bluuebunny/crossref_metadata_2025 huggingface dataset:
Study Designs for Extending Causal Inferences From a Randomized Trial to a Target Population
Authors: Dahabreh Issa J , Haneuse Sebastien J-P A , Robins James M , Robertson Sarah E , Buchanan Ashley L , Stuart Elizabeth A , Hernán Miguel A
Published: December 2020

In this article, we examine study designs for extending (generalizing or transporting) causal inferences from a randomized trial to a target population. Specifically, we consider nested trial designs, where randomized individuals are nested within a sample from the target population, and nonnested trial designs, including composite data-set designs, where observations from a randomized trial are combined with those from a separately obtained sample of nonrandomized individuals from the target population. We show that the counterfactual quantities that can be identified in each study design depend on what is known about the probability of sampling nonrandomized individuals. For each study design, we examine identification of counterfactual outcome means via the g-formula and inverse probability weighting. Last, we explore the implications of the sampling properties underlying the designs for the identification and estimation of the probability of trial participation.
An Update on the Posterior Earlobe/Concha Mastoid Suspension Suture to Correct “Pixie Ear” Following Facelift: Review of 40 Cases
Authors: Kaye Kai O , Casabona Gabriela R , Paprottka Felix J
Published: December 2020

Background

Auricular displacement (AD) and earlobe distortion, such as “pixie ear,” are commonly seen deformities after rhytidectomies. In 2018, the authors of this article published a prophylactic technique (posterior earlobe rotation flap [PERF] and concha-mastoid suspension suture [CMSS]) to prevent such cosmetic-related complications in primary facelift surgery. Here, the authors review the utilization of this technique to correct such deformities in patients receiving revision facelift surgeries.

Objectives

The authors sought to demonstrate the usefulness of this technique in reconstructive cases suffering from such aesthetic deformities.

Methods

A total 25 secondary and 15 tertiary rhytidectomies were operated between 2015 and 2018. A combination PERF/CMSS technique was performed bilaterally during each revision facelift surgery (n = 80). A retrospective data analysis (preoperatively; 1 year postoperatively) was conducted to detect any deformities.

Results

No “pixie ear” deformities were seen in any of our patients postoperatively. AD was detected twice and unilateral hypertrophic scarring once. The postoperative photometric analysis showed a natural ptosis grade I/II in all our patients. The total rate of aesthetic-related complications in our patient cohort was 3.75% (AD: 2.5%; hypertrophic scarring: 1.25%).

Conclusions

After demonstrating the effectiveness of the PERF and CMSS techniques in primary facelifts, the authors reviewed the technique’s effectiveness for restoring earlobe distortion and AD in secondary or tertiary rhytidectomy cases. In addition to its prophylactic utilization, this method also possesses strong reconstructive power to change tension vectors applied on the face (CMSS) and/or to correct pre-existing aesthetic complications, such as “pixie ear” formation (PERF).

Level of Evidence: 4
DeepNOG: fast and accurate protein orthologous group assignment
Authors: Feldbauer Roman , Gosch Lukas , Lüftinger Lukas , Hyden Patrick , Flexer Arthur , Rattei Thomas
Published: December 2020

Motivation

Protein orthologous group databases are powerful tools for evolutionary analysis, functional annotation or metabolic pathway modeling across lineages. Sequences are typically assigned to orthologous groups with alignment-based methods, such as profile hidden Markov models, which have become a computational bottleneck.

Results

We present DeepNOG, an extremely fast and accurate, alignment-free orthology assignment method based on deep convolutional networks. We compare DeepNOG against state-of-the-art alignment-based (HMMER, DIAMOND) and alignment-free methods (DeepFam) on two orthology databases (COG, eggNOG 5). DeepNOG can be scaled to large orthology databases like eggNOG, for which it outperforms DeepFam in terms of precision and recall by large margins. While alignment-based methods still provide the most accurate assignments among the investigated methods, computing time of DeepNOG is an order of magnitude lower on CPUs. Optional GPU usage further increases throughput massively. A command-line tool enables rapid adoption by users.

Availabilityand implementation

Source code and packages are freely available at https://github.com/univieCUBE/deepnog. Install the platform-independent Python program with $pip install deepnog.

Supplementary information

Supplementary data are available at Bioinformatics online.
Data-driven noise modeling of digital DNA melting analysis enables prediction of sequence discriminating power
Authors: Langouche Lennart , Aralar April , Sinha Mridu , Lawrence Shelley M , Fraley Stephanie I , Coleman Todd P
Published: December 2020

Motivation

The need to rapidly screen complex samples for a wide range of nucleic acid targets, like infectious diseases, remains unmet. Digital High-Resolution Melt (dHRM) is an emerging technology with potential to meet this need by accomplishing broad-based, rapid nucleic acid sequence identification. Here, we set out to develop a computational framework for estimating the resolving power of dHRM technology for defined sequence profiling tasks. By deriving noise models from experimentally generated dHRM datasets and applying these to in silico predicted melt curves, we enable the production of synthetic dHRM datasets that faithfully recapitulate real-world variations arising from sample and machine variables. We then use these datasets to identify the most challenging melt curve classification tasks likely to arise for a given application and test the performance of benchmark classifiers.

