bluuebunny/crossref_metadata_2025 huggingface dataset:
LBERT: Lexically aware Transformer-based Bidirectional Encoder Representation model for learning universal bio-entity relations
Authors: Warikoo Neha , Chang Yung-Chun , Hsu Wen-Lian
Published: August 2020

Motivation

Natural Language Processing techniques are constantly being advanced to accommodate the influx of data as well as to provide exhaustive and structured knowledge dissemination. Within the biomedical domain, relation detection between bio-entities known as the Bio-Entity Relation Extraction (BRE) task has a critical function in knowledge structuring. Although recent advances in deep learning-based biomedical domain embedding have improved BRE predictive analytics, these works are often task selective or use external knowledge-based pre-/post-processing. In addition, deep learning-based models do not account for local syntactic contexts, which have improved data representation in many kernel classifier-based models. In this study, we propose a universal BRE model, i.e. LBERT, which is a Lexically aware Transformer-based Bidirectional Encoder Representation model, and which explores both local and global contexts representations for sentence-level classification tasks.

Results

This article presents one of the most exhaustive BRE studies ever conducted over five different bio-entity relation types. Our model outperforms state-of-the-art deep learning models in protein–protein interaction (PPI), drug–drug interaction and protein–bio-entity relation classification tasks by 0.02%, 11.2% and 41.4%, respectively. LBERT representations show a statistically significant improvement over BioBERT in detecting true bio-entity relation for large corpora like PPI. Our ablation studies clearly indicate the contribution of the lexical features and distance-adjusted attention in improving prediction performance by learning additional local semantic context along with bi-directionally learned global context.

Availability and implementation

Github. https://github.com/warikoone/LBERT.

Supplementary information

Supplementary data are available at Bioinformatics online.
FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts
Authors: Gupta Rajinder , Schrooders Yannick , Verheijen Marcha , Roth Adrian , Kleinjans Jos , Caiment Florian
Published: August 2020

Typical RNA sequencing (RNA-Seq) analyses are performed either at the gene level by summing all reads from the same locus, assuming that all transcripts from a gene make a protein or at the transcript level, assuming that each transcript displays unique function. However, these assumptions are flawed, as a gene can code for different types of transcripts and different transcripts are capable of synthesizing similar, different or no protein. As a consequence, functional changes are not well illustrated by either gene or transcript analyses. We propose to improve RNA-Seq analyses by grouping the transcripts based on their similar functions. We developed FuSe to predict functional similarities using the primary and secondary structure of proteins. To estimate the likelihood of proteins with similar functions, FuSe computes two confidence scores: knowledge (KS) and discovery (DS) for protein pairs. Overlapping protein pairs exhibiting high confidence are grouped to form ‘similar function protein groups’ and expression is calculated for each functional group. The impact of using FuSe is demonstrated on in vitro cells exposed to paracetamol, which highlight genes responsible for cell adhesion and glycogen regulation which were earlier shown to be not differentially expressed with traditional analysis methods.

Availability and implementation

The source code is available at https://github.com/rajinder4489/FuSe. Data for APAP exposure are available in the BioStudies database (http://www.ebi.ac.uk/biostudies) under accession numbers S-HECA143, S-HECA(158) and S-HECA139.

Supplementary information

Supplementary data are available at Bioinformatics online.
Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species
Authors: Sun Yidan Eden , Zhou Heather J , Li Jingyi Jessica
Published: August 2020

Motivation

Gene clustering is a widely used technique that has enabled computational prediction of unknown gene functions within a species. However, it remains a challenge to refine gene function prediction by leveraging evolutionarily conserved genes in another species. This challenge calls for a new computational algorithm to identify gene co-clusters in two species, so that genes in each co-cluster exhibit similar expression levels in each species and strong conservation between the species.

Results

Here, we develop the bipartite tight spectral clustering (BiTSC) algorithm, which identifies gene co-clusters in two species based on gene orthology information and gene expression data. BiTSC novelly implements a formulation that encodes gene orthology as a bipartite network and gene expression data as node covariates. This formulation allows BiTSC to adopt and combine the advantages of multiple unsupervised learning techniques: kernel enhancement, bipartite spectral clustering, consensus clustering, tight clustering and hierarchical clustering. As a result, BiTSC is a flexible and robust algorithm capable of identifying informative gene co-clusters without forcing all genes into co-clusters. Another advantage of BiTSC is that it does not rely on any distributional assumptions. Beyond cross-species gene co-clustering, BiTSC also has wide applications as a general algorithm for identifying tight node co-clusters in any bipartite network with node covariates. We demonstrate the accuracy and robustness of BiTSC through comprehensive simulation studies. In a real data example, we use BiTSC to identify conserved gene co-clusters of Drosophila melanogaster and Caenorhabditis elegans, and we perform a series of downstream analysis to both validate BiTSC and verify the biological significance of the identified co-clusters.

Availability and implementation

The Python package BiTSC is open-access and available at https://github.com/edensunyidan/BiTSC.

Supplementary information

Supplementary data are available at Bioinformatics online.
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes
Authors: Moshiri Niema
Published: August 2020

Motivation

In molecular epidemiology, the identification of clusters of transmissions typically requires the alignment of viral genomic sequence data. However, existing methods of multiple sequence alignment (MSA) scale poorly with respect to the number of sequences.

