bluuebunny/crossref_metadata_2025 huggingface dataset:
The functional impact of 1,570 SNP-accessible missense variants in humanOTC
Authors: Lo Russell S. , Cromie Gareth A. , Tang Michelle , Teng Kevin , Owens Katherine , Sirr Amy , Kutz J. Nathan , McLaughlin Richard N. , Morizono Hiroki , Caldovic Ljubica , Mew Nicholas Ah , Gropman Andrea , Dudley Aimée M.
Published: October 2022

Deleterious mutations in the X-linked gene encoding ornithine transcarbamylase (OTC) cause the most common urea cycle disorder, OTC deficiency. This rare, but highly actionable disease can present with severe neonatal onset in males or with later onset in either sex. Neonatal onset patients appear normal at birth but rapidly develop hyperammonemia, which can progress to cerebral edema, coma and death, outcomes ameliorated by rapid diagnosis and treatment. Existing biochemical assays have limitations, including the sensitivity of the citrulline assays used in newborn screening panels. With prior knowledge of variant pathogenicity, DNA sequence-based diagnostics would provide an alternative screening method. Here, we develop a high throughput functional assay for human OTC and measure the impact of 1,570 variants, 84% of all SNP-accessible missense mutations. Our assay scores agree well with existing clinical significance calls, distinguishing known benign from pathogenic variants and variants with neonatal onset from late-onset disease presentation. Further, use of an intronless expression construct allows us to measure the impact of amino acid changes at splice sites independent of their effect on splicing, thereby separating the contribution of splicing and protein coding changes to aid the analysis of molecular mechanisms underlying pathogenicity. Finally, we assess the utility of our functional data onOTCvariant curation by using the current ACMG/AMP guidelines to reclassify variants. Inclusion of our data as PS3/BS3 substantially improves variant interpretation. Thus, our dataset is of high clinical utility and illustrates the power of functional assays to inform interpretation of existing and novel genetic variation.
Statistically Consistent Rooting of Species Trees under the Multispecies Coalescent Model
Authors: Tabatabaee Yasamin , Roch Sebastien , Warnow Tandy
Published: October 2022

Rooted species trees are used in several downstream applications of phylogenetics. Most species tree estimation methods produce unrooted trees and additional methods are then used to root these unrooted trees. Recently, Quintet Rooting (QR) (Tabatabaee et al., ISMB and Bioinformatics 2022), a polynomial-time method for rooting an unrooted species tree given unrooted gene trees under the multispecies coalescent, was introduced. QR, which is based on a proof of identifiability of rooted 5-taxon trees in the presence of incomplete lineage sorting, was shown to have good accuracy, improving over other methods for rooting species trees when incomplete lineage sorting was the only cause of gene tree discordance, except when gene tree estimation error was very high. However, the statistical consistency of QR was left as an open question. Here, we present QR-STAR, a polynomial-time variant of QR that has an additional step for determining the rooted shape of each quintet tree. We prove that QR-STAR is statistically consistent under the multispecies coalescent model. Our simulation study under a variety of model conditions shows that QR-STAR matches or improves on the accuracy of QR. QR-STAR is available in open source form athttps://github.com/ytabatabaee/Quintet-Rooting.
Targeting IRS-1/2 in uveal melanoma inhibitsin vitrocell growth, survival and migration, andin vivotumor growth
Authors: Chattopadhyay Chandrani , Bhattacharya Rajat , Roszik Jason , Khan Fatima S. , Wells Gabrielle A. , Villanueva Hugo , Qin Yong , Bhattacharya Rishav , Patel Sapna , Grimm Elizabeth A.
Published: October 2022

Uveal melanoma (UM) originating in the eye and metastasizing to the liver is associated with poor prognosis and has only one approved therapeutic option. We hypothesized that liver-borne growth factors may contribute to UM growth. Therefore, we investigated the role of insulin-like growth factor −1 and its receptor (IGF-1/IGF-1R) signaling in UM. We found that the insulin receptor substrate −1 (IRS-1) is overexpressed in UM cells and tumors. Since we previously observed that IGF-1R antibody therapy was not clinically effective in UM, we investigated the potential of NT157, a small molecule inhibitor of IRS-1/2 in blocking this pathway in UM. NT157 treatment in UM cells resulted in reduced cell survival and migration, and increased apoptosis. This treatment also significantly inhibited UM tumor growthin vivo, in the chicken egg chorioallantoic membrane (CAM) and subcutaneous mouse models, validating thein vitroeffect. Mechanistically, through reverse phase protein array (RPPA), we identified significant proteomic changes in the PI3K/AKT pathway, a downstream mediator of IGF-1 signaling, with NT157 treatment. Together, these results suggest that NT157 inhibits cell survival, migrationin vitroand tumor growthin vivovia inhibiting IGF-1 signaling in UM.
Highlight Results, Don’t Hide Them: Enhance interpretation, reduce biases and improve reproducibility
Authors: Taylor Paul A. , Reynolds Richard C. , Calhoun Vince , Gonzalez-Castillo Javier , Handwerker Daniel A. , Bandettini Peter A. , Mejia Amanda F. , Chen Gang
Published: October 2022