Results

This toolbox enables the in silico design and testing of broad-based dHRM screening assays and the selection of optimal classifiers. For an example application of screening common human bacterial pathogens, we show that human pathogens having the most similar sequences and melt curves are still reliably identifiable in the presence of experimental noise. Further, we find that ensemble methods outperform whole series classifiers for this task and are in some cases able to resolve melt curves with single-nucleotide resolution.

Availability and implementation

Data and code available on https://github.com/lenlan/dHRM-noise-modeling.

Supplementary information

Supplementary data are available at Bioinformatics online.
The COVID-19 Ontology
Authors: Sargsyan Astghik , Kodamullil Alpha Tom , Baksi Shounak , Darms Johannes , Madan Sumit , Gebel Stephan , Keminer Oliver , Jose Geena Mariya , Balabin Helena , DeLong Lauren Nicole , Kohler Manfred , Jacobs Marc , Hofmann-Apitius Martin
Published: December 2020

Motivation

The COVID-19 pandemic has prompted an impressive, worldwide response by the academic community. In order to support text mining approaches as well as data description, linking and harmonization in the context of COVID-19, we have developed an ontology representing major novel coronavirus (SARS-CoV-2) entities. The ontology has a strong scope on chemical entities suited for drug repurposing, as this is a major target of ongoing COVID-19 therapeutic development.

Results

The ontology comprises 2270 classes of concepts and 38 987 axioms (2622 logical axioms and 2434 declaration axioms). It depicts the roles of molecular and cellular entities in virus-host interactions and in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19. The performance of the ontology has been tested on Medline and the COVID-19 corpus provided by the Allen Institute.

Availabilityand implementation

COVID-19 Ontology is released under a Creative Commons 4.0 License and shared via https://github.com/covid-19-ontology/covid-19. The ontology is also deposited in BioPortal at https://bioportal.bioontology.org/ontologies/COVID-19.

Supplementary information

Supplementary data are available at Bioinformatics online.
Estimation of the generation interval using pairwise relative transmission probabilities
Authors: Leavitt Sarah V , Jenkins Helen E , Sebastiani Paola , Lee Robyn S , Horsburgh C Robert , Tibbs Andrew M , White Laura F
Published: December 2020

The generation interval (the time between infection of primary and secondary cases) and its often used proxy, the serial interval (the time between symptom onset of primary and secondary cases) are critical parameters in understanding infectious disease dynamics. Because it is difficult to determine who infected whom, these important outbreak characteristics are not well understood for many diseases. We present a novel method for estimating transmission intervals using surveillance or outbreak investigation data that, unlike existing methods, does not require a contact tracing data or pathogen whole genome sequence data on all cases. We start with an expectation maximization algorithm and incorporate relative transmission probabilities with noise reduction. We use simulations to show that our method can accurately estimate the generation interval distribution for diseases with different reproductive numbers, generation intervals, and mutation rates. We then apply our method to routinely collected surveillance data from Massachusetts (2010–2016) to estimate the serial interval of tuberculosis in this setting.
Genetic variations in microRNA-binding sites of solute carrier transporter genes as predictors of clinical outcome in colorectal cancer
Authors: Bendova Petra , Pardini Barbara , Susova Simona , Rosendorf Jachym , Levy Miloslav , Skrobanek Pavel , Buchler Tomas , Kral Jan , Liska Vaclav , Vodickova Ludmila , Landi Stefano , Soucek Pavel , Naccarati Alessio , Vodicka Pavel , Vymetalkova Veronika
Published: December 2020

One of the principal mechanisms of chemotherapy resistance in highly frequent solid tumors, such as colorectal cancer (CRC), is the decreased activity of drug transport into tumor cells due to low expression of important membrane proteins, such as solute carrier (SLC) transporters. Sequence complementarity is a major determinant for target gene recognition by microRNAs (miRNAs). Single-nucleotide polymorphisms (SNPs) in target sequences transcribed into messenger RNA may therefore alter miRNA binding to these regions by either creating a new site or destroying an existing one. miRSNPs may explain the modulation of expression levels in association with increased/decreased susceptibility to common diseases as well as in chemoresistance and the consequent inter-individual variability in drug response. In the present study, we investigated whether miRSNPs in SLC transporter genes may modulate CRC susceptibility and patient’s survival. Using an in silico approach for functional predictions, we analyzed 26 miRSNPs in 9 SLC genes in a cohort of 1368 CRC cases and 698 controls from the Czech Republic. After correcting for multiple tests, we found several miRSNPs significantly associated with patient’s survival. SNPs in SLCO3A1, SLC22A2 and SLC22A3 genes were defined as prognostic factors in the classification and regression tree analysis. In contrast, we did not observe any significant association between miRSNPs and CRC risk. To the best of our knowledge, this is the first study investigating miRSNPs potentially affecting miRNA binding to SLC transporter genes and their impact on CRC susceptibility or patient’s prognosis.
3D Ultrastructure of Synaptic Inputs to Distinct GABAergic Neurons in the Mouse Primary Visual Cortex
Authors: Hwang Yang-Sun , Maclachlan Catherine , Blanc Jérôme , Dubois Anaëlle , Petersen Carl C H , Knott Graham , Lee Seung-Hee
Published: December 2020