Results

ViralMSA is a user-friendly reference-guided MSA tool that leverages the algorithmic techniques of read mappers to enable the MSA of ultra-large viral genome datasets. It scales linearly with the number of sequences, and it is able to align tens of thousands of full viral genomes in seconds. However, alignments produced by ViralMSA omit insertions with respect to the reference genome.

Availability and implementation

ViralMSA is freely available at https://github.com/niemasd/ViralMSA as an open-source software project.

Supplementary information

Supplementary data are available at Bioinformatics online.
Regional extracorporeal membrane oxygenation retrieval service during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic: an interdisciplinary team approach to maintain service provision despite increased demand
Authors: Rafiq Muhammad U , Valchanov Kamen , Vuylsteke Alain , Taghavi Fouad J , Iyer Swetha B , Sudarshan Catherine D , Fowles Jo-Anne , Anderson Simon , Govender Pooveshni , Holmes Miranda , White Alexander , Mishra Abhi , Mwaura Lucy , Jenkins David P
Published: August 2020

OBJECTIVES

Coronavirus disease 2019 is a new contagious disease that has spread rapidly across the world. It is associated with high mortality in those who develop respiratory complications and require admission to intensive care. Extracorporeal membrane oxygenation (ECMO) is a supportive therapy option for selected severely ill patients who deteriorate despite the best supportive care. During the coronavirus disease 2019 pandemic, extra demand led to staff reorganization; hence, cardiac surgery consultants joined the ECMO retrieval team. This article describes how we increased service provisions to adapt to the changes in activity and staffing.

METHODS

The data were collected from 16 March 2020 to 8 May 2020. The patients were referred through a dedicated Web-based referral portal to cope with increasing demand. The retrieval team attended the referring hospital, reviewed the patients and made the final decision to proceed with ECMO.

RESULTS

We reported 41 ECMO retrieval runs during this study period. Apart from staffing changes, other retrieval protocols were maintained. The preferred cannulation method for veno-venous ECMO was drainage via the femoral vein and return to the right internal jugular vein. There were no complications reported during cannulation or transport.

CONCLUSIONS

Staff reorganization in a crisis is of paramount importance. For those with precise transferrable skills, experience can be gained quickly with appropriate supervision. Therefore, the team members were selected based on skill mix rather than on roles that are more traditional. We have demonstrated that an ECMO retrieval service can be reorganized swiftly and successfully to cope with the sudden increase in demand by spending cardiac surgeons services to supplement the anaesthetic-intensivist roles.
The effect of minimally invasive pectus excavatum repair on thoracic scoliosis
Authors: İşcan Mehlika , Kılıç Burcu , Turna Akif , Kaynak Mehmet Kamil
Published: August 2020

OBJECTIVES

The Nuss technique comprises the placement of an intrathoracic bar behind the sternum. However, besides improving the body posture through the correction of the pectus excavatum (PE), this procedure may cause or worsen thoracic scoliosis as a result of the considerable stress loaded on the chest wall and the thorax. Our goal was to investigate the impact of the Nuss procedure on the thoracic spinal curvature in patients with PE.

METHODS

A total of 100 patients with PE who underwent the Nuss procedure were included in the study and evaluated retrospectively. The Haller index (HI), asymmetry index and sternal torsion angle were calculated from thoracic computed tomography images before the operation. To evaluate the scoliosis in the T2–T8 thoracic vertebrae, Cobb angles were calculated on a plain chest X-ray before the Nuss operation and after the removal of the bar. Cobb angles were classified as normal (5°), scoliotic posture (5°–10°) and scoliosis (>10°). All angles before and after the Nuss operation were compared. The patients were followed up for a mean of 41 months. Substernal bars were removed after a mean of 33 months.

RESULTS

The mean age of the patients was 19.6 ± 6.7 years. The Cobb angle was statistically significantly increased in all patients (P = 0.01), male patients (P = 0.01) and children (P = 0.046) but not in adults (P = 0.11) and female patients (P = 0.54). The Cobb angle was increased in patients with severe (HI ≥ 3.5) but not in patients with moderate (3.2 < HI < 3.5) or mild (2.0 < HI < 3.2) PE deformity.

CONCLUSIONS

The present study shows that the Cobb angle indicates that the severity of thoracic scoliosis increases following the Nuss procedure, particularly in male patients, in patients with mild and moderate sternal torsion angle and in those with a high preoperative HI. This alteration might be due to correctional forces and torque applied by the bar. Patients undergoing the Nuss procedure for the correction of PE should be followed up strictly for timely diagnosis and management of the scoliosis.
Clinical outcomes of complete versus incomplete revascularization in patients treated with coronary artery bypass grafting: insights from the TiCAB trial
Authors: Schaefer Andreas , Conradi Lenard , Schneeberger Yvonne , Reichenspurner Hermann , Sandner Sigrid , Tebbe Ulrich , Nowak Bernd , Stritzke Jan , Kastrati Adnan , Schunkert Heribert , Scheidt Moritz von ,   for the TiCAB investigators
Published: August 2020

OBJECTIVES

In this post hoc analysis of the Ticagrelor in coronary artery bypass grafting (CABG) trial, we aimed to analyse patients treated with CABG receiving either complete revascularization (CR) or incomplete revascularization (ICR) independent from random allocation to either ticagrelor or aspirin.

