age‐related hearing loss. We investigated the prevalence of tinnitus among a general aging population, across age strata and hearing status.

Study Design

Cross‐sectional.

Setting

The population‐based Rotterdam Study.

Methods

A total of 6098 participants underwent tinnitus assessment, and 4805 had additional hearing assessment. We determined tinnitus prevalence per 5‐year age groups. Hearing impairment was defined as ≥25–dB HL worse ear pure tone average (0.5, 1, 2, 4 kHz). We investigated with multivariable logistic regression the association between hearing impairment and tinnitus. Tinnitus handicap was assessed in 663 participants with daily tinnitus via the Tinnitus Handicap Inventory–screening version (THI‐s).

Results

Tinnitus was prevalent in 21.4% (n = 1304). Prevalent tinnitus was evenly distributed over 5‐year age groups. Participants with hearing impairment were more likely to have tinnitus (odds ratio, 2.27; 95% CI, 1.92‐2.69) as compared with those without hearing impairment. The median THI‐s score was 4 (interquartile range, 0‐10), indicating a slight handicap, and 14.6% of the participants reported a moderate or severe handicap (THI‐s ≥16).

Conclusions

In a general elderly population, 1 in 5 persons has tinnitus. Of those with tinnitus, for 1 per 10 persons, the presence of tinnitus interfered with daily life. Participants with hearing impairment were twice as likely to have tinnitus. Despite the age‐dependent occurrence of hearing impairment, no such age dependency was found for tinnitus.
Prevalence of and Associations With Distress and Professional Burnout Among Otolaryngologists: Part I, Trainees
Authors: Larson David P. , Carlson Matthew L. , Lohse Christine M. , O’Brien Erin K. , Kircher Matthew L. , Gurgel Richard K. , Hunter Jacob B. , Micco Alan G. , Nogan Stephen J. , O’Connell Brendan P. , Rangarajan Sanjeet V. , Rivas Alejandro , Sweeney Alex D. , Wanna George B. , Weisskopf Peter A. , Choby Garret
Published: September 2020

Objective

To assess the prevalence of distress and burnout in otolaryngology trainees, including associations with relevant sociodemographic and professional factors, and to compare these results with those of attending otolaryngologists.

Study Design

A cross‐sectional survey of trainees and attending physicians.

Setting

Twelve academic otolaryngology programs.

Methods

Distress and burnout were measured with the Expanded Physician Well‐being Index and the 2‐item Maslach Burnout Inventory. The Patient Health Questionnaire–2 and Generalized Anxiety Disorder–2 were used to screen for depressive disorders and anxiety disorders, respectively. Associations with sociodemographic and professional characteristics were assessed.

Results

Of the 613 surveys administered to trainees and attending physicians, 340 were completed (56%). Among 154 trainees, distress was present in 49%, professional burnout in 35%, positive depressive disorder screening in 5%, and positive anxiety disorder screening in 16%. In univariable analysis, female gender, hours worked in a typical week (HW), and nights on call in a typical week (NOC) were significantly associated with distress. In multivariable analysis, female gender (odds ratio, 3.91; P =. 001) and HW (odds ratio for each 10 HW, 1.89; P =. 003) remained significantly associated with distress. Female gender, HW, and NOC were significantly associated with burnout univariably, although only HW (odds ratio for each 10 HW, 1.92; P =. 003) remained significantly associated with burnout in a multivariable setting. Attending physicians had less distress than trainees (P =. 02) and felt less callous and less emotionally hardened than trainees (P <. 001).

Conclusion

Otolaryngology trainees experience significant work‐place distress (49%) and burnout (35%). Gender, HW, and NOC had the strongest associations with distress and burnout.
Visualising the dynamics of COVID-19 cases leading to inbound transmission in Hong Kong
Authors: Zhou Long , Li Sihong , Li Chaosu
Published: September 2020

As a global city, Hong Kong directly connects more than 120 cities worldwide and transfers nearly 20 million passengers each year. The current COVID-19 pandemic has put the major transport hub in Asia under severe threat of potential imported cases. This Featured Graphic visualizes inbound confirmed COVID-19 cases to Hong Kong globally from January to June 2020, which could greatly help to assess risks from imported cases and improve air transport control policy for mitigating the global spread of COVID-19.
Change and continuity in Finnish drinking in the 21st century
Authors: Tigerstedt Christoffer , Makela Pia , Karlsson Thomas , Härkönen Janne , Lintonen Tomi , Warpenius Katariina
Published: September 2020

Aim:

Alcohol consumption and policy in Finland have undergone a variety of changes in the two last decades. In several cases, trends in both consumption and policy have shifted direction when moving from the first decade of the 21st century to the second one. The aim of the overview is to summarise the trends.