Synapses are the fundamental elements of the brain’s complicated neural networks. Although the ultrastructure of synapses has been extensively studied, the difference in how synaptic inputs are organized onto distinct neuronal types is not yet fully understood. Here, we examined the cell-type-specific ultrastructure of proximal processes from the soma of parvalbumin-positive (PV+) and somatostatin-positive (SST+) GABAergic neurons in comparison with a pyramidal neuron in the mouse primary visual cortex (V1), using serial block-face scanning electron microscopy. Interestingly, each type of neuron organizes excitatory and inhibitory synapses in a unique way. First, we found that a subset of SST+ neurons are spiny, having spines on both soma and dendrites. Each of those spines has a highly complicated structure that has up to eight synaptic inputs. Next, the PV+ and SST+ neurons receive more robust excitatory inputs to their perisoma than does the pyramidal neuron. Notably, excitatory synapses on GABAergic neurons were often multiple-synapse boutons, making another synapse on distal dendrites. On the other hand, inhibitory synapses near the soma were often single-targeting multiple boutons. Collectively, our data demonstrate that synaptic inputs near the soma are differentially organized across cell types and form a network that balances inhibition and excitation in the V1.
Functional Connectivity Predicts Individual Development of Inhibitory Control during Adolescence
Authors: Wang Haiyan , Fan Lingzhong , Song Ming , Liu Bing , Wu Dongya , Jiang Rongtao , Li Jin , Li Ang , Banaschewski Tobias , Bokde Arun L W , Quinlan Erin Burke , Desrivières Sylvane , Flor Herta , Grigis Antoine , Garavan Hugh , Chaarani Bader , Gowland Penny , Heinz Andreas , Ittermann Bernd , Martinot Jean-Luc , Martinot Marie-Laure Paillère , Artiges Eric , Nees Frauke , Orfanos Dimitri Papadopoulos , Poustka Luise , Millenet Sabina , Fröhner Juliane H , Smolka Michael N , Walter Henrik , Whelan Robert , Schumann Gunter , Jiang Tianzi
Published: December 2020

Derailment of inhibitory control (IC) underlies numerous psychiatric and behavioral disorders, many of which emerge during adolescence. Identifying reliable predictive biomarkers that place the adolescents at elevated risk for future IC deficits can help guide early interventions, yet the scarcity of longitudinal research has hindered the progress. Here, using a large-scale longitudinal dataset in which the same subjects performed a stop signal task during functional magnetic resonance imaging at ages 14 and 19, we tracked their IC development individually and tried to find the brain features predicting their development by constructing prediction models using 14-year-olds’ functional connections within a network or between a pair of networks. The participants had distinct between-subject trajectories in their IC development. Of the candidate connections used for prediction, ventral attention-subcortical network interconnections could predict the individual development of IC and formed a prediction model that generalized to previously unseen individuals. Furthermore, we found that connectivity between these two networks was related to substance abuse problems, an IC-deficit related problematic behavior, within 5 years. Our study reveals individual differences in IC development from mid- to late-adolescence and highlights the importance of ventral attention-subcortical network interconnections in predicting future IC development and substance abuse in adolescents.
Configural Cues Associated with Reward Elicit Theta Oscillations of Rat Retrosplenial Cortical Neurons Phase-Locked to LFP Theta Cycles
Authors: Yoshida Masashi , Chinzorig Choijiljav , Matsumoto Jumpei , Nishimaru Hiroshi , Ono Taketoshi , Yamazaki Mitsuaki , Nishijo Hisao
Published: December 2020

Previous behavioral studies implicated the retrosplenial cortex (RSC) in stimulus–stimulus associations, and also in the retrieval of remote associative memory based on EEG theta oscillations. However, neural mechanisms involved in the retrieval of stored information of such associations and memory in the RSC remain unclear. To investigate the neural mechanisms underlying these processes, RSC neurons and local field potentials (LFPs) were simultaneously recorded from well-trained rats performing a cue-reward association task. In the task, simultaneous presentation of two multimodal conditioned stimuli (configural CSs) predicted a reward outcome opposite to that associated with the individual presentation of each elemental CS. Here, we show neurophysiological evidence that the RSC is involved in stimulus–stimulus association where configural CSs are discriminated from each elementary CS that is a constituent of the configural CSs, and that memory retrieval of rewarding CSs is associated with theta oscillation of RSC neurons during CS presentation, which is phase-locked to LFP theta cycles. The results suggest that cue (elementary and configural CSs)-reinforcement associations are stored in the RSC neural circuits, and are retrieved in synchronization with LFP theta rhythm.
Temporal Encoding is Required for Categorization, But Not Discrimination
Authors: Yao Justin D , Sanes Dan H
Published: December 2020

Core auditory cortex (AC) neurons encode slow fluctuations of acoustic stimuli with temporally patterned activity. However, whether temporal encoding is necessary to explain auditory perceptual skills remains uncertain. Here, we recorded from gerbil AC neurons while they discriminated between a 4-Hz amplitude modulation (AM) broadband noise and AM rates >4 Hz. We found a proportion of neurons possessed neural thresholds based on spike pattern or spike count that were better than the recorded session’s behavioral threshold, suggesting that spike count could provide sufficient information for this perceptual task. A population decoder that relied on temporal information outperformed a decoder that relied on spike count alone, but the spike count decoder still remained sufficient to explain average behavioral performance. This leaves open the possibility that more demanding perceptual judgments require temporal information. Thus, we asked whether accurate classification of different AM rates between 4 and 12 Hz required the information contained in AC temporal discharge patterns. Indeed, accurate classification of these AM stimuli depended on the inclusion of temporal information rather than spike count alone. Overall, our results compare two different representations of time-varying acoustic features that can be accessed by downstream circuits required for perceptual judgments.
Assessment of the Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Reinfection in an Intense Reexposure Setting
Authors: Abu-Raddad Laith J , Chemaitelly Hiam , Malek Joel A , Ahmed Ayeda A , Mohamoud Yasmin A , Younuskunju Shameem , Ayoub Houssein H , Al Kanaani Zaina , Al Khal Abdullatif , Al Kuwari Einas , Butt Adeel A , Coyle Peter , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul Rahim Hanan F , Yassine Hadi M , Al Kuwari Mohamed G , Al Romaihi Hamad Eid , Al-Thani Mohamed H , Bertollini Roberto
Published: December 2020