METHODS

Of 1859 patients enrolled in the Ticagrelor in CABG trial, 1550 patients (83.4%) received CR and 309 patients (16.6%) ICR. Outcomes were evaluated regarding all-cause mortality, cardiovascular death, myocardial infarction (MI), repeat revascularization, stroke and bleeding within 12 months after CABG.

RESULTS

Baseline parameters revealed significant differences regarding clinical presentation (stable angina pectoris: CR 68.9% vs ICR 71.2%, instable angina pectoris: 14.1% vs 7.8%, non-ST elevation MI: 17.0% vs 21.0%, P ˂ 0.01), lesion characteristics (chronic total occlusion: CR 91.3% vs ICR 96.8%, P ˂ 0.01), operative technique [off-pump coronary artery bypass surgery (OPCAB): CR 3.0% vs ICR 6.1%, P ˂ 0.01] and number of utilized grafts (total number of grafts: 2.69/patient vs 2.49/patient, P ˂ 0.001). ICR patients displayed a significantly increased risk of repeat revascularization [hazard ratio (HR) 1.91, 95% confidence interval (CI) 1.16–3.16; P < 0.01] and percutaneous coronary intervention (HR 1.95, 95% CI 1.13–3.35; P < 0.05) within 12 months after CABG. Higher risk for repeat revascularization in ICR patients was independent from random allocation to either ticagrelor or aspirin and persisted after adjustment for baseline imbalances.

CONCLUSIONS

Patients with ICR presented more stable at the time of admission, but received less grafts, highly likely due to a higher rate of chronic total occlusion lesions and performed OPCAB. Although mortality presented no difference between groups, our results suggest that patients benefit from CR with regard to prevention of repeat revascularization.
Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids
Authors: Nakabachi Atsushi , Piel Jörn , Malenovský Igor , Hirose Yuu
Published: August 2020

The Asian citrus psyllid Diaphorina citri (Insecta: Hemiptera: Psylloidea), a serious pest of citrus species worldwide, harbors vertically transmitted intracellular mutualists, Candidatus Profftella armatura (Profftella_DC, Gammaproteobacteria: Burkholderiales) and Candidatus Carsonella ruddii (Carsonella_DC, Gammaproteobacteria: Oceanospirillales). Whereas Carsonella_DC is a typical nutritional symbiont, Profftella_DC is a unique defensive symbiont with organelle-like features, including intracellular localization within the host, perfect infection in host populations, vertical transmission over evolutionary time, and drastic genome reduction down to much less than 1 Mb. Large parts of the 460-kb genome of Profftella_DC are devoted to genes for synthesizing a polyketide toxin; diaphorin. To better understand the evolution of this unusual symbiont, the present study analyzed the genome of Profftella_Dco, a sister lineage to Profftella_DC, using Diaphorina cf. continua, a host psyllid congeneric with D. citri. The genome of coresiding Carsonella (Carsonella_Dco) was also analyzed. The analysis revealed nearly perfect synteny conservation in these genomes with their counterparts from D. citri. The substitution rate analysis further demonstrated genomic stability of Profftella which is comparable to that of Carsonella. Profftella_Dco and Profftella_DC shared all genes for the biosynthesis of diaphorin, hemolysin, riboflavin, biotin, and carotenoids, underlining multiple roles of Profftella, which may contribute to stabilizing symbiotic relationships with the host. However, acyl carrier proteins were extensively amplified in polyketide synthases DipP and DipT for diaphorin synthesis in Profftella_Dco. This level of acyl carrier protein augmentation, unprecedented in modular polyketide synthases of any known organism, is not thought to influence the polyketide structure but may improve the synthesis efficiency.
Food Fingerprinting: Using a Two-Tiered approach to Monitor and Mitigate Food Fraud in Rice
Authors: McGrath Terence F , Shannon Maeve , Chevallier Olivier P , Ch Ratnasekhar , Xu Fei , Kong Fanzhou , Peng Hong , Teye Ernest , Akaba Selorm , Wu Di , Wu Libiao , Cai Qiang , Le Nguyen Doan Duy , Le Van Viet Man , Pandor Sufyan , Kapil Arun P , Zhang Guangtao , McBride Mary , Elliott Christopher T
Published: August 2020

Background

Rice is an important staple food that is consumed around the world. Like many foods, the price of rice varies considerably, from very inexpensive for a low-quality product to premium pricing for highly prized varieties from specific locations. Therefore, like other foods it is vulnerable to economically motivated adulteration through substitution or misrepresentation of inferior-quality rice for more expensive varieties.

Objective

In this article we describe results of a research project focused on addressing potential food fraud issues related to rice supplies in China, India, Vietnam, and Ghana. Rice fraud manifests differently in each country; therefore, tailored solutions were required.

Method

Here we describe a two-tiered testing regime of rapid screening using portable Near Infrared technology supported by second tier testing using mass spectrometry-based analysis of suspicious samples.