Most neuroimaging studies display results that represent only a tiny fraction of the collected data. While it is conventional to present “only the significant results” to the reader, here we suggest that this practice has several negative consequences for both reproducibility and understanding. This practice hides away most of the results of the dataset and leads to problems of selection bias and irreproducibility, both of which have been recognized as major issues in neuroimaging studies recently. Opaque, all-or-nothing thresholding, even if well-intentioned, places undue influence on arbitrary filter values, hinders clear communication of scientific results, wastes data, is antithetical to good scientific practice, and leads to conceptual inconsistencies. It is also inconsistent with the properties of the acquired data and the underlying biology being studied. Instead of presenting only a few statistically significant locations and hiding away the remaining results, we propose that studies should “highlight” the former while also showing as much as possible of the rest. This is distinct from but complementary to utilizing data sharing repositories: the initial presentation of results has an enormous impact on the interpretation of a study. We present practical examples for voxelwise, regionwise and cross-study analyses using publicly available data that was analyzed previously by 70 teams (NARPS; Botvinik-Nezer, et al., 2020), showing that it is possible to balance the goals of displaying a full set of results with providing the reader reasonably concise and “digestible” findings. In particular, the highlighting approach sheds useful light on the kind of variability present among the NARPS teams’ results, which is primarily a varied strength of agreement rather than disagreement. Using a meta-analysis built on the informative “highlighting” approach shows this relative agreement, while one using the standard “hiding” approach does not. We describe how this simple but powerful change in practice---focusing on highlighting results, rather than hiding all but the strongest ones---can help address many large concerns within the field, or at least to provide more complete information about them. We include a list of practical suggestions for results reporting to improve reproducibility, cross-study comparisons and meta-analyses.

Highlights

Most studies do not present all results of their analysis, hiding subthreshold ones.

Hiding results negatively affects the interpretation and understanding of the study.

Neuroimagers should present all results of their study, highlighting key ones.

Using the public NARPS data, we show several benefits of the “highlighting” approach.

The highlighting approach improves individual studies and meta-analyses.
BATCH-SCAMPP: Batch Scaled Phylogenetic Placement Large Trees
Authors: Wedell Eleanor , Shen Chengze , Warnow Tandy
Published: October 2022

Phylogenetic placement, the problem of placing sequences into phylogenetic trees, has been limited either by the number of sequences placed in a single run or by the size of the placement tree. The most accurate scalable phylogenetic placement method with respect to the number of query sequences placed, EPA-ng, has a runtime that scales sublinearly to the number of query sequences. However, larger phylogenetic trees cause an increase in EPA-ng memory usage, limiting the method to placement trees of up to 10,000 sequences. Our recently designed SCAMPP framework has been shown to scale EPA-ng to larger placement trees of up to 200,000 sequences by building a subtree for the placement of each query sequence. The approach of SCAMPP does not take advantage of EPA-ng parallel efficiency since it only places a single query for each run of EPA-ng. Here we present BATCH-SCAMPP, a new technique that overcomes this barrier and enables EPA-ng and other phylogenetic placement methods to scale to ultra-large backbone trees and many query sequences. BATCH-SCAMPP is freely available at https://github.com/ewedell/BSCAMPP_code.
Low Temperature and High Hydrostatic Pressure Have Compounding Negative Effects on Marine Microbial Motility
Authors: Mullane Kelli K. , Nishiyama Masayoshi , Kurihara Tatsuo , Bartlett Douglas H.
Published: October 2022

Approximately three fourths of all pelagic marine prokaryotes live in the deep-sea, an environment characterized by low temperature and high hydrostatic pressure. Within deep-sea environments labile organic matter is often scarce and motility can serve as a competitive advantage for microorganisms. Experimental work with a handful of species suggests motility is one of the most temperature- and pressure-sensitive cellular processes, however the combined effects of temperature and pressure together have yet to be investigated in detail. Here we employed growth-dependent motility agar assays and growth-independent microscopy assays to assess how changes in these two physical factors impact motility both individually and in combination, using ecologically relevant model organisms from the cosmopolitan generaHalomonas, Alcanivorax, andMarinobacter. At pressures equivalent to bathyal and abyssal depths, changes in temperature from 30°C to 4°C (motility assays) or 23°C to 7°C (microscopy assays) had a greater influence on motility than pressure. In addition, low-temperature and high-pressure impacts were additive. Exposure to high pressure had varying degrees of effect on flagellar function, depending on the strain and the magnitude of the pressure. These ranged from short-term impacts that were quickly reversible to long-term impacts that were detrimental to the function of the flagellum, leading to complete loss of motility. These findings highlight the sensitivity of deep-sea bacterial motility systems to combined temperature/pressure conditions, phenotypes that will contribute to the modulation of diverse microbial activities at depth.