Background

Risk of reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unknown. We assessed the risk and incidence rate of documented SARS-CoV-2 reinfection in a cohort of laboratory-confirmed cases in Qatar.

Methods

All SARS-CoV-2 laboratory-confirmed cases with at least 1 polymerase chain reaction–positive swab that was ≥45 days after a first positive swab were individually investigated for evidence of reinfection. Viral genome sequencing of the paired first positive and reinfection viral specimens was conducted to confirm reinfection.

Results

Out of 133 266 laboratory-confirmed SARS-CoV-2 cases, 243 persons (0.18%) had at least 1 subsequent positive swab ≥45 days after the first positive swab. Of these, 54 cases (22.2%) had strong or good evidence for reinfection. Median time between the first swab and reinfection swab was 64.5 days (range, 45–129). Twenty-three of the 54 cases (42.6%) were diagnosed at a health facility, suggesting presence of symptoms, while 31 (57.4%) were identified incidentally through random testing campaigns/surveys or contact tracing. Only 1 person was hospitalized at the time of reinfection but was discharged the next day. No deaths were recorded. Viral genome sequencing confirmed 4 reinfections of 12 cases with available genetic evidence. Reinfection risk was estimated at 0.02% (95% confidence interval [CI], .01%–.02%), and reinfection incidence rate was 0.36 (95% CI, .28–.47) per 10 000 person-weeks.

Conclusions

SARS-CoV-2 reinfection can occur but is a rare phenomenon suggestive of protective immunity against reinfection that lasts for at least a few months post primary infection.
Tariffs and Politics: Evidence from Trump’s Trade Wars
Authors: Fetzer Thiemo , Schwarz Carlo
Published: December 2020

We use the recent trade escalation between the USA and its trade partners to study whether retaliatory tariffs are politically targeted. We find comprehensive evidence using individual and aggregate voting data suggesting that retaliation is carefully targeted to hurt Trump. We develop a simulation approach to construct counterfactual retaliation responses allowing us to quantify the extent of political targeting while also studying potential trade-offs. China appears to place great emphasis on achieving maximal political targeting. The EU seems to have been successful in maximising political targeting while at the same time minimising the potential damage to its economy.
Hybrid robotic versus hybrid laparoscopic Ivor Lewis oesophagectomy: a case-matched analysis
Authors: Giulini Luca , Nasser Corinna A , Tank Julian , Papp Marton , Stein Hubert J , Dubecz Attila
Published: December 2020

OBJECTIVES

Robotic-assisted oesophagectomy for cancer has been increasingly employed worldwide; however, the benefits of this technique compared to conventional minimally invasive oesophagectomy are unclear. Since 2016, hybrid robotic minimally invasive oesophagectomy (R-HMIE) has increasingly replaced hybrid laparoscopic minimally invasive oesophagectomy (HMIE) as the standard of care in our institution. The aim of this study was to compare these procedures.

METHODS

Over a 10-year period, 686 patients underwent oesophagectomy at our institution. Out of these patients, 128 patients with cancer were treated with a hybrid minimally invasive technique. Each patient who underwent R-HMIE was matched according to gender, age, comorbidity, American Society of Anesthesiologists classification, Union International Contre le Cancer stage, localization, histology and neoadjuvant treatment with a patient who underwent HMIE. Perioperative parameters were extracted from our database and compared between the 2 groups.

RESULTS

After the matching procedure, 88 patients were included in the study. Between HMIE and R-HMIE, no significant differences (P > 0.05) were found in operating time (median 281 vs 300 min), R0 resection rate (n = 42 vs 42), harvested lymph nodes (median 28 vs 24), hospital stay (median 19 vs 17 days) and intensive care unit stay (median 7 vs 6.5 days). Regarding surgical complications, no difference could be observed either (n = 42 vs 44).

CONCLUSIONS

Minimally invasive oesophagectomy remains a challenging operation with high morbidity even in a high-volume institution. According to our intra- and short-term results, we have found no difference between R-HMIE and HMIE.
Education and health: long-run effects of peers, tracking and years
Authors: Fischer Martin , Gerdtham Ulf-G , Heckley Gawain , Karlsson Martin , Kjellsson Gustav , Nilsson Therese
Published: December 2020

We investigate two parallel school reforms in Sweden to assess the long-run health effects of education. One reform only increased years of schooling, while the other increased years of schooling but also removed tracking leading to a more mixed socioeconomic peer group. By differencing the effects of the parallel reforms we separate the effect of de-tracking and peers from that of more schooling. We find that the pure years of schooling reform reduced mortality and improved current health. Differencing the effects of the reforms shows significant differences in the estimated impacts, suggesting that de-tracking and subsequent peer effects resulted in worse health.
Novel left ventricular cardiac synchronization: left ventricular septal pacing or left bundle branch pacing?
Authors: Wu Shengjie , Sharma Parikshit S , Huang Weijian
Published: December 2020