Results

Portable Near Infrared spectroscopy models and laboratory-based Gas Chromatography-Mass Spectrometry methods were developed to differentiate between: high-value Basmati rice varieties and their potential adulterants; six Geographic Indicated protected rice varieties from specific regions within China; various qualities of rice in Ghana and Vietnam; and locally produced and imported rice in Ghana. Furthermore, an Inductively Coupled Plasma-Mass Spectrometry method was developed to support the Chinese rice varieties methods as well as a Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry method for quality differentiation in Vietnam.

Conclusions/Highlights

This two-tier approach can provide a substantially increased level of testing through rapid screening outside of the laboratory with the reassurance of corroborating mass spectrometry-based laboratory analysis to support decision making.
Setting Up an Abbreviated Breast MRI Program: Our Two-year Implementation Experience
Authors: Marshall Holly N , Plecha Donna M
Published: August 2020

Mammography is the long-standing screening tool for detecting breast cancer. Breast MRI is the most sensitive screening modality; however, it has been reserved for patients who are at an increased risk of developing breast cancer. Abbreviated breast MRI (AB-MRI) overcomes the limitations of cost and scanner time when considering screening patients at average or slightly elevated risk. This paper discusses the practical considerations for implementing an AB-MRI program on many levels, after our two-year experience. One of the first steps in introducing an AB-MRI program, since there is no standardized protocol, is determining and implementing a protocol. Since there is no Current Procedural Terminology code for an AB-MRI, a self-pay charge should be established. Adjusting MRI scheduling templates to accommodate the 10-minute AB-MRI exam is helpful. Communication with the breast team and the education of referring physicians is a key step to ensure awareness of a new screening option. As the AB-MRI program is incorporated into a practice, auditing of routine screening outcomes several months after commencement is invaluable to the continued success of the program.
Effects of medium-chain fatty acids as alternatives to ZnO or antibiotics in nursery pig diets
Authors: Dahmer Payton L , Leubcke Grace E , Lerner Annie B , Jones Cassandra K
Published: August 2020

The objective of this experiment was to evaluate the effects of medium-chain fatty acids (MCFA) on nursery pig performance in place of ZnO and carbadox. In this trial, 360 weanling pigs (DNA 200 × 400; 5.4 ± 0.07 kg BW) were fed for 35 d, with 6 pigs/pen and 10 replicate pens/treatment. Upon weaning, pigs were weighed and allotted to pens based on BW in a completely randomized design to one of six treatment diets: 1) Negative control (no added ZnO or carbadox); 2) Control + 3,000 ppm ZnO in phase 1 and 2,000 ppm ZnO in phase 2; 3) Control + 50 g/ton carbadox; 4) Control + C6:C8:C10 MCFA blend; 5) Control + Proprietary Oil Blend (Feed Energy Corp.); and 6) Control + monolaurate blend (FORMI GML from ADDCON). Treatment diets were fed through two dietary phases and a common diet fed through phase three. Pigs and feeders were individually weighed on a weekly basis to determine average daily gain (ADG) and average daily feed intake (ADFI). From days 0 to 19, pigs being fed the ZnO or Carbadox diets had the greatest ADG. These pigs had significantly higher (P < 0.05) ADG than pigs fed the control or Feed Energy Proprietary Oil Blend, whereas pigs fed the C6:C8:C10 blend or FORMI GML diets had similar (P > 0.05) ADG compared with those fed carbadox. These effects were primarily driven by feed intake, which was greatest (P < 0.05) in pigs fed ZnO and carbadox. Treatment diet had a marginally significant effect (P = 0.078) on G:F. Increased day 19 BW (P < 0.05) was observed for pigs fed ZnO and carbadox compared with the negative control, whereas other treatments were intermediate. Additionally, blood data and fecal scores were collected throughout the trial. On day 21, pigs fed ZnO or carbadox had higher (P < 0.0001) glucose values than those fed the Feed Energy Proprietary Oil Blend, with other diets being intermediate, showing potential health benefits of carbadox. Although ZnO resulted in higher glucose values, it may also contribute to hepatic issues. Although replacing ZnO and carbadox with MCFA did not result in significant changes in gut microflora, it did affect fecal consistency by softening the feces during the treatment period. Overall, these results show that ZnO and carbadox are valuable additives to help maximize growth performance in early stages of the nursery. Some MCFA products, like FORMI GML, may result in similar performance, whereas others restrict it. Thus, additional research is needed to study the effectiveness of MCFA to replace ZnO or feed-based antibiotics.
Dollar Spot Suppression on Creeping Bentgrass in Response to Repeated Foliar Nitrogen Applications
Authors: Townsend Ronald , Millican Michael D. , Smith Damon , Nangle Ed , Hockemeyer Kurt , Soldat Doug , Koch Paul L.
Published: August 2020