Data:

The overview draws on results primarily from the cross-sectional Finnish Drinking Habits Survey (FDHS) in 2000, 2008 and 2016, and also from the whole series including altogether seven separate data collections carried out every eight years from 1968 to 2016 and mainly covering Finns aged 15–69 years. Response rates show a falling trend (78% in 2000, 74% in 2008 and 60% in 2016). The overview also makes use of data collected within the European School Survey Project on Alcohol and other Drugs (ESPAD) and, for the elderly, the National FinSote study carried out by the Finnish Institute for Health and Welfare (THL).

Results:

After an all-time high of 12.7 litres of pure alcohol per capita 15 years and over in 2007, total consumption of alcohol had decreased by 21% by the year 2019. Underage drinking has decreased ever since the millennium shift. Older people’s drinking has continued increasing or levelled out. Along with reduced total consumption, heavy episodic drinking (HED) has also decreased, but the differences between manual and white-collar workers in HED have continued to grow. Drinking alcoholic beverages with meals has also declined since 2008. Liberal and restrictive alcohol policy measures have alternated.

Conclusions:

Finnish drinking culture seems to change at a slow pace; several typical drinking habits have remained unchanged.
Meso–macro-scale computational analysis of boron nitride nanotube-reinforced aluminium and epoxy nanocomposites: A case study on crack propagation
Authors: Padmanabhan Srikant , Gupta Ankit , Arora Gaurav , Pathak Himanshu , Burela Ramesh G , Bhatnagar Anant S
Published: September 2020

In this paper, an outline of mean-field homogenization and fracture toughness of boron nitride nanotube-reinforced aluminium and epoxy composites have been presented. The meso-scale material modelling has been achieved using Mori-Tanaka and double inclusion homogenization schemes. To examine the effectiveness of Mori-Tanaka and double inclusion schemes, a comparison has been drawn with the rule of mixture. Meso-scale numerical results of boron nitride nanotube-reinforced aluminium and epoxy composites are presented for various design parameters such as aspect ratio and volume fraction of boron nitride nanotubes. The validation studies of the developed transversely isotropic composites model have been documented with the experiments performed and existing literature. Finally, macro-scale fracture toughness simulations incorporating the transversely isotropic properties have been performed using the domain integral method. It is observed that aluminium and epoxy with elastoplastic and viscoelastic nature, respectively, have shown a significant effect on the fracture properties of the composites.
Three-dimensional virtual surgical planning (3D-VSP) in orthognathic surgery: Advantages, disadvantages and pitfalls
Authors: Donaldson Chris D , Manisali Mehmet , Naini Farhad B
Published: September 2020

In this article, the advantages, disadvantages and pitfalls of three-dimensional virtual surgical planning (3D-VSP) compared to traditional two-dimensional (2D) planning methods in orthognathic surgery are discussed, alongside a standardised protocol that can be utilised. A skeletal Class II, skeletal Class III and an anterior open bite clinical case along with their 3D-VSP management are presented, highlighting modifications that can be made to computer-aided design/computer-aided manufacture (CAD/CAM) cutting guide and plate designs.
Effectiveness and Cost of Implementing Evidence-Based Interventions to Increase Colorectal Cancer Screening Among an Underserved Population in Chicago
Authors: Kim Karen E. , Tangka Florence K. L. , Jayaprakash Manasi , Randal Fornessa T. , Lam Helen , Freedman David , Carrier Laurie A. , Sargant Coletta , Maene Chieko , Hoover Sonja , Joseph Djenaba , French Cynthia , Subramanian Sujha
Published: September 2020

With funding from the Centers for Disease Control and Prevention’s Colorectal Cancer Control Program, The University of Chicago Center for Asian Health Equity partnered with a federally qualified health center (FQHC) to implement multiple evidence-based interventions (EBIs) in order to improve colorectal cancer (CRC) screening uptake. The purpose of this study is to determine the effectiveness and cost of implementing a provider reminder system entered manually and supplemented with patient reminders and provider assessment and feedback. The FQHC collected demographic characteristics of the FQHC and outcome data from January 2015 through December 2015 (preimplementation period) and cost from January 2016 through September 2017 (implementation period). Cost data were collected for the implementation period. We report on the demographics of the eligible population, CRC screening order, completion rates by sociodemographic characteristics, and, overall, the effectiveness and cost of implementation. From the preimplementation phase to the implementation phase, there was a 21.2 percentage point increase in CRC screens completed. The total cost of implementing EBIs was $40908.97. We estimated that an additional 283 screens were completed because of the interventions, and the implementation cost of the interventions was $144.65 per additional screen. With the interventions, CRC screening uptake in Chicago increased for all race/ethnicity and demographic backgrounds at the FQHC, particularly for patients aged 50 to 64 years and for Asian, Hispanic, and uninsured patients.
Mapping the time course of semantic activation in mediated false memory: Immediate classification, naming, and recognition
Authors: Huff Mark J , Di Mauro Alyssa , Coane Jennifer H , O’Brien Liam M
Published: September 2020