IMPORTANCE

Microorganisms perform critical functions in biogeochemical cycles at depth, as well as likely modulating the carbon sequestration potential of the deep ocean. However, their activities under in situ conditions are poorly constrained. One aspect of microbial activity is motility, generally mediated by the energy-consuming rotation of one or more flagellar filaments that enables swimming behavior. This provides a competitive advantage for microbes in the environment, such as by enhancing nutrient acquisition. Here we report on culture-based and microscopy-based analyses of pressure-temperature (P-T) effects on the motility of three ecologically relevant marine microbes. The results in all cases indicate that high pressure and low temperature exert compounding inhibitory effects. This argues for the need for further investigations into P-T effects on deep-sea microbial processes.
Electron diffraction characterization of nanocrystalline materials using a Rietveld-based approach. Part II. Application to microstructural analysis
Authors: Sinha Ankur , Ischia Gloria , Lutterotti Luca , Gialanella Stefano
Published: October 2022

This is the second in a two-paper series concerning the quantitative characterization of nanocrystalline materials using an electron-diffraction-based approach, in which a full-pattern fitting Rietveld-based refinement is applied to electron powder diffraction data in transmission electron microscopy (TEM). Part I [Sinha et al. (2022). J. Appl. Cryst.
55, 953–965] established a standard calibration protocol to determine the instrumental effects, with special emphasis on the camera length and the diameter of the selected area apertures. Possible application cases are now considered to demonstrate the capabilities of the approach, including the evaluation of the phase composition of TEM specimens, an operation that reveals new application fields for this powerful materials characterization technique. In this regard, different types of material specimen are examined: nanocrystalline yttrium oxide, silicon, titanium dioxide and debris from disc brake wear, each one featuring specific aspects to be tackled with the proposed methodology. To demonstrate the limits of the proposed approach as concerns the material characteristics, an analysis of a hematite sample obtained from the heat treatment of natural goethite, displaying a relatively coarse crystallite size, is performed and a critical discussion of the results is given.
Discussion of “local government turnover and capital structure: evidence from China”
Authors: Li Jingjing
Published: October 2022

Purpose

This paper aims to identify and evaluate the limitations related to Xin et al. (2022). The discussant also provide suggestions for future research along this line.

Design/methodology/approach

In this discussion, the discussant will attempt to identify the main limitations and provide suggestions for future improvement. This written discussion focuses on three main points. First, the discussant will focus on the incremental contribution. Second, the discussant will discuss some remaining issues with the empirical design and propose suggestions for further improvement. Lastly, the discussant will go over the underlying reasons behind the documented results.

Findings

Xin et al. (2022) investigate the original and important question of whether local leadership turnover leads to lower financial leverage.

Originality/value

Xin et al. (2022) contribute to the research line of the economic impact of political uncertainty by investigating the turnover year effect of local top leadership in the Chinese setting. Future research can improve our understanding by investigating the underlying mechanisms behind the documented results.
Balancing work and family in the context of the COVID-19 pandemic: the role of work conditions and family-friendly policy
Authors: Fan Yangyang , Tulepbayev Erbolat , Lee Hyun Jung , Lyu Xiaojun
Published: October 2022

Purpose

Work from home has become as regular as the traditional commuting system after the outbreak of the COVID-19 pandemic. Previous studies have discussed the influence of working at home on the work–family interface. However, there is limited understanding of how diverse workforces manage their work–family issues with various family-friendly policies. This study aims to bridge this research gap by examining the collective influence of work conditions and family-friendly policies on work–family balance.

Design/methodology/approach

A survey experiment featuring two working conditions (work from home or commuting) × four family-friendly policies (household subsidy, family-friendly supervisor, financial profit, paid leave vs no policy) was approached based on 703 valid responses in China.

Findings

The results indicate that family-friendly policies are more effective under the work-from-home condition than the commuting condition, household subsidies and financial profits are considered more helpful for work–family balance under the work-from-home condition and employees’ policy preferences depend on personal identity and work conditions, which help them maintain work and family issues concurrently.

Originality/value

This study explores the joint impact of work conditions and family-friendly policies from a situational perspective. This study indicated that professional organizations need to perform delicacy management considering policy preferences. Moreover, changing working arrangements help employees facilitate their work–family balance.
Social capital and performance of farmers' groups in producer organizations in India: examining the mediating role of self-efficacy
Authors: Pant Satish Chandra , Kumar Sathyendra , Joshi Sanjay Kumar
Published: October 2022

Purpose

This paper aims to examine the impact of social capital and self-efficacy in the performance of producer organizations. It also tests the mediating influence of self-efficacy in the relationship of social capital and performance of producer organizations.

Design/methodology/approach

The study used data from a survey of 226 members of farmer producer organizations (FPO) in India. The model was tested through structural equation modeling wherein all hypotheses were tested using “R” studio.

Findings

The findings reveal that social capital and self-efficacy play a significant role in predicting the performance of FPO. It was found that in the process of social capital influencing the performance of FPO, self-efficacy plays a significant role as a partial mediator with a mediating effect of approximately 69.28%.