It is well recognized that a high burden of right ventricular pacing results in deleterious clinical outcomes over the long term. His bundle pacing can achieve optimal ventricular synchronization; however, relatively high pacing thresholds, low R-wave amplitudes, and the long-term performance have been concerns. Recently, left ventricular (LV) septal endocardium pacing (LVSP) has demonstrated improved acute haemodynamics. Another novel technique of intraseptal left bundle branch pacing (LBBP) via transvenous approach has been adopted rapidly and has demonstrated its feasibility and effectiveness. This article reviews the clinical application and differences between LVSP and LBBP. Compared with LVSP, LBBP has strict criteria for left conduction system capture and lead location. In addition to LV septal capture it also stimulates the proximal left bundle branch, resulting in rapid and physiological LV activation. With a uniformity and standardization of the implant procedure and definitions, it may be possible to achieve widespread application of this form of physiological pacing.
Evaluation of a Novel Technology-Based Program Designed to Assess and Train Everyday Skills in Older Adults
Authors: Czaja Sara J , Kallestrup Peter , Harvey Philip D
Published: December 2020

Background and Objectives

Performance of everyday activities is often challenging for older adults. We evaluated a novel computer-based functional skills assessment and training (CFSAT) program, which includes simulations of everyday tasks (e.g., money and medication management).

Research Design and Methods

The sample included noncognitively impaired (NC) older adults (n = 51) and cognitively impaired (CI) older adults (n = 43), who ranged in age from 60 to 86 years (M = 73.12; SD = 6.06), were primarily female (90%), and ethnically diverse (23% Hispanic, 51% African American). Participants (stratified by cognitive status) were randomized to 1 of the 2 conditions training alone (CFSAT) or CFSAT with computerized cognitive training and trained up to 24 training sessions. Task performance, using measures of completion time and efficiency (accuracy/completion time), was evaluated at baseline, the final training session, and immediately posttraining with an alternate form of the CFSAT assessment.

Results

Both NC and CI participants demonstrated significant performance improvements across all tasks following training (all ps < .001). The CI participants demonstrated reduced training gains compared to the NC participants (all ps < .001). Training gains did not vary as a function of training conditions.

Discussion and Implications

The findings suggest that CFSAT is an efficacious program for assessing and training everyday task performance. CFSAT can ultimately be used as an intervention strategy to enhance functional independence for aging adults with and without cognitive impairments.
Overall Work and Practice Satisfaction of Licensed Clinical Social Workers in the National Health Service Corps Loan Repayment Program
Authors: Yun Jonathan , Zerden Lisa de Saxe , Cuddeback Gary , Konrad Thomas , Pathman Donald E
Published: December 2020

Little is known about the job satisfaction of licensed clinical social workers (LCSWs) participating in the National Health Service Corps (NHSC) federal Loan Repayment Program (LRP). Employee satisfaction in organizations is important for organizational well-being and to decrease turnover. A satisfied NHSC LCSW workforce is also important given the array of services it provides, especially in rural and underserved areas. This study examined the work satisfaction of 386 LCSWs participating in the NHSC LRP in 21 states. Rural upbringing, being older than 40 years, and a higher salary were significantly associated with overall work and practice satisfaction. In addition, satisfaction with administration, staff and the practices’ linkages to other health providers, the mission of the practice, and connection with patients were strongly associated with overall work and practice satisfaction. To our knowledge, this is the first study to examine the work and practice satisfaction of LCSWs participating in the NHSC LRP, and our findings have the potential to inform the NHSC’s strategies in managing and retaining LCSWs.
Estimating individual fish school biomass using digital omnidirectional sonars, applied to mackerel and herring
Authors: Peña Héctor , Macaulay Gavin J , Ona Egil , Vatnehol Sindre , Holmin Arne J
Published: December 2020

Economic profitability and responsible fisheries are objectives of fishermen and fisheries managers. In purse seine fisheries, an accurate biomass estimate of the targeted school is crucial to accomplish this. For this study, omnidirectional fisheries sonar was used to estimate individual school biomass of Norwegian spring spawning herring (Clupea harengus) and Atlantic mackerel (Scomber scombrus). A sonar sampling design based on professional skipper’s experience provided detailed information on school dimensions and acoustic backscattering. Using calibrated digital sonar data, school volume and fish densities were obtained, and school biomass computed. A positive linear relation was found between the estimated sonar school biomass and purse seine catches for both species (r2 = 0.92; residual standard error, RSE = 4.7 t). Large variability in volume backscattering coefficient and uncertainty in side-aspect target strength (TS) are the main sources of discrepancy between the estimates and the catch. Using a 4 dB (39%) weaker mean TS for mean side-aspect TS than the normal mean dorsal aspect TS was needed for optimizing the 1:1 relationship between sonar biomass estimate and catch. Accurate estimation of single school biomass can reduce the catch of unexpectedly large schools, leading to improvements in economic efficiency and reduced release of dead or dying fish.
Oncological outcomes of unsuspected pN2 in patients with non-small-cell lung cancer: a systematic review and meta-analysis
Authors: IJsseldijk Michiel A , ten Broek Richard P G , Wiering Bastiaan , Hekma Edo , de Roos Marnix A J
Published: December 2020

OBJECTIVES

Optimal treatment of stage IIIA (N2) non-small-cell lung cancer (NSCLC) is controversial. Guidelines advise induction therapy before surgical resection. A proportion of patients with cN0 NSCLC are postoperatively upstaged due to unsuspected N2 disease. Survival of unsuspected N2 NSCLC treated with surgery varies and technical feasibility of video-assisted thoracic surgery (VATS) is unknown. The purpose of this study was to assess prevalence and survival of unsuspected N2 NSCLC treated with thoracotomy or VATS.