We evaluated the time course of persistent automatic spreading activation from a mediated list of indirect associates (e.g., meow, day, and basement) that all converged upon a non-presented critical item (CI; e.g., black). Mediated lists were related to CIs through non-presented mediators (e.g., cat, night, and bottom). Three speeded tasks were used to evaluate the time course of semantic activation of the CI: a continuous semantic classification task (concrete/abstract decisions), a naming task (reading words aloud), or a recognition test (old/new memory decisions). Test lists were presented immediately following the mediated lists, and CIs were presented in the first, third, or eighth positions. The results revealed that in both the classification and naming tasks, CI priming was greatest in the first test position and declined across the remaining test positions. Importantly, priming was statistically reliable in the late test positions, providing evidence for long-term semantic priming (i.e., across positions on immediate tasks). False recognition, however, was stable across test positions. Collectively, these patterns suggest that spreading-activation processes decline, consistent with implicit spreading activation, and these processes may contribute to long-term false recognition.
Faecal microbiota transplantation for Clostridioides difficile infection: Four years’ experience of the Netherlands Donor Feces Bank
Authors: Terveer Elisabeth M , Vendrik Karuna EW , Ooijevaar Rogier E , van Lingen Emilie , Boeije‐Koppenol Eline , van Nood Els , Goorhuis Abraham , Bauer Martijn P , van Beurden Yvette H , Dijkgraaf Marcel GW , Mulder Chris JJ , Vandenbroucke‐Grauls Christina MJE , Seegers Jos FML , van Prehn Joffrey , Verspaget Hein W , Kuijper Ed J , Keller Josbert J
Published: September 2020

Background

The Netherlands Donor Feces Bank provides standardized ready‐to‐use donor faecal suspensions for faecal microbiota transplantation treatment of patients with recurrent Clostridioides difficile infection.

Objective

The purpose of this study was evaluation of safety, feasibility and outcome of faecal microbiota transplantation facilitated by a national stool bank.

Methods

The methods used included: observational cohort study of donors and recipients of faecal suspensions; assessment of donor screening and patient selection performed by an expert panel of medical microbiologists, gastroenterologists and infectious disease specialists; and patient outcome evaluated at different timepoints after faecal microbiota transplantation.

Results

Of 871 volunteers who registered as a potential faeces donor, 16 (2%) became active donors. Nine donors stopped or were excluded after a mean donation period of 5.7 months. In 2016–2019, 47 (27%) of 176 requests for faecal microbiota transplantations were deemed not indicated by the expert panel. In total, 129 patients with recurrent C. difficile infection were treated with 143 faecal suspensions in 40 different hospitals. The cure rate at two months after a single infusion was 89% (107/120). Of 84 patients, long‐term follow‐up (median 42 weeks) was available and sustained cure was achieved in 61 (73%). Early C. difficile infection relapses (within two months after faecal microbiota transplantation) and late recurrences (after more than two months) occurred more frequently in patients who received non‐C. difficile antibiotics within three weeks after faecal microbiota transplantation and in moderately to severely immunocompromised patients. Of 21 patients with C. difficile infection after faecal microbiota transplantation, 14 were cured with anti‐C. difficile antibiotics and seven with a second transplantation. No faecal microbiota transplantation‐related serious adverse events were observed, but gastro‐intestinal complaints (nausea, abdominal pain or diarrhoea) persisted in 32% of the treated patients at long‐term follow‐up.

Conclusion

Faecal suspensions provided by a centralized stool bank, supported by a multidisciplinary expert team, resulted in effective, appropriate and safe application of faecal microbiota transplantation for recurrent C. difficile infection.