Research limitations/implications

The study considered only one antecedent while identifying the reasons for perceived performance of FPOs. Hence, further studies of the various other constructs such as attitude, subjective norms, etc., may be considered.

Originality/value

No previous work has examined the mediating role of self-efficacy in the relationship between social capital and perceived performance of FPO. This study is possibly the only one that joins two streams of thought – social capital and self-efficacy – to examine the performance of FPO.
Changing plant species composition and richness benefit soil carbon sequestration under climate warming
Authors: Yan Yingjie , Niu Shuli , He Yicheng , Wang Song , Song Lei , Peng Jinlong , Chen Xinli , Quan Quan , Meng Cheng , Zhou Qingping , Wang Jinsong
Published: October 2022

Anthropogenic warming and land‐use change are expected to accelerate global soil organic carbon (SOC) losses and change plant species composition and richness. However, how changes in plant composition and species richness mediate SOC responses to climate warming and land‐use change remains poorly understood.

Using data from a 7‐year warming and clipping field experiment in an alpine meadow on the Qinghai–Tibetan Plateau, we examined the direct effects of warming and clipping on SOC storage versus their indirect effects mediated by plant functional type and species richness.

We found that warming significantly increased SOC storage by 8.1% and clipping decreased it by 6.4%, which was closely correlated with the corresponding response of below‐ground net primary productivity (BNPP). We also found a negative correlation between SOC storage and species richness, which was ascribed to the increased BNPP via enhancing the dominance of grasses and decreasing species richness under warming. The lower SOC storage under clipping was caused by the clipping‐induced decrease in BNPP via weakening the dominance of grasses and increasing species richness.

Our findings highlight that the SOC storage in this alpine meadow under climate warming and clipping was primarily governed by BNPP changes, which was mediated by changes in the dominance of grasses and species richness. Overall, our study demonstrates that shifting to the dominance of grasses and changing species richness would benefit soil C sequestration under climate warming, but this positive effect would be dampened by grazing or hay harvest.

Read the free Plain Language Summary for this article on the Journal blog.
The employment effects of intra‐African exports
Authors: Poumie Boker , Kaffo Fotio Herve , Dazoue Dongue Guy P.
Published: October 2022

The establishment of the continental free trade area in Africa is an important step forward for the creation of a market of significant size in a context of sluggish job creation. This study examines the effects of intra‐African exports on aggregate and sectoral employment using the fixed‐effects model with Driscoll‐Kraay standard errors. The data covers 44 African countries over the period 1995–2018. The results show that intra‐African exports increase both sectoral and aggregate employment. Despite the marginal size of intra‐African trade, its effect on employment is greater than that of extra‐African exports. Our results also show that intra‐African exports of primary products create jobs in the agricultural sector, while its effect on employment in the two other sectors is not statistically significant. African countries should therefore increase employment through higher processing of primary products.
Sex education's community problem
Authors: Howlett Caitlin
Published: October 2022

Legislating comprehensive sex education curricula has long been believed to be essential to aligning education about sex, sexuality and human relationships with the values of equality, inclusivity and autonomy. Defences of the need for ‘good’ sex education in public schools are contingent upon arguments about whose experiences ought to guide us in determining what sufficient alignment with such values might look like. The aim of this paper is to explore the assumptions underlying one prevailing norm in such defences: what I call parental deference or the practice of heeding to the rights of parents in debates about sex education. The question at the heart of this paper is, then, who in our communities does this deference exclude? I begin with a brief consideration of the appeal of parental deference within theories of education in general, and sex education in particular, before problematising its normalisation through a consideration of the exclusions such deference creates. In the process, I aim to explore the limits of parental deference for addressing the intersection of sexuality, sex, gender and race with violence in curricula and argue instead that one way of mitigating the consequences of these limits is to take seriously what I call sex education's community problem: If schools are to serve communities, why are so many community members’ experiences excluded?
Artificial light at night decreases the pupillary light response of dark‐adapted toads to bright light
Authors: SECONDI Jean , SCRIBA Madeleine F. , MONDY Nathalie , LENGAGNE Thierry
Published: October 2022

Artificial light at night (ALAN) is expanding worldwide. Many physiological effects have been reported in animals, but we still know little about the consequences for the visual system. The pupil contributes to control incoming light onto the retina. Sudden increases in light intensity evokes the pupil light reflex (PLR). Intrinsically photosensitive retinal ganglion cells (ipRGC) affect PLR and melatonin expression, which largely regulate circadian rhythms and PLR itself. IpRCG receive inputs from various photoreptors with different peak sensitivities implying that PLR could be altered by a broad range of light sources. We predicted ALAN to enhance PLR. Contrary to our prediction, dark‐adapted cane toads Rhinella marina, exposed to ALAN (5 lx) for 12 days, exhibited a lower PLR than controls and individuals exposed to 0.04 lx, even after 1 h in bright light. We cannot conclude whether ALAN induced a larger pupil size in dark‐adapted toads or a slower initial contraction. Nevertheless, the response was triggered by a light source with an emission peak (590 nm) well above the sensitivity peak of melanopsin, the main photoreceptor involved in PLR. Therefore, ALAN alters the capacity of toads to regulate the incoming light in the eye at night, which may reduce the performance of visually guided behaviors, and increase mortality by predators or road kills at night. This first study emphasizes the need to focus on the effect of ALAN on the vision of nocturnal organisms to better understand how this sensory system is altered and anticipate the consequences for organisms.
Fermentation conditions for yeast selection and effect of yeast–bacterial interaction in developing a starter culture for tequila fermentation
Authors: Aldrete‐Tapia J. Alejadro , Escalante‐Minakata Pilar , Miranda‐Castilleja Dalia Elizabeth , Hernández‐Iturriaga Montserrat
Published: October 2022