METHODS

A systematic review and meta-analysis was performed of all available literatures through Pubmed, Cochrane, EMBASE, Web of Science, Trials registries and System for Information on Grey Literature (SIGLE) from 2000 to 2019. Outcomes of interest were prevalence, overall survival (OS) and disease-free survival of unsuspected N2 NSCLC. Secondary outcomes were number of harvested lymph nodes, postoperative complications and survival of unsuspected N2 NSCLC treated with VATS.

RESULTS

Seventeen studies with patients with clinical stage N0-1 and unsuspected pN2 NSCLC were included. Prevalence of unsuspected pN2 was 8.6%. Three- and 5-year OS was 58% [95% confidence interval (CI) 37–78%) (N = 4337] and 35% (95% CI 28–43%) (N = 4337). Three- and 5-y ear disease-free survival was 48% (95% CI 30–66%) (N = 109) and 35% (95% CI 24–46%) (N = 517). VATS resulted in a low complication rate with similar 5-year OS as thoracotomy.

CONCLUSIONS

In patients with cN0-1 NSCLC, a minority has unsuspected pN2 NSCLC. Even for these patients, 5-year OS and disease-free survival are reasonable. VATS with adequate lymph node dissection is the treatment of choice when in experienced hands. Adjuvant therapy should be provided in absence of relevant comorbidity.
The combined impact of smoking, obesity and alcohol on life-expectancy trends in Europe
Authors: Janssen Fanny , Trias-Llimós Sergi , Kunst Anton E
Published: December 2020

Background

Smoking, obesity and alcohol abuse greatly affect mortality and exhibit a distinct time dynamic, with their prevalence and associated mortality rates increasing and (eventually) declining over time. Their combined impact on secular trends in life expectancy is unknown but is relevant for understanding these trends. We therefore estimate the combined impact of smoking, obesity and alcohol on life-expectancy trends in Europe.

Methods

We used estimated national age-specific smoking-, obesity- and alcohol-attributable mortality fractions for 30 European countries by sex, 1990–2014, which we aggregated multiplicatively to obtain lifestyle-attributable mortality. We estimated potential gains in life expectancy by eliminating lifestyle-attributable mortality and compared past trends in life expectancy at birth (e0) with and without lifestyle-attributable mortality. We examined all countries combined, by region and individually.

Results

Among men, the combined impact of smoking, obesity and alcohol on e0 declined from 6.6 years in 1990 to 5.8 years in 2014, mainly due to declining smoking-attributable mortality. Among women, the combined impact increased from 1.9 to 2.3 years due to mortality increases in all three lifestyle-related factors. The observed increase in e0 over the 1990–2014 period was 5.0 years for men and 4.0 years for women. After excluding lifestyle-attributable mortality, this increase would have been 4.2–4.3 years for both men and women.

Conclusion

Without the combined impact of smoking, obesity and alcohol, the increase over time in life expectancy at birth would have been smaller among men but larger among women, resulting in a stable increase in e0, parallel for men and women.
Mechanisms Underlying the Comorbidity of Schizophrenia and Type 2 Diabetes Mellitus
Authors: Mizuki Yutaka , Sakamoto Shinji , Okahisa Yuko , Yada Yuji , Hashimoto Nozomu , Takaki Manabu , Yamada Norihito
Published: December 2020

The mortality rate of patients with schizophrenia is high, and life expectancy is shorter by 10 to 20 years. Metabolic abnormalities including type 2 diabetes mellitus (T2DM) are among the main reasons. The prevalence of T2DM in patients with schizophrenia may be epidemiologically frequent because antipsychotics induce weight gain as a side effect and the cognitive dysfunction of patients with schizophrenia relates to a disordered lifestyle, poor diet, and low socioeconomic status. Apart from these common risk factors and risk factors unique to schizophrenia, accumulating evidence suggests the existence of common susceptibility genes between schizophrenia and T2DM. Functional proteins translated from common genetic susceptibility genes are known to regulate neuronal development in the brain and insulin in the pancreas through several common cascades. In this review, we discuss common susceptibility genes, functional cascades, and the relationship between schizophrenia and T2DM. Many genetic and epidemiological studies have reliably associated the comorbidity of schizophrenia and T2DM, and it is probably safe to think that common cascades and mechanisms suspected from common genes’ functions are related to the onset of both schizophrenia and T2DM. On the other hand, even when genetic analyses are performed on a relatively large number of comorbid patients, the results are sometimes inconsistent, and susceptibility genes may carry only a low or moderate risk. We anticipate future directions in this field.
Impacts of Digitalisation on Employment Relationships and the Need for more Democracy at Work
Authors: Pärli Kurt
Published: December 2020