Level of evidence

Level II, prospective cohort study
Fusion partner–specific mutation profiles and KRAS mutations as adverse prognostic factors in MLL-rearranged AML
Authors: Matsuo Hidemasa , Yoshida Kenichi , Nakatani Kana , Harata Yutarou , Higashitani Moe , Ito Yuri , Kamikubo Yasuhiko , Shiozawa Yusuke , Shiraishi Yuichi , Chiba Kenichi , Tanaka Hiroko , Okada Ai , Nannya Yasuhito , Takeda June , Ueno Hiroo , Kiyokawa Nobutaka , Tomizawa Daisuke , Taga Takashi , Tawa Akio , Miyano Satoru , Meggendorfer Manja , Haferlach Claudia , Ogawa Seishi , Adachi Souichi
Published: September 2020

Mixed-lineage leukemia (MLL) gene rearrangements are among the most frequent chromosomal abnormalities in acute myeloid leukemia (AML). MLL fusion patterns are associated with the patient’s prognosis; however, their relationship with driver mutations is unclear. We conducted sequence analyses of 338 genes in pediatric patients with MLL-rearranged (MLL-r) AML (n = 56; JPLSG AML-05 study) alongside data from the TARGET study’s pediatric cohorts with MLL-r AML (n = 104), non–MLL-r AML (n = 581), and adult MLL-r AML (n = 81). KRAS mutations were most frequent in pediatric patients with high-risk MLL fusions (MLL-MLLLT10, MLL-MLLT4, and MLL-MLLT1). Pediatric patients with MLL-r AML (n = 160) and a KRAS mutation (KRAS-MT) had a significantly worse prognosis than those without a KRAS mutation (KRAS-WT) (5-year event-free survival [EFS]: 51.8% vs 18.3%, P < .0001; 5-year overall survival [OS]: 67.3% vs 44.3%, P = .003). The adverse prognostic impact of KRAS mutations was confirmed in adult MLL-r AML. KRAS mutations were associated with adverse prognoses in pediatric patients with both high-risk (MLLT10+MLLT4+MLLT1; n = 60) and intermediate-to-low–risk (MLLT3+ELL+others; n = 100) MLL fusions. The prognosis did not differ significantly between patients with non–MLL-r AML with KRAS-WT or KRAS-MT. Multivariate analysis showed the presence of a KRAS mutation to be an independent prognostic factor for EFS (hazard ratio [HR], 2.21; 95% confidence interval [CI], 1.35-3.59; P = .002) and OS (HR, 1.85; 95% CI, 1.01-3.31; P = .045) in MLL-r AML. The mutation is a distinct adverse prognostic factor in MLL-r AML, regardless of risk subgroup, and is potentially useful for accurate treatment stratification. This trial was registered at the UMIN (University Hospital Medical Information Network) Clinical Trials Registry (UMIN-CTR; http://www.umin.ac.jp/ctr/index.htm) as #UMIN000000511.
TRIP - T cell receptor/immunoglobulin profiler
Authors: Kotouza Maria Th. , Gemenetzi Katerina , Galigalidou Chrysi , Vlachonikola Elisavet , Pechlivanis Nikolaos , Agathangelidis Andreas , Sandaltzopoulos Raphael , Mitkas Pericles A. , Stamatopoulos Kostas , Chatzidimitriou Anastasia , Psomopoulos Fotis E. ,   on behalf of the Hellenic Precision Medicine Network in Oncology
Published: September 2020

Background

Antigen receptors are characterized by an extreme diversity of specificities, which poses major computational and analytical challenges, particularly in the era of high-throughput immunoprofiling by next generation sequencing (NGS). The T cell Receptor/Immunoglobulin Profiler (TRIP) tool offers the opportunity for an in-depth analysis based on the processing of the output files of the IMGT/HighV-Quest tool, a standard in NGS immunoprofiling, through a number of interoperable modules. These provide detailed information about antigen receptor gene rearrangements, including variable (V), diversity (D) and joining (J) gene usage, CDR3 amino acid and nucleotide composition and clonality of both T cell receptors (TR) and B cell receptor immunoglobulins (BcR IG), and characteristics of the somatic hypermutation within the BcR IG genes. TRIP is a web application implemented in R shiny.

Results

Two sets of experiments have been performed in order to evaluate the efficiency and performance of the TRIP tool. The first used a number of synthetic datasets, ranging from 250k to 1M sequences, and established the linear response time of the tool (about 6 h for 1M sequences processed through the entire BcR IG data pipeline). The reproducibility of the tool was tested comparing the results produced by the main TRIP workflow with the results from a previous pipeline used on the Galaxy platform. As expected, no significant differences were noted between the two tools; although the preselection process seems to be stricter within the TRIP pipeline, about 0.1% more rearrangements were filtered out, with no impact on the final results.

Conclusions

TRIP is a software framework that provides analytical services on antigen receptor gene sequence data. It is accurate and contains functions for data wrangling, cleaning, analysis and visualization, enabling the user to build a pipeline tailored to their needs. TRIP is publicly available at https://bio.tools/TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler.
Proteome of larval metamorphosis induced by epinephrine in the Fujian oyster Crassostrea angulata
Authors: Di Guilan , Xiao Xiaohuo , Tong Ming Him , Chen Xinhua , Li Li , Huang Miaoqin , Zhou Long , Ke Caihuan
Published: September 2020

Background

The Fujian oyster Crassostrea angulata is an economically important species that has typical settlement and metamorphosis stages. The development of the oyster involves complex morphological and physiological changes, the molecular mechanisms of which are as yet unclear.