Similar to other beverages, tequila fermentation can be improved using selected native strains. During fermentation, yeast and bacteria frequently act together and can improve product quality. However, their influence during tequila fermentation is not fully understood. Three Saccharomyces cerevisiae strains isolated in a previous study were used to determine their fermentation parameters. Fermentation of agave juice by a selected yeast strain in the presence of seven native bacterial species (individually and in consortium) was also evaluated. Optimal temperature, initial fructose, and pH were determined using a rotatory central composite design, and concomitant fermentative parameters were used to select the best tequila yeast strain. The yeast strain Teq‐199 presented the best fructose consumption (91.0%), ethanol production (33.5 g/L), and yield (72%), as well as produced low concentrations of acetic acid (0.2 g/L). The optimal fermentation temperature was 32°C, similar to that used at distilleries. During fermentation of agave juice by strain Teq‐199 in the presence of individual native bacteria, the yeast dominated fermentation, while bacterial species impaired its quality due to lactic acid production (>3.3 g/L). In the presence of a bacterial consortium, strain Teq‐199 also dominated fermentation; however, a high concentration of acetic acid (6.5 g/L) was generated, reducing the quality of the fermentation parameters. A comparison with a commercial wine strain K1‐V1116, revealed that the strain Teq‐199 exhibited the best fermentation parameters, indicating its potential use as an inoculant in industrial processing. Since bacteria were detrimental, distilleries should exert efforts to reduce their impact.

Practical Application

The optimal fermentation conditions for pre‐selected yeast strains isolated during tequila production were determined, which led to the selection of the best‐adapted yeast strain to fulfill the actual requirements and conditions in the tequila industry. This study allows the selection of yeast strains that could be used by local producers. In addition, this yeast was able to overcome a well‐adapted bacterial consortium, showing dominance throughout the fermentation process. This study is unique since it explored bacterial interactions during fermentation process and proposes a method to assess the effect of these concomitant microorganisms to properly select and design a starter culture.
Learning to predict spatiotemporal movement dynamics from weather radar networks
Authors: Lippert Fiona , Kranstauber Bart , Forré Patrick D. , van Loon E. Emiel
Published: October 2022

Weather radar networks provide wide‐ranging opportunities for ecologists to quantify and predict movements of airborne organisms over unprecedented geographical expanses. The typically sparse spatial distribution of radar measurements poses, however, a major challenge to spatiotemporal predictive modelling.

We propose FluxRGNN, a recurrent graph neural network that is based on a generic mechanistic description of population‐level movements across the Voronoi tessellation of radar sites. The resulting hybrid model capitalises on local associations between environmental conditions and animal density as well as on spatiotemporal dependencies inherent to the movement process. We applied FluxRGNN to make 72‐h forecasts of nocturnal bird migration over Western Europe using simulated trajectories and measurements from the European weather radar network.

For both datasets, FluxRGNN achieves higher predictive performance than baseline models based on environmental conditions alone. It effectively disentangles local take‐off and landing dynamics from aerial movements and correctly predicts migration directions with an accuracy of 87%.

Continental‐scale forecasts of animal density and biomass fluxes have the potential to improve the impact and cost‐effectiveness of wildlife management and conservation efforts. With FluxRGNN this becomes feasible for nocturnal bird migration. In the future, other migration systems could benefit from applying the proposed method to similar static sensor networks.
Estimating the size of colorectal polyps endoscopically: random guess or systematic error?
Authors: Liang Jennifer , Church James M.
Published: October 2022

Background

Size of colorectal polyps reflects potential for malignancy and helps define advanced lesions. Studies measuring ability of endoscopists to estimate polyp size show significant variation. The aim of this study was to determine if there is a linear relationship between endoscopic and pathologic polyp size.

Methods

Data for adenomas removed completely by snare, in one piece, were retrieved from a prospectively recorded polyp database. Endoscopic estimate of maximum diameter was compared to that on the pathology report by linear regression analysis.