The world of labour is in transformation due to automation, digitalisation and platform work. Digitalisation is changing the classic relationship between employer and employee; this also affects workers’ participation rights within the company. New forms of work demand very high self-organisation and active commitment on the part of employees to solving process problems and optimising processes. If at the same time management and organisational structures remain largely top-down and employees hardly have any say, this is contradictory. Co-determination is a central component of qualified work. Without the expansion of democratic processes within the company, the opportunities offered by digitalisation will not be fully exploited. Digital processes require cooperation across technical, departmental, and hierarchical boundaries, which must inevitably lead to the democratisation of company decisions. Digitalisation may also act as a catalyst for the dormant debate about “democracy in the workplace”.
HFE at the frontiers of COVID-19. Human factors/ergonomics to support the communication for safer care in Italy during the COVID-19 pandemic
Authors: Albolino Sara , Dagliana Giulia , Tanzini Michela , Beleffi Elena , Ranzani Francesco , Flore Elisabetta
Published: December 2020

Italy was the first country after China to be affected by COVID-19. The wave of the emergency found our country unprepared to cope with the surge of patients going to first aid departments to seek assistance in the almost complete paralysis of community health. Human factors and ergonomics (HFE) can effectively contribute to, and improve the effectiveness of, a pandemic response working on several key areas: training, adapting workflows and processes, restructuring teams and tasks, effective mechanisms and tools for communication, engaging patients and families and learning from failures and successes. In Italy, HFE expertise has been able to provide our healthcare systems with some easy-to-realize solutions (particularly dedicated to improving communication, team work and situational awareness) in order to cope with the need for rapid adaptations to new and unknown scenarios: ensuring information and communication continuity in the different levels of the healthcare system; identifying hazard opportunity through risk management tool; providing training through simulation; organizing regular briefing and debriefing; enhancing the reporting and learning system as an informal way of communicating adverse events and supporting information campaign and education initiatives for the public.
The Oil Nouveau-Riche and Arms Imports
Authors: Vézina Pierre-Louis
Published: December 2020

Countries that strike it rich when exploring for oil and gas often fail to see growth materialise. This paper shows that one way things can go awry is via squandering new wealth, based on future resource revenues, on arms imports. Across developing countries, in the 5 years following a giant oil or gas discovery, arms imports increase by 30% on average. This effect only occurs in non-democracies with high levels of corruption, and there is suggestive evidence that it is driven in part by arms imports from China and Russia, and not by imports from other major arms exporters. These estimates can be interpreted causally as the timing of giant oil discoveries is unpredictable due to the uncertain nature of exploration.
Binding of collagen gene products with titanium oxide
Authors: Song Qin , Iku Shouhei , Sammons Rachel , Yagami Kimitoshi , Furusawa Toshitake , Morimoto Koichi , Rahaman Md Shiblur , Kurasaki Masaaki , Tokura Seiichi , Kuboki Yoshinori
Published: December 2020

Titanium is the only metal to which osteoblasts can adhere and on which they can grow and form bone tissue in vivo, resulting in a strong bond between the implant and living bone. This discovery provides the basis for the universal medical application of Ti. However, the biochemical mechanism of bond formation is still unknown. We aimed to elucidate the mechanism of bond formation between collagen, which constitutes the main organic component of bone, and TiO2, of which the entire surface of pure Ti is composed. We analysed the binding between the soluble collagen and TiO2 by chromatography with a column packed with Ti beads of 45 µm, and we explored the association between collagen fibrils and TiO2 (anatase) powders of 0.2 µm. We ran the column of chromatography under various elution conditions. We demonstrated that there is a unique binding affinity between Ti and collagen. This binding capacity was not changed even in the presence of the dissociative solvent 2M urea, but it decreased after heat denaturation of collagen, suggesting the contribution of the triple-helical structure. We propose a possible role of periodically occurring polar amino acids and the collagen molecules in the binding with TiO2.
Cutaneous Thermal Injury Modulates Blood and Skin Metabolomes Differently in a Murine Model
Authors: Alkhalil Abdulnaser , Ball Robert L , Garg Gaurav , Day Anna , Carney Bonnie C , Kumar Raina , Hammamieh Rasha , Moffatt Lauren T , Shupp Jeffrey W
Published: December 2020

As the field of metabolomics develops further, investigations of how the metabolome is affected following thermal injury may be helpful to inform diagnostics and guide treatments. In this study, changes to the metabolome were tested and validated in a murine burn injury model. After a 30% total body surface scald injury or sham procedure sera and skin biopsies were collected at 1, 2, 6, or 24 hr.

Burn-specific changes in the metabolome were detected compared to sham animals. The sera metabolome exhibited a more rapid response to burn injury than that of the skin and it peaked more proximal to injury (6 vs 24 hr). Progression of metabolic response in the skin was less synchronous and showed a higher overlap of the significantly modified metabolites (SMMs) among tested time-points. Top affected pathways identified by SMMs of skin included inositol phosphate metabolism, ascorbate and alderate metabolism, caffeine metabolism, and the pentose phosphate pathway. Future research is warranted in human and larger animal models to further elucidate the role of metabolomic perturbations and the pathophysiology following burn injury.
Aedes Albopictus (Diptera: Culicidae) Susceptibility Status to Agrochemical Insecticides Used in Durian Planting Systems in Southern Thailand
Authors: Ratisupakorn Sakda , Lorn Sokchan , Dada Nsa , Ngampongsai Aran , Chaivisit Pawit , Ritthison Wanapa , Tainchum Krajana
Published: December 2020