Results

In this study, changes in proteins were investigated during larval settlement and metamorphosis of Crassostrea angulata using epinephrine induction. Protein abundance and identity were characterized using label-free quantitative proteomics, tandem mass spectrometry (MS/ MS), and Mascot methods. The results showed that more than 50% (764 out of 1471) of the quantified proteins were characterized as differentially expressed. Notably, more than two-thirds of the differentially expressed proteins were down-regulated in epinephrine-induced larvae. The results showed that “metabolic process” was closely related to the development of settlement and metamorphosis; 5 × 10− 4 M epinephrine induced direct metamorphosis of larvae and was non-toxic. Calmodulin and MAPK pathways were involved in the regulation of settlement of the oyster. Expression levels of immune-related proteins increased during metamorphosis. Hepatic lectin-like proteins, cadherins, calmodulin, calreticulin, and cytoskeletal proteins were involved in metamorphosis. The nervous system may be remodeled in larval metamorphosis induced by epinephrine. Expression levels of proteins that were enriched in the epinephrine signaling pathway may reflect the developmental stage of the larvae, that may reflect whether or not larvae were directly involved in metamorphosis when the larvae were treated with epinephrine.

Conclusion

The study provides insight into proteins that function in energy metabolism, immune responses, settlement and metamorphosis, and shell formation in C. angulata. The results contribute valuable information for further research on larval settlement and metamorphosis.

Graphical abstract
Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis
Authors: Vu Nga T. T. , Zenger Kyall R. , Guppy Jarrod L. , Sellars Melony J. , Silva Catarina N. S. , Kjeldsen Shannon R. , Jerry Dean R.
Published: September 2020

Background

Restrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely distributed throughout the Indian and Pacific Oceans including along the western, northern and eastern coastline of Australia, where it is an important aquaculture and fishery species. Understanding the genetic structure and the influence of environmental factors leading to adaptive differences among populations of this species is important for farm genetic improvement programs and sustainable fisheries management.

Results

Based on 278 individuals obtained from seven geographically disparate Australian locations, 10,624 high-quality SNP loci were used to characterize genetic diversity, population structure, genetic connectivity, and adaptive divergence. Significant population structure and differentiation were revealed among wild populations (average FST = 0.001–0.107; p <  0.05). Eighty-nine putatively outlier SNPs were identified to be potentially associated with environmental variables by using both population differentiation (BayeScan and PCAdapt) and environmental association (redundancy analysis and latent factor mixed model) analysis methods. Clear population structure with similar spatial patterns were observed in both neutral and outlier markers with three genetically distinct groups identified (north Queensland, Northern Territory, and Western Australia). Redundancy, partial redundancy, and multiple regression on distance matrices analyses revealed that both geographical distance and environmental factors interact to generate the structure observed across Australian P. monodon populations.

Conclusion

This study provides new insights on genetic population structure of Australian P. monodon in the face of environmental changes, which can be used to advance sustainable fisheries management and aquaculture breeding programs.
Molecular epidemiology and risk factors of Stenotrophomonas maltophilia infections in a Chinese teaching hospital
Authors: Duan Zhongliang , Qin Juanxiu , Liu Yao , Li Cui , Ying Chunmei
Published: September 2020

Background

Stenotrophomonas maltophilia (S. maltophilia) is an important opportunistic pathogen that can be isolated in hospitals. With the abuse of broad spectrum antibiotics and invasive surgical devices, the rate of S. maltophilia infection is increasing every year. This study was an epidemiological analysis of the clinical and molecular characteristics of S. maltophilia infection in a Chinese teaching hospital. The goal was to obtain a comprehensive understanding of the status of S. maltophilia infection to provide strong epidemiological data for the prevention and treatment of S. maltophilia infection.

Results

A total of 93 isolates from Renji Hospital affiliated with the Shanghai Jiaotong University School of Medicine were included, in which 62 isolates were from male patients. In addition, 81 isolates were isolated from sputum samples. A total of 86 patients had underlying diseases. All patients received antibiotics. Multilocus sequence typing (MLST) analysis indicated that 61 different sequence types (STs) were found (including 45 novel STs), and MLST did not show significantly dominant STs. Pulsed field gel electrophoresis (PFGE) results showed that 93 isolates could be divided into 73 clusters, and they also showed weak genetic linkages between isolates. The resistant rates to trimethoprim/sulfamethoxazole (TMP/SMX) and levofloxacin were 9.7 and 4.3%, respectively, and all isolates were susceptible to minocycline. Four virulence gene’s loci Stmpr1, Stmpr2, Smf-1, and Smlt3773 were positive in 79.6, 91.4, 94.6, and 52.7% of the isolates, respectively. Three biofilm genes rmlA, spgM, and rpfF were positive in 82.8, 92.5, and 64.5% of the isolates, respectively. Mean biofilm forming level of OD492 was 0.54 ± 0.49. We did not find any significant difference between different genders and different age-groups. We retrospectively analyzed data from patients in the intensive care unit (ICU) and the control group. The independent risk factors of those who were infected in the ICU included immunosuppression and the increased antibiotic usage.