Results

There were 126 polyps in 126 patients, 85 men and 41 women. Mean age was 63.2 ± 12.9 years. Mean endoscopic polyp size was 12.2 ± 9.3 mm and mean pathology size was 9.3 ± 6.9 mm. Endoscopically, 16 polyps were ≤ 5 mm, 62 were from 6 to 10 mm, 21 were from 11 to 15 mm, and 27 were from 16 to 55 mm. Twenty‐nine polyps were right sided, 86 were left and 11 were rectal. Regression of endoscopic size against pathology size yielded a significant r2 of 0.761. Using the regression formula of endoscopic size = 0.7 + 1.175× pathology size an endoscopic estimate of 10 mm (= advanced adenoma) means a pathologic size of 8 mm. For a pathologic size of 10 mm, an endoscopic estimate of 12 mm is needed. A large polyp is ≥20 mm; for this endoscopist a 20 mm polyp is really 16.4 mm.

Conclusions

The relationship between endoscopic and directly measured size is linear over all polyp diameters, and likely represents a systematic error.
Validation of appendiceal stump invagination in laparoscopic appendectomy
Authors: Bekki Tomoaki , Abe Tomoyuki , Namba Yosuke , Okimoto Sho , Mukai Shoichiro , Saito Yasufumi , Oishi Koichi , Fujisaki Seiji , Ohdan Hideki , Fukuda Toshikatsu
Published: October 2022

Introduction

There are various methods for appendiceal stump dissection, but the necessity for stump invagination remains unclear. This study aimed to assess the efficacy of appendiceal stump invagination in patients with acute appendicitis after laparoscopic appendectomy (LA).

Methods

We enrolled 327 patients with acute appendicitis who underwent LA between 2012 and 2020. Perioperative variables and surgical outcomes were analyzed between the invagination of the appendiceal stump and noninvagination groups. Propensity score‐matched analysis (PSM) was performed.

Results

More patients experienced severe inflammation and severe intra‐abdominal contamination in the noninvagination group than in the invagination group. Patients in the noninvagination group had an older age, higher body mass index, and poorer American Society of Anesthesiologists physical status than the invagination group. Severe inflammation in the noninvagination group was associated with longer hospital stays and poorer postoperative complications than in the invagination group. PSM analysis was performed to minimize bias in the two groups. After PSM analysis, there were no significant differences in surgical site infection, postoperative intra‐abdominal abscess, Clavien–Dindo class ≥IIIa, or postoperative stay between the two groups. During the follow‐up period, the postoperative adhesive ileus was not significantly different between the invagination and noninvagination groups.

Conclusion

Invagination of the appendiceal stump during LA is not necessary to prevent short‐ and long‐term complications. Even in cases dissected using a laparoscopic endostapler, the appendiceal stump per se is not related to postoperative adhesive ileus.
Effects of feeding wood kraft pulp silage containing sweet‐potato shochu distillery by‐product on feed intake, feed digestibility, rumen fermentation, blood components, and growth performance in Japanese Black fattening steers during early period
Authors: Maeda Yuka , Nishimura Keiko , Kurosu Kazuhiro , Mizuguchi Hitoshi , Terada Fuminori , Kushibiki Shiro
Published: October 2022

The effects of long‐term feeding of wood kraft pulp (KP) silage containing sweet‐potato shochu distillery by‐product (SDP) on feed intake, feed digestibility, rumen fermentation, and growth performance of Japanese Black steers were investigated during the early fattening period. Ten Japanese Black steers (9.8 ± 0.6 months of age) were used in this study. Five steers (KP group) were fed KP silage as a replacement for 10% timothy hay (dry matter bases), in contrast to the other five (control group). KP silage consisted of 92.9% KP and 7.1% SDP (dry matter bases). The experiment was conducted for 18 weeks. No significant differences were observed in terms of feed intake, feed digestibility, or daily body weight gain between the groups. In addition, diurnal changes in the rumen pH and ruminal lipopolysaccharide activity did not differ between the groups. However, the plasma concentration of aspartate transaminase in the KP group was slightly lower (P = 0.078) than that in the control group. Thus, our study suggested that feeding KP silage does not reduce feed intake or affect the rumen fermentation or growth performance of Japanese Black fattening steer.
Teachers' perceptions of the barriers to assessment of mental health in schools with implications for educational policy: A systematic review
Authors: O'Farrell Pia , Wilson Charlotte , Shiel Gerry
Published: October 2022

Background

Assessment of mental health in schools has garnered increased interest in recent years. Children spend a large proportion of their waking hours in schools. Teachers can act as gatekeepers by playing a key role in identifying children with mental health difficulties in the classroom and making the necessary onward referrals to external services. The prevalence of mental health difficulties, their impact on schooling (and beyond) and the importance of early intervention means that it is incumbent on schools to identify and support potentially affected children.

Aims

Previous reviews focused on mental healthinterventionsin schools; however, this review focuses onthe assessment ofmental health in schools and on teachers' perceptions of this, as such a review is still lacking. Therefore, the study fills a gap in the existing literature while also providing new, highly relevant evidence that may inform policy making in this area.

Composition of studies included in this review

This review included 19 studies. Five studied teachers exclusively at primary/elementary level, and seven focused on secondary level, while six included both primary and secondary teachers. Three studies employed mixed methods, ten were primarily qualitative studies, and five were primarily quantitative.