High rates of dengue morbidity occur in southern Thailand. The intensive application of insecticides in orchards could affect not only agricultural insect pests, but also nontarget mosquitoes or beneficial insects. In this study, the type and quantity of insecticides commonly used across durian plantations in southern Thailand were characterized, along with the population density of Aedes albopictus (Skuse) (Diptera: Culicidae). Our primary aim was to determine the susceptibility status of field-derived Ae. albopictus to typical application concentrations of four agrochemical insecticides; cypermethrin, chlorpyrifos, carbaryl, and imidacloprid. Mosquito eggs were collected from durian cultivation sites in five provinces in southern Thailand and used to generate adults for susceptibility tests. The cultivation sites were categorized into three groups based on insecticide application: intensive application of insecticides, low application of insecticides, and no application of insecticides. Twenty ovitraps were deployed for at least three consecutive days at each study site to collect mosquito eggs and to determine Ae. albopictus population density. WHO tube assays were used to determine the susceptibility of adult mosquitoes derived from field-collected eggs to selected insecticides. This represents the first report of the susceptibility status of Ae. albopictus from durian orchards in southern Thailand to agrochemical insecticides. Results showed complete susceptibility of these Ae. albopictus to chlorpyrifos, but reduced mortality following exposure to λ-cyhalothrin, carbaryl, and imidacloprid, which is suggestive of the development of resistance. These findings provide new insights into the status of insecticide susceptibility in Ae. albopictus populations, with important implications for mosquito and mosquito-borne disease control in Thailand.
The External Morphology of the Eggs of Culex (Culex) saltanensis (Diptera: Culicidae) Under Scanning Electron Microscopy
Authors: Santos-Mallet J R , Balthazar T D , Oliveira A A , Marques W A , Bastos A Q , Freitas S P C
Published: December 2020

The aim of the present study was to describe the morphology of the eggs of Culex (Culex) saltanensis Dyar that occurs in the Neotropical region. Eggs of the Cx. (Cux.) saltanensis were collected at the Mata Atlântica FIOCRUZ campus, fixed in 1% osmium tetroxide, prepared for mounting on metal supports, observed under a scanning electron microscope, and described morphologically. The eggs had a coniform shape with a length of approximately 0.5 mm (505–510 µm) and a width in the median portion of 117 µm (113–123 µm). Upper portion is lined with tubers of irregular shape and varying sizes (0.64–1.31 µm), located on a cross-linked matrix forming bands observed under optical microscopy. The micropyle is encased in a necklace of approximately 6.6-µm plates arranged in a flower-like shape. Comparing Cx. (Cux.) saltanensis eggs with several species of different genera, important divergent characteristics can be observed. However, this study points to the need for new descriptions of eggs of species belonging to the same subgenus in order to analyze if there will be differences between them. Culex (Cux.) saltanensis eggs have particular characteristics not observed in eggs of other Culicidae genera.
Concordance Between Tumor and Germline BRCA Status in High-Grade Ovarian Carcinoma Patients in the Phase III PAOLA-1/ENGOT-ov25 Trial
Authors: Callens Céline , Vaur Dominique , Soubeyran Isabelle , Rouleau Etienne , Just Pierre-Alexandre , Guillerm Erell , Golmard Lisa , Goardon Nicolas , Sevenet Nicolas , Cabaret Odile , Harter Philipp , Gonzalez-Martin Antonio , Fujiwara Keiichi , Cecere Sabrina Chiara , Colombo Nicoletta , Marth Christian , Vergote Ignace , Maenpaa Johanna , Pujade-Lauraine Eric , Ray-Coquard Isabelle
Published: December 2020

Background

PAOLA1 is a phase III study assessing olaparib maintenance therapy in advanced high-grade ovarian carcinoma patients responding to first-line platinum-taxane–based chemotherapy plus bevacizumab as standard of care. Randomization was stratified by treatment outcome and tumor BRCA1/2 status (tBRCA) at screening.

Methods

tBRCA was tested on formalin-fixed, paraffin-embedded tumor blocks on 5 French platforms using 2 next-generation sequencing methods based either on hybrid capture or amplicon technology. One of the exploratory objectives was to assess the concordance between germline (gBRCA) and tBRCA testing in French patients. gBRCA testing was performed on blood samples on the same platforms.

Results

From May 2015 to July 2017, tBRCA tests were performed for 1176 screened patients. Only 52 (4.4%) tumor samples were noncontributive. The median interval between reception of the tumor sample and availability of the tBRCA status result was 37 days (range = 8-260). A pathogenic variant was reported in 27.1% tumor samples (319 of 1176 screened patients). tBRCA and gBRCA testing were performed for 451 French patients with negative results for both tests in 306 patients (67.8%) and positive results for both tests in 85 patients (18.8%). Only 1 large genomic rearrangement of BRCA1 was detected, exclusively in the blood sample. Interestingly, tBRCA testing revealed 6.4% of pathogenic variant (29 of 451) not detected by gBRCA testing.

Conclusions

tBRCA testing is an appropriate tool with an acceptable turnaround time for clinical practice and a low failure rate, ensuring reliable identification of patients likely to benefit from poly(ADP-ribose) polymerase inhibitor therapy.