Conclusions

Most of the patients had prior medical usage histories and baseline diseases. The positive rate of virulence genes was high, the drug resistance rate of S. maltophilia was low, and the biofilm formation ability was strong. The increased use of antibiotics was an independent risk factor for S. maltophilia infection, which should receive more attention. No obvious clonal transmissions were found in the same departments.
Transcriptome analysis reveals underlying immune response mechanism of fungal (Penicillium oxalicum) disease in Gastrodia elata Bl. f. glauca S. chow (Orchidaceae)
Authors: Wang Yanhua , Gao Yugang , Zang Pu , Xu Yue
Published: September 2020

Background

Gastrodia elata Bl. f. glauca S. Chow is a medicinal plant. G. elata f. glauca is unavoidably infected by pathogens in their growth process. In previous work, we have successfully isolated and identified Penicillium oxalicum from fungal diseased tubers of G. elata f. glauca. As a widespread epidemic, this fungal disease seriously affected the yield and quality of G. elata f. glauca. We speculate that the healthy G. elata F. glauca might carry resistance genes, which can resist against fungal disease. In this study, healthy and fungal diseased mature tubers of G. elata f. glauca from Changbai Mountain area were used as experimental materials to help us find potential resistance genes against the fungal disease.

Results

A total of 7540 differentially expressed Unigenes (DEGs) were identified (FDR < 0.01, log2FC > 2). The current study screened 10 potential resistance genes. They were attached to transcription factors (TFs) in plant hormone signal transduction pathway and plant pathogen interaction pathway, including WRKY22, GH3, TIFY/JAZ, ERF1, WRKY33, TGA. In addition, four of these genes were closely related to jasmonic acid signaling pathway.

Conclusions

The immune response mechanism of fungal disease in G. elata f. glauca is a complex biological process, involving plant hormones such as ethylene, jasmonic acid, salicylic acid and disease-resistant transcription factors such as WRKY, TGA.
Mild hypercapnia improves brain tissue oxygen tension but not diffusion limitation in asphyxial cardiac arrest: an experimental study in pigs
Authors: Zhou Dawei , Li Zhimin , Zhang Shaolan , Wu Lei , Li Yiyuan , Shi Guangzhi , Zhou Jianxin
Published: September 2020

Background

We sought to evaluate the effect of mild hypercapnia on brain tissue oxygen tension (Pbto2) and diffusion limitation (impaired ability of oxygen extraction) in a porcine post asphyxial cardiac arrest model.

Methods

In 16 Bama pigs, asphyxial cardiac arrest was induced by endotracheal tube clamping and remained untreated for another 4 min. After return of spontaneous circulation (ROSC), animals were randomly assigned to mild hypercapnia (end-tidal carbon dioxide (EtCO2): 45 ~ 50 mmHg) and normocapnia (EtCO2: 35 ~ 40 mmHg) groups for 12 h. Intracranial pressure (ICP), Pbto2, and brain tissue temperature were invasively measured by multimodality monitors. Blood gas analysis, neuron specific enolase (NSE), and S100β were tested at baseline, ROSC 1 h, 6 h, and 12 h. Generalized mixed model with a compound symmetry covariance matrix was used to compare the time-variables of the two groups.

Results

Twelve (75%) pigs had ROSC and 11 pigs survived for the study period, with 6 pigs in mild hypercapnia group and 5 in the normocapnia group. The mean EtCO2 in the mild hypercapnia was significantly higher than normocapnia group (48 vs 38 mmHg, p <  0.001). Compared with normocapnia, mild hypercapnia group had higher Pbto2 (p <  0.001), slightly higher mean arterial pressure (p = 0.012) and ICP (p = 0.009). There were no differences in cerebral perfusion pressure (p = 0.106), gradient of partial pressure of jugular venous bulb oxygen (Pjvo2) and Pbto2 (p = 0.262), difference of partial pressure of jugular venous CO2 and arterial CO2 (p = 0.546), cardiac output (p = 0.712), NSE (p = 0.822), and S100β (p = 0.759) between the two groups.