Methods

Bronfenbrenner's (The ecology of human development: Experiments by nature and design, Harvard University Press, 1979) framework, adapted by Harvest (How can EPs best support secondary school staff to work effectively with children and young people who experience social, emotional and mental health difficulties?2018), which includes the mature version of the theory (Tudgeet al., 2009,J. Fam. Theory Rev., 1, 198), was used to analyse the literature.

Results

Results found that lack of training in assessment of mental health and ‘role conflict’ were key barriers; some teachers attributed this to their lack of knowledge, skills and confidence in the area.

Conclusion

Implications for practice and research are discussed in relation to the importance of sustained training both pre‐service and in‐service.
Two efficient selection methods for high‐dimensional CD‐CAT utilizing max‐marginals factor from MAP query and ensemble learning approach
Authors: Luo Fen , Wang Xiaoqing , Cai Yan , Tu Dongbo
Published: October 2022

Computerized adaptive testing for cognitive diagnosis (CD‐CAT) needs to be efficient and responsive in real time to meet practical applications' requirements. For high‐dimensional data, the number of categories to be recognized in a test grows exponentially as the number of attributes increases, which can easily cause system reaction time to be too long such that it adversely affects the examinees and thus seriously impacts the measurement efficiency. More importantly, the long‐time CPU operations and memory usage of item selection in CD‐CAT due to intensive computation are impractical and cannot wholly meet practice needs. This paper proposed two new efficient selection strategies (HIA and CEL) for high‐dimensional CD‐CAT to address this issue by incorporating the max‐marginals from the maximum a posteriori query and integrating the ensemble learning approach into the previous efficient selection methods, respectively. The performance of the proposed selection method was compared with the conventional selection method using simulated and real item pools. The results showed that the proposed methods could significantly improve the measurement efficiency with about 1/2–1/200 of the conventional methods' computation time while retaining similar measurement accuracy. With increasing number of attributes and size of the item pool, the computation time advantage of the proposed methods becomes more significant.
Virtual indigo carmine dyeing: New artificial intelligence‐based chromoendoscopy technique
Authors: Yuan Xianglei , Gong Wei , Hu Bing
Published: October 2022

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Challenging method of endoscopic ultrasound‐guided gastroenterostomy using a novel electrocautery‐enhanced lumen‐apposing metal stent for afferent and efferent loop obstruction
Authors: Lee Seung Hyun , Lee Kyong Joo , Park Se Woo
Published: October 2022

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Overtreatment of older people with type 2 diabetes—a high impact frequent occurrence in need of a new definition
Authors: Christiaens Antoine , Henrard Séverine , Boland Benoit , Sinclair Alan J.
Published: October 2022

Background

Diabetes overtreatment is a frequent and major issue in older people with type 2 diabetes but its definition is often inconsistent and may be misleading. This critical review has aimed at examining the definitions of diabetes overtreatment in older people used in research studies.

Methods

Studies addressing diabetes overtreatment in people aged 65 or older were identified by searching the PubMed database according to an extensive search equation.

Results

Twenty‐two research studies providing a definition of diabetes overtreatment in people aged were found. Overall, 12 different definitions of diabetes overtreatment were used. All studies defined overtreatment according to a HbA1c threshold (varying from <42 mmol/mol [<6.0%] to <64 mmol/mol [<8%]). Amongst them, 2 definitions had no consideration about glucose‐lowering (GL) treatment, 6 required the prescribing of ≥1 GL agent(s), and 4 the prescribing of ≥1 GL agent(s) inducing the high risk of hypoglycaemia (i.e., sulfonylurea(s) or insulin(s)). Only 4 definitions (four studies) were individualised, using varying HbA1c thresholds according to patients' age or health status.

Conclusions

Definitions of diabetes overtreatment are heterogeneous across research studies, which is confusing. A standardised definition, based on the individual risk of hypoglycaemia and/or its complications must be promoted in order to bring clarity and greater insight into this field, as well as to improve the quality of management of diabetes in older patients.
Toward an understanding of the implementation of management innovation in international joint ventures: A multilevel perspective
Authors: Bahri Korbi Fadia , Geraudel Mickael , Nakara Walid A.
Published: October 2022

Implementing management innovation (MI) is a great challenge for international joint ventures (IJVs), specifically for those between multinational enterprises (MNEs) and local firms. Different multilevel factors have been shown in the international business literature to play a role in MI implementation within IJVs. In this paper, we add to this literature by showing that these factors do not act in isolation and that their interplay must be considered. To this aim, we draw on qualitative data from 35 CEOs and TMT members of five IJVs between European MNEs and Tunisian local firms. Overall, our study reveals that depending on the type of IJV, the multilevel factors playing a role in the implementation of MI are different.
BAP1 depletion in human B‐lymphoblast cells affects the production of innate immune cytokines and chemokines
Authors: Takagi‐Kimura Misato , Tada Akio , Kijima Takashi , Kubo Shuji , Ohmuraya Masaki , Yoshikawa Yoshie
Published: October 2022