Dollar spot is caused by the fungus Clarireedia spp. and is the most economically important disease of golf course turfgrass in temperate regions of the United States. Previous research has demonstrated that nitrogen (N) fertilization may reduce dollar spot severity, but the results have been inconsistent, and the impact of N as part of repeated foliar fertilization applications to golf course putting greens remains unclear. Two independent trials were replicated in Madison, Wisconsin and Glenview, Illinois in the 2015, 2016, and 2017 growing seasons. The objective of the first trial was to evaluate the effect of four different N rates applied as urea (4.9, 9.8, 19.4, and 29.3 kg N/ha applied every 2 weeks) on dollar spot severity, and the objective of the second trial was to evaluate the effect of three N sources (calcium nitrate, ammonium sulfate, and ammonium nitrate applied every 2 weeks) on dollar spot severity. Results from the N rate trial at both locations indicated that only the highest (29.3 kg N/ha) rate consistently reduced dollar spot severity relative to the nontreated control. Nitrogen source had minimal and inconsistent impacts on dollar spot severity based on location and year. Although these results show that meaningful reductions in dollar spot severity can be achieved by manipulating N fertilizer application rates, the rate of N needed for disease suppression may be impractical for most superintendents to apply and result in undesirable nontarget impacts.
Identification of Novel Sources of Resistance to Ascochyta Blight in a Collection of Wild Cicer Accessions
Authors: Newman Toby E. , Jacques Silke , Grime Christy , Kamphuis Fiona L. , Lee Robert C. , Berger Jens , Kamphuis Lars G.
Published: August 2020

Chickpea production is constrained worldwide by the necrotrophic fungal pathogen Ascochyta rabiei, the causal agent of Ascochyta blight (AB). To reduce the impact of this disease, novel sources of resistance are required in chickpea cultivars. Here, we screened a new collection of wild Cicer accessions for AB resistance and identified accessions resistant to multiple, highly pathogenic isolates. In addition to this, analyses demonstrated that some collection sites of C. echinospermum harbor predominantly resistant accessions, knowledge that can inform future collection missions. Furthermore, a genome-wide association study identified regions of the C. reticulatum genome associated with AB resistance and investigation of these regions identified candidate resistance genes. Taken together, these results can be utilized to enhance the resistance of chickpea cultivars to this globally yield-limiting disease.
Cognitive declines after perioperative covert stroke: Recent advances and perspectives
Authors: Yu Shiqiu , Li Peiying
Published: August 2020

Purpose of review

With the aging of the population, there are increasing number of aged patients who require surgical interventions. Perioperative covert stroke is emerging as an important health threat and social burden that could affect patients’ long-term neurological outcomes.

Recent findings

Recent findings of the association between perioperative covert stroke with long-term cognitive declines of surgical patients highlighted the significance of the silent cognitive function killer—perioperative covert stroke. Considering the devastating long-term consequence of the asymptomatic covert stroke, early diagnosis and prevention are turning out as crucial problems to tackle. The evolving brain imaging techniques, such as multimodel MRI sequences are not only able to detect early, small and subtle injuries of the acute ischemic lesions, but also quite advantageous in capturing the preexisting brain vascular diseases that are considered as important risk factors of covert stroke. However, effective predictive markers are still lacking to identify high risk patients for perioperative covert stroke, rendering an unmet need of investigations in this regard.

The present review will summarize recent findings in perioperative covert stroke and highlight future perspectives of its early diagnosis and the impact of postoperative cognitive impairments.
SoftVoice Improves Speech Recognition and Reduces Listening Effort in Cochlear Implant Users
Authors: Stronks H. Christiaan , Apperloo Eline , Koning Raphael , Briaire Jeroen J. , Frijns Johan H. M.
Published: August 2020

Objectives:

The ability to perceive soft speech by cochlear implant (CI) users is restricted in part by the inherent system noise produced by the speech processor, and in particular by the microphone(s). The algorithm “SoftVoice” (SV) was developed by Advanced Bionics to enhance the perception of soft speech by reducing the system noise in speech processors. The aim of this study was to examine the effects of SV on speech recognition and listening effort.

Design:

Seventeen adult Advanced Bionics CI recipients were recruited and tested in two sessions. The effect of SV on speech recognition was tested by determining the SRT in quiet using the Matrix test. Based on the individual subjects’ SRTs, we investigated speech-recognition scores at fixed speech levels, namely SRT −5 dB, SRT +0 dB, SRT +5 dB, and SRT +10 dB, again in quiet and using the Matrix test. Listening effort was measured at each of these speech levels subjectively by using a rating scale, and objectively by determining pupil dilation with pupillometry. To verify whether SoftVoice had any negative effects on speech perception in noise, we determined the SRT in steady state, speech-weighted noise of 60 dBA.

Results:

Our results revealed a significant improvement of 2.0 dB on the SRT in quiet with SoftVoice. The average SRT in quiet without SoftVoice was 38 dBA. SoftVoice did not affect the SRT in steady state, speech-weighted noise of 60 dB. At an average speech level of 33 dBA (SRT –5 dB) and 38 dBA (SRT +0 dB) in quiet, significant improvements of 17% and 9% on speech-recognition scores were found with SoftVoice, respectively. At higher speech levels, SoftVoice did not significantly affect speech recognition. Pupillometry did not show significant effects of SoftVoice at any speech level. However, subjective ratings of listening effort indicated a decrease of listening effort with SoftVoice at a speech level of 33 dBA.