Conclusions

Short term mild hypercapnia post-resuscitation could improve Pbto2. However, no corresponding improvements in the gradient of Pjvo2 to Pbto2 and biomarkers of neurological recovery were observed in the porcine asphyxial cardiac arrest model.
Frailty phenotype and multi-domain impairments in older patients with chronic kidney disease
Authors: Vettoretti Simone , Caldiroli Lara , Porata Giulia , Vezza Carlotta , Cesari Matteo , Messa Piergiorgio
Published: September 2020

Background

Older subjects with chronic kidney disease (CKD) are often affected by multiple geriatric impairments that may benefit from a comprehensive geriatric assessment (CGA). However, ordinary execution of CGA in all these individuals would be unaffordable. We evaluated if Frailty Phenotype (FP) could identify older CKD-patients that may benefit the most from a CGA.

Methods

We evaluated 112 CKD patients not yet on dialysis (age ≥ 65 years, eGFR < 45 ml/min). FP was defined according to the criteria proposed by Fried and co-authors. CGA evaluated four domains (nutrition, physical performance, cognition and depression). Malnutrition was defined in accordance to Malnutrition-Inflammation Score (MIS) and/or by the presence of Protein Energy Wasting syndrome (PEW). Physical performance was evaluated using Short Physical Performance Battery (SPPB) and handgrip strength. Cognitive status was assessed by using Mini Mental State Examination (MMSE) and Clock Drawing Test. Mood was investigated with Geriatric Depression Scale (GDS).

Results

Average age of our cohort was 80 ± 6 years and mean eGFR 24 ± 11 ml/min/1.73 m2. Prevalence of frailty was 45%. Frail patients (F-CKD) had higher prevalence of malnutrition (58 vs 29%, p = 0.0005), physical impairment (100% vs 78%; p < 0.0001), cognitive dysfunction (83% vs 37%; p < 0.0001) and depression (50% vs 21%; p < 0.001) compared to robust ones (NF-CKD).

Moreover, F-CKD patients had higher probability to have > 2 impaired domains (83% sensitivity and 76% specificity) respect to NF-CKD individuals.

Conclusions

FP is a reliable screening tool to identify older CKD-patients that may benefit from a CGA.
The associations of the number of medications and the use of anticholinergics with recovery from tubal feeding: a longitudinal hospital-based study
Authors: Takata Keiji , Oniki Kentaro , Tateyama Yuki , Yasuda Hiroki , Yokota Miu , Yamauchi Sae , Sugawara Norio , Yasui-Furukori Norio , Saruwatari Junji
Published: September 2020

Background

Several medications, such as anticholinergics, are considered to affect the swallowing function adversely; however, whether or not anticholinergics or polypharmacy should be avoided to prevent eating dysfunction in elderly populations remains unclear. We therefore examined whether or not the number of medications or the use of anticholinergics was associated with recovery from tubal feeding in elderly inpatients.

Methods

We conducted a retrospective 1-year observation study in 95 Japanese hospitalized patients (83.3 ± 9.7 years old) receiving nutrition through a feeding tube. The anticholinergic cognitive burden scale (ACBs) was used as an index for quantifying the anticholinergic action.

Results

Thirty-six (37.9%) subjects recovered from tubal to oral feeding during the observation period. The logistic regression models showed that an increased number of prescribed medications and an increase in ACBs decreased the incidence of recovery from tubal feeding (odds ratio [95% confidence interval]: 0.66 [0.50–0.87],P = 0.003 and 0.52 [0.29–0.92],P = 0.024, respectively). Furthermore, the cumulative incidence of recovery from tubal feeding was significantly lower in the subjects who were given an additional ≥3 medications during the observation period than in those who were not (hazard ratio [95% confidence interval]: 0.08 [0.01–0.59],P = 0.014).

Conclusions

The findings of this study suggest that an increased exposure to medications, especially anticholinergics, may be an important factor interfering with recovery from tubal feeding in hospitalized elderly patients.
The prediction for development of COVID-19 in global major epidemic areas through empirical trends in China by utilizing state transition matrix model
Authors: Zheng Zhong , Wu Ke , Yao Zhixian , Zheng Xinyi , Zheng Junhua , Chen Jian
Published: September 2020

Background

Since pneumonia caused by coronavirus disease 2019 (COVID-19) broke out in Wuhan, Hubei province, China, tremendous infected cases has risen all over the world attributed to its high transmissibility. We aimed to mathematically forecast the inflection point (IFP) of new cases in South Korea, Italy, and Iran, utilizing the transcendental model from China.