BRCA1 associated protein 1 (BAP1) is a ubiquitin C‐terminal hydrolase that deubiquitinates histone H2AK119ub and other proteins and regulates the expression of multiple genes. The knockout of this tumor suppressor gene results in severe thymic atrophy, complete loss of the T cell lineage, and abnormal B cell development in mice. In the current study, we investigated in vitro effects of BAP1 knockout on cytokine and chemokine production using the human B‐lymphoblast cell line TSCE5. We confirmed that knockout changed the production of innate immune‐associated genes and their receptors. The CCL19, CCR7, CCL2, and CXCR5 genes associated with T and B cell migration were upregulated. Knockout cells producing high levels of CCL19 showed acceleration of actin polymerization, which is essential for cell migration. CD69, PTPRC, and TLR3 genes that activate inflammation were downregulated. The tumor necrosis factor ligand genes TNF, LTA, and TNFSF10 were downregulated by knockout. In knockout cells, TNFα production was strongly downregulated upon the addition of H2O2, but NF‐κB in the basal condition and when TNFα was added was augmented, suggesting that these cells could respond to TNFα. These results indicated that BAP1 affects the expression of chemokines and cytokines, T and B cell migration, and activated inflammation associating with innate immunity.
Early‐phase prothrombin time‐international normalized ratio in acute liver injury indicates the timing of therapeutic intervention and predicts prognostic improvement
Authors: Kumagai Kotaro , Mawatari Seiichi , Moriuchi Akihiro , Oda Kohei , Takikawa Yasuhiro , Kato Naoya , Oda Shigeto , Inoue Kazuaki , Terai Shuji , Genda Takuya , Shimizu Masahito , Sakaida Isao , Mochida Satoshi , Ido Akio
Published: October 2022

Aim

We investigated whether an early‐phase prothrombin time‐international normalized ratio (PT‐INR) is an interventional prognostic indicator for patients with acute liver injury, including acute liver failure.

Methods

This was a multicenter retrospective observational study. We included 595 patients with alanine aminotransferase levels ≥300 U/L due to acute liver injury who were admitted to Kagoshima University Hospital or other collaborative investigation organizations between January 1, 2010, and December 31, 2015. Patients with alanine aminotransferase levels ≥300 U/L and no previous liver disease were defined as having an acute liver injury. Acute liver failure was defined by PT‐INR ≥1.5 with or without hepatic encephalopathy in acute liver injury patients. Data were obtained retrospectively from case reports and analyzed.

Results

The PT‐INR on day 1 was the most accurate independent prognosis predictor in patients with acute liver injury and acute liver failure. On day 1, the transplant‐free survival rates were significantly lower in patients with PT‐INR ≥1.3. The transplant‐free survival rates were also significantly higher in patients with acute liver injury and acute liver failure, in whom the PT‐INR had recovered from ≥1.3 on day 1 to <1.3 by day 8.

Conclusion

Early‐phase changes in the PT‐INR can predict the prognosis of patients with acute liver injury and acute liver failure. Furthermore, PT‐INR ≥1.3 could be an interventional marker, whereas PT‐INR <1.3 after 1 week could reflect prognostic improvement.
Towards a functional classification of poorly known tropical insects: The case of rhinoceros beetles (Coleoptera, Dynastinae) in Panama
Authors: Basset Yves , Blažek Petr , Souto‐Vilarós Daniel , Vargas Gersey , Ramírez Silva José Alejandro , Barrios Héctor , Perez Filonila , Bobadilla Ricardo , Lopez Yacksecari , Ctvrtecka Richard , Šípek Petr , Solís Angel , Segar Simon T. , Lamarre Greg P. A.
Published: October 2022

The population dynamics of most tropical insects are unknown and long‐term monitoring programmes are urgently needed to evaluate a possible insect decline in the tropics. In this context, functional groups can be used effectively to summarise time‐series for species‐rich taxa. Neotropical dung beetles have often been catalogued into functional groups, but close relatives also of ecological significance, the Dynastinae, are awaiting such a classification.

Here, we examine the functional groups of Dynastinae at the regional (Panama: 147 species) and local (Barro Colorado Island, BCI: 56 species) scales. Our optimum classification of Panamanian species distinguished five groups, one of which is probably artificial and accounts for species ecologically poorly known.

Ecological attributes or species traits mainly influencing the delineation of groups were geographical distribution, body length, seasonal aggregation, larval food and whether the adult may be present in decaying wood.

Our analyses indicated that (1) missing trait values and the high percentage of ‘cryptic’ species (25%) influenced the delineation of groups; (2) the dendrogram similarity of functional groups versus phylogenetic tree was low, although some traits were phylogenetically conserved; and (3) the overall structure of functional groups was conserved when comparing regional and local data, suggesting no drastic loss of functional groups locally.

To proceed with the functional classification of poorly known tropical insects, we recommend a cautious selection of traits a priori, inclusion of ‘cryptic’ species recognised by DNA barcoding, and building phylogenies, which may allow a careful taxonomic imputation to complete species‐traits matrices.