Conclusions:

We conclude that SoftVoice substantially improves recognition of soft speech and lowers subjective listening effort at low speech levels in quiet. However, no significant effect of SoftVoice was found on pupil dilation. As SRTs in noise were not statistically significantly affected by SoftVoice, we conclude that SoftVoice can be used in noisy listening conditions with little negative impact on speech recognition, if any. The increased power demands of the algorithm are considered to be negligible. It is expected that SoftVoice will reduce power consumption at low ambient sound levels. These results support the use of SoftVoice as a standard feature of Advanced Bionics CI fittings for everyday use.
Workforce, Workload, and Burnout in Critical Care Organizations: Survey Results and Research Agenda*
Authors: Lilly Craig M. , Oropello John M. , Pastores Stephen M. , Coopersmith Craig M. , Khan Roozehra A. , Sessler Curtis N. , Christman John W.
Published: August 2020

Objectives:

This report provides analyses and perspective of a survey of critical care workforce, workload, and burnout among the intensivists and advanced practice providers of established U.S. and Canadian critical care organizations and provides a research agenda.

Design:

A 97-item electronic survey questionnaire was distributed to the leaders of 27 qualifying organizations.

Setting:

United States and Canada.

Participants:

Leaders of critical care organizations in the United States and Canada.

Interventions:

None.

Data Synthesis and Main Results:

We received 23 responses (85%). The critical care organization survey recorded substantial variability of most organizational aspects that were not restricted by the critical care organization definition or regulatory mandates. The most common physician staffing model was a combination of full-time and part-time intensivists. Approximately 80% of critical care organizations had dedicated advanced practice providers that staffed some or all their ICUs. Full-time intensivists worked a median of 168 days (range 42–192 d) in the ICU (168 shifts = 24 7-d wk). The median shift duration was 12 hours (range, 7–14 hr), and the median number of consecutive shifts allowed was 7 hours (range 7–14 hr). More than half of critical care organizations reported having burnout prevention programs targeted to ICU physicians, advanced practice providers, and nurses.

Conclusions:

The variability of current approaches suggests that systematic comparative analyses could identify best organizational practices. The research agenda for the study of critical care organizations should include studies that provide insights regarding the effects of the integrative structure of critical care organizations on outcomes at the levels of our patients, our workforce, our work practices, and sustainability.
Blinded Evaluation of Hyaluronic Acid Hand Filler Injections and Effects on First Impressions
Authors: Cristel Robert T. , Demesh Daniel , Lombard Rachel , Russell Parker T. , Gandhi Nimit D. , Kola Eljona , Dayan Steven H.
Published: August 2020

BACKGROUND

The hands are the second most common body part visible after the face. In the aging hand, the dorsum loses volume, becomes uneven, veins become more prominent, and there is an increase in spots and wrinkles.

OBJECTIVE

To determine the effects of large-particle hyaluronic acid filler injection into the dorsal hand on first impressions.

MATERIALS AND METHODS

Ten subjects underwent filler injections in the bilateral dorsal hands with large-particle hyaluronic acid filler. Photographs of the hands were taken at baseline and 2 weeks after the optimal correction result. A survey to evaluate first impressions was then completed by blinded evaluators on defined categories of perception.

RESULTS

A total of 209 evaluators completed the first impression questionnaire. Overall, 10,032 individual assessments of first impressions were completed. There was a significant improvement in mean first impressions in all categories of perception and overall first impression scores.

CONCLUSION

Cosmetic treatments to the hands is a growing field with the use of hyaluronic acid fillers to restore volume, decrease wrinkles, and improve the appearance of prominent veins. This study revealed an improvement in first impression scores in all categories following treatment with large-particle hyaluronic acid filler to the dorsal hands.
The comparison of different antiviral therapies on the prognosis of hepatitis B virus-related hepatocellular carcinoma after curative treatments
Authors: Xia Zijing , He Linye , Xiong Li , Wen Tianfu
Published: August 2020

Objective:

The purpose of this study was to evaluate the efficacy of different nucleos(t)ide analogues in the prognosis of HBV-related hepatocellular carcinoma (HCC) patients after curative treatment by network meta-analysis.

Methods:

Literature retrieval was conducted in globally recognized databases, namely, PubMed, EMBASE, Cochrane Library databases, and Science Citation Index Expanded, to address relative studies investigating nucleot(s)ide analogues for HBV-related HCC patients after curative resection. Relative parametric data, including 1-, 3-, and 5-year overall survival rate and 1-, 3-, and 5-year recurrence-free survival rate were quantitatively pooled and estimated. The inconsistency factor, the cumulative ranking curve, and the publication bias were evaluated.

Results:

Fourteen observational studies of 2481 adults performed between 2000 and 2019 were eligible. In terms of overall survival, ADV (Adefovir dipivoxil) (Odds ratio (OR): 2.35, 95% confidence interval (CI): 1.17–4.73), Lamivudine (OR: 2.08, 95% CI: 1.78–5.58), and Entecavir (OR: 2.14, 95% CI: 1.59–2.88) were found to be more beneficial than control group while ADV has the highest probability of having the most efficacious treatment (SCURA values 66.3) for 5-year overall survival. In late recurrence-free survival, ADV (OR = 1.88, 95% CI: 1.77–4.60), Entecavir (OR = 1.96, 95% CI: 1.36–2.55), and Lamivudine (OR = 1.73, 95% CI: 1.06–2.82) all had better significant prognosis than patients without antiviral therapy postoperatively and patients with ADV as postoperative antiviral therapy has significantly recurrence-free survival benefit at 5-year follow-up compared to those undertaking Entecavir (OR = 1.96, 95% CI: 1.52–7.38) and Lamivudine (OR = 1.39, 95% CI: 1.09–3.01). Moreover, the application of ADV possessed the highest possibility of having the best clinical effects on 1- (surface under the cumulative ranking probabilities (SUCRA), 64.7), 3- (SUCRA, 64.7), and 5-year (SUCRA, 70.4) recurrence survival rate for HBV-related HCC patients.