Methods

Data from reports released by the National Health Commission of the People’s Republic of China (Dec 31, 2019 to Mar 5, 2020) and the World Health Organization (Jan 20, 2020 to Mar 5, 2020) were extracted as the training set and the data from Mar 6 to 9 as the validation set. New close contacts, newly confirmed cases, cumulative confirmed cases, non-severe cases, severe cases, critical cases, cured cases, and death were collected and analyzed. We analyzed the data above through the State Transition Matrix model.

Results

The optimistic scenario (non-Hubei model, daily increment rate of − 3.87%), the cautiously optimistic scenario (Hubei model, daily increment rate of − 2.20%), and the relatively pessimistic scenario (adjustment, daily increment rate of − 1.50%) were inferred and modeling from data in China. The IFP of time in South Korea would be Mar 6 to 12, Italy Mar 10 to 24, and Iran Mar 10 to 24. The numbers of cumulative confirmed patients will reach approximately 20 k in South Korea, 209 k in Italy, and 226 k in Iran under fitting scenarios, respectively. However, with the adoption of different diagnosis criteria, the variation of new cases could impose various influences in the predictive model. If that happens, the IFP of increment will be earlier than predicted above.

Conclusion

The end of the pandemic is still inapproachable, and the number of confirmed cases is still escalating. With the augment of data, the world epidemic trend could be further predicted, and it is imperative to consummate the assignment of global medical resources to curb the development of COVID-19.
Correction to: Vogesella perlucida-induced bacteremia in an advanced-age patient: first case report
Authors: Yu Zengxian , Zhu Fang , Tao Xinghe , Zhang Lu , Wu Suliu , Dong Chunfu , Dong Yeqing , Chen Ge , Zhou Xinyang , Fang Yinfei , Xu Kechen
Published: September 2020

An amendment to this paper has been published and can be accessed via the original article.
Salivary microbiome in patients undergoing hemodialysis and its associations with the duration of the dialysis
Authors: Duan Xiaobo , Chen Xiaolei , Gupta Megha , Seriwatanachai Dutmanee , Xue Hanxiao , Xiong Qiuchan , Xu Tong , Li Dan , Mo Anchun , Tang Xi , Zhou Xuedong , Li Yuqing , Yuan Quan
Published: September 2020

Background

Chronic kidney disease (CKD) patients, especially those with end stage renal disease (ESRD) undergoing hemodialysis (HD), exhibit high prevalence of periodontitis. This cross-sectional study aimed to investigate the periodontal status of HD patients and its relationship with salivary microbiome.

Methods

One hundred eight HD patients and one hundred healthy control individuals were recruited. They were subjected to periodontal examination followed by saliva samples collection for 16S rRNA gene sequencing.

Results

The HD patients were with worse periodontal health status, and exhibited higher salivary microbial diversity and lower richness. The periodontal pathogens were significantly enriched in the HD patients. The inferred functional analyze showed microbes enriched in the HD patients were mainly related to metabolism. Despite the periodontal status and overall structure of the microbiome were not significantly altered as the HD duration prolonged, the abundance of Lachnospiraceae [G-2] sp. |HMT_096| is positively correlated with the duration of HD and the community periodontal index (CPI). Five OTUs (operational taxonomic units) belonging to the phyla Firmicutes were enriched as the duration prolonged, and four OTUs originated from the phyla Proteobacteria were negatively related with the CPI index. ESRD patients undergoing HD exhibited microbiota structural, compositional and functional differences compared with the healthy controls. And the species changed as the duration of hemodialysis prolonged.

Conclusions

End stage renal disease changes salivary microbiome and is a risk factor for oral dysbiosis.
A qualitative study exploring the needs related to the health system in women with experience of pregnancy termination due to fetal anomalies in Iran
Authors: Kamranpour Bahareh , Noroozi Mahnaz , Bahrami Masoud
Published: September 2020

Background

In order to provide appropriate and adequate care to women who have experienced termination of pregnancy due to fetal anomalies, the health needs of this group should be assessed. Considering the lack of information about the care and services required by these women in Iran, this study was conducted with the aim of exploring the needs related to the health system in women with experience of pregnancy termination due to fetal anomalies.

Methods

This study was conducted with a qualitative approach. 40 participants were selected through purposive sampling, and the data were collected through in-depth semi structured interviews and field notes, and analyzed using conventional qualitative content analysis.

Results

After analyzing the texts, the needs related to the health system in women with experience of pregnancy termination due to fetal anomalies were categorized in the three main categories: “efficient treatment team”, “optimal organizational structure in providing services” and “financial support for families”.

Conclusions

The findings of the present study by exploring and highlighting the needs related to the health system in different dimensions in women with experience of pregnancy termination due to fetal anomalies can be helpful for designing and providing basic and comprehensive care programs.