Conclusions:

Patients with postoperative nucleos(t)ide analogues antiviral therapy had better survival benefit than those without antiviral therapy for HBV-related HCC patients after curative treatment. Additionally, nucleotide analogues like ADV and Tenofovir disoproxil fumarate has better impact on early and late recurrence-free survival of patients after curative treatment than those undertaking nucleoside analogues.
Can early switch to rituximab-bendamustine in a patient with follicular non-Hodgkin lymphoma progressing during R-CHOP be considered frontline treatment?
Authors: Cerchione Claudio , Nappi Davide , Musuraca Gerardo , Lucchesi Alessandro , Cimmino Ilaria , Pane Fabrizio , De Renzo Amalia , Martinelli Giovanni
Published: August 2020

Rationale:

Follicular non-Hodgkin lymphoma (fNHL) is a neoplasm characterized by an indolent course and chemosensitivity, but also by disease recurrence. Bendamustine is often used as frontline treatment or second line.

Heading diagnosis:

fNHL.

Patient concerns:

A 63-year-old Caucasian male with diagnosis of fNHL lymphoma underwent to cyclophosphamide, doxorubicin, vincristine, and prednisone associated with rituximab chemoimmunotherapy, during which interim reevaluation showed progressive disease and severe toxicity.

Interventions:

Early switch to rituximab-bendamustine.

Outcomes:

This regimen was well tolerated, patient compliance was optimal, there were no delays in administration and no infectious episodes. An interim reevaluation after 3 courses revealed that the patient was fit, the blood cell count was normal, and lymphadenopathies and nocturnal sweating had completely regressed. Of note, the PET/CT scan did not show fluorodeoxyglucose pathological uptake, clearly confirming disease regression.

Lessons:

Early switching to a bendamustine-rituximab-based scheme, even during conventional chemotherapy, decreases toxicity and reduces the risk of treatment interruption or delay, with favorable effects on overall response and prognosis.
The value of microRNA-21 as a biomarker for the prognosis of lung cancer
Authors: Zhang Wei , Wei Lin , Luo Rong , Liu Hui , Chen Jing
Published: August 2020

Backgroud:

More and more studies are investigating the influence of the expression of MicroRNA-21 (miRNA-21) on prognosis and clinical significance in patients with lung cancer, but the results are contradictory and uncertain. A meta-analysis was conducted with controversial data to accurately assess the issue.

Methods:

A detailed search of relevant research in Wanfang, Chinese Biomedical Literature Database, Chinese National Knowledge Infrastructure (CNKI), the Chongqing VIP Chinese Science and Technology Periodical Database, PubMed, Embase, Web of Science and other databases. Two reviewers independently conducted data extraction and literature quality evaluation. Odd ratio and its 95% confidence intervals were used to evaluate the relationship between miRNA-21 and clinicopathological characteristics of lung cancer patients. Hazard ratios and its 95% confidence intervals To assess the prognostic effect of miRNA-21 on overall survival and disease-free survival. Meta analysis was performed using RevMan 5.3 and Stata 14.0 software.

Results:

This study will provide a high-quality evidence-based medical evidence of the correlations between miRNA-21 expression and overall survival, disease-free survival and clinicopathological features.

Conclusion:

The study will provide updated evidence to evaluate whether the expression of miRNA-21 is in association with poor prognosis in patients with lung cancer.

Ethics and dissemination:

The private information from individuals will not publish. This systematic review also will not involve endangering participant rights. Ethical approval is not available. The results may be published in a peer- reviewed journal or disseminated in relevant conferences.

OSF REGISTRATION NUMBER:

DOI 10.17605/OSF.IO/X3MD6
Human coronavirus OC43 infection associated pneumonia in a girl with acute lymphoblastic leukemia
Authors: Chang Tsung-Yen , Du Chia-Jui , Chang Chih-Chen , Chen Shih-Hsiang , Chen Chih-Jung , Chiu Chih-Yung , Chiu Cheng-Hsun
Published: August 2020

Rationale:

Information regarding the clinical features and outcomes of pneumonia due to an infection with human coronavirus (HCoV)-OC43 in children with cancer is rare. This report presents the clinical features in terms of chest CT scan images which may be used to identify cases of HCoV-OC43 infection induced pneumonia in immunocompromised children.

Patient concerns:

We report here a girl with acute lymphoblastic leukemia who developed respiratory symptoms during febrile neutropenia. Rapid clinical progression and nodular lesions on her chest X-ray and computed tomography scans were suggestive of a pulmonary fungal infection.

Diagnosis:

A series of tests eventually confirmed the exclusive presence of HCoV-OC43 by the FilmArray Respiratory Panel from a throat swab sample.

Interventions:

After the diagnosis was confirmed, the antimicrobial agents initially administered were discontinued.

Outcomes:

Although the chest CT scan images looked severe, the clinical course of the infection induced pneumonia was benign. The respiratory status of the patient was completely resolved in 2 weeks.

Lessons:

This report highlights the importance of early identification of respiratory viruses, via the realization of their clinical characteristics, which helps reduce the duration of administration of antimicrobial agents in this setting.
Quality grade classification of China commercial moxa floss using electronic nose
Authors: Lim Min Yee , Huang Jian , He Fu-rong , Zhao Bai-xiao , Zou Hui-qin , Yan Yong-hong , Hu Hui , Qiu Dong-sheng , Xie Jun-jie
Published: August 2020

Moxa floss is the primary material used in moxibustion, an important traditional Chinese medicine therapy that uses ignited moxa floss to apply heat to the body for disease treatment. Till date, there is no available data regarding quality control of different grades of moxa floss. The objectives of this study were to explore the probative value of the electronic nose (e-nose) in differentiating different quality grades of commercial moxa floss sold in China, and to investigate if data mining techniques could be used to optimize the sensor array while retaining classification accuracy of the samples. The e-nose with 12 metal oxide semiconductor type sensors was used to analyze the odor profiles of 15 commercial moxa floss samples of different quality grades. Feature selection algorithms using principal component analysis (PCA) and BestFirst (BC) coupled with correlation-based feature subset selection (CfsSubsetEval) method were used to obtain the most efficient feature subsets. Results for the BC feature selection method identified 3 optimized sensors (S2, S6, and S11), suggesting that aromatic compounds relate more to the identification of the samples. Radial basis function (RBF), multilayer perceptron (MLP), and random forests (RF) performed well in discriminating the samples, retaining prediction accuracies above 85%, which achieved cost-effectiveness and operational simplicity, while retaining prediction accuracy. The e-nose could be a rapid and nondestructive method for objective preliminary classification of quality grades of moxa floss and may be used for future studies related to moxa products safety and quality.
Antiemetic regimen with aprepitant in the prevention of chemotherapy-induced nausea and vomiting
Authors: Qiu Tingting , Men Peng , Xu Xiaohan , Zhai Suodi , Cui Xiangli
Published: August 2020

Objective:

To systematically evaluate the efficacy and safety of antiemetic regimen with aprepitant in the prevention of chemotherapy-induced nausea and vomiting (CINV) and provide updated information for clinical practice.

Methods:

Pubmed, Embase, the Cochrane Library, and 3 Chinese literature databases were systematically searched. Randomized controlled trials comparing standard regimen (5-hydroxytryptamine-3 receptor antagonist and glucocorticoid) with aprepitant triple regimen (aprepitant plus the standard regimen) for preventing CINV were screened. Literature selection, data extraction, and quality evaluation were performed by 2 reviewers independently. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated in the meta-analysis using RevMan 5.3 software.

Results:

A total of 51 randomized controlled trials were finally included in the systematic review. Compared with the standard regimen, the aprepitant triple regimen significantly improved the complete response in the overall (OR 1.88, 95% CI 1.71–2.07), acute (OR 1.96, 95% CI 1.65–2.32) and delayed (OR 1.96, 95% CI 1.70–2.27) phases, regardless of emetogenic risk of chemotherapy. Aprepitant could also significantly enhance the proportions of patients who have no emesis, nausea, or use of rescue medication respectively in the overall, acute and/or delayed phases. Aprepitant was found to be associated with decreased risk of constipation (OR 0.85, 95% CI 0.74–0.97), but increased the incidence of hiccup (OR 1.26, 95% CI 1.05, 1.51). There were no statistically significant differences between the 2 groups on other safety outcomes.

Conclusion:

The aprepitant triple regimen is effective for the prevention of CINV in patients being treated with moderately or highly emetogenic chemotherapy, and has a significant tendency to reduce the risk of constipation and increase the incidence of hiccup.
Multiple schwannoma of the seminal vesicle
Authors: Zhang Yan , Zhao Jing , Xu Pan , Qi Qi
Published: August 2020

Rationale:

Schwannomas of the seminal vesicles are extremely rare, and only cases of single seminal vesicle schwannomas have been reported. Here, we report a case of multiple schwannoma of the seminal vesicle.

Patient concerns:

We report a rare case of multiple schwannoma of the seminal vesicle that occurred in a 48-year-old man during physical examination. Multiple mixed masses in the left region of the seminal vesicle were documented with transrectal ultrasonography and magnetic resonance imaging. The patient presented no clinical symptoms, no family history of the disease and no history of genetic disease.

Diagnosis:

Postoperative pathology revealed a diagnosis of seminal vesical schwannoma.

Interventions:

The patient underwent robotic-assisted laparoscopic surgery to remove the mass.

Outcomes:

The patient recovered rapidly and the length of hospitalization was 6 days after operation. At present, there is no recurrence in 10 month follow up.

Lessons:

Whether benign or malignant, single or multiple, schwannomas still need to be diagnosed by pathology because of the limitations of examination methods. Surgical resection is still the preferred treatment.