bluuebunny/crossref_metadata_2025 huggingface dataset:
A latent variable approach to decoding neural population activity
Authors: Whiteway Matthew R , Averbeck Bruno , Butts Daniel A
Published: January 2020

Decoding is a powerful approach for measuring the information contained in the activity of neural populations. As a result, decoding analyses are now used across a wide range of model organisms and experimental paradigms. However, typical analyses employ general purpose decoding algorithms that do not explicitly take advantage of the structure of neural variability, which is often low-dimensional and can thus be effectively characterized using latent variables. Here we propose a new decoding framework that exploits the low-dimensional structure of neural population variability by removing correlated variability that is unrelated to the decoded variable, then decoding the resulting denoised activity. We demonstrate the efficacy of this framework using simulated data, where the true upper bounds for decoding performance are known. A linear version of our decoder provides an estimator for the decoded variable that can be more efficient than other commonly used linear estimators such as linear discriminant analysis. In addition, our proposed decoding framework admits a simple extension to nonlinear decoding that compares favorably to standard feed-forward neural networks. By explicitly modeling shared population variability, the success of the resulting linear and nonlinear decoders also offers a new perspective on the relationship between shared variability and information contained in large neural populations.
Neurodegenerative disease-associated protein aggregates are poor inducers of the heat shock response in neuronal-like cells
Authors: Gil R. San , Cox D. , McAlary L. , Berg T. , Walker A. K. , Yerbury J. J. , Ooi L. , Ecroyd H.
Published: January 2020

Protein aggregation that results in the formation of inclusions is strongly correlated with neuronal death and is a pathological hallmark common to many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and Huntington’s disease. Cells are thought to dramatically up-regulate the levels of heat shock proteins during periods of cellular stress via induction of the heat shock response (HSR). Heat shock proteins are well-characterised molecular chaperones that interact with aggregation-prone proteins to either stabilise, refold, or traffic protein for degradation. The reason why heat shock proteins are unable to maintain the solubility of particular proteins in neurodegenerative disease is unknown. We sought to determine whether neurodegenerative disease-associated protein aggregates can induce the HSR. Here, we generated a neuroblastoma cell line that expresses a fluorescent reporter under conditions of HSR induction, for example heat shock. Using these cells, we show that the HSR is not induced by exogenous treatment with aggregated forms of Parkinson’s disease-associatedα-synuclein or the ALS-associated G93A mutant of superoxide dismutase-1 (SOD1G93A). Furthermore, flow cytometric analysis revealed that intracellular expression of SOD1G93Aor a pathogenic form of polyQ-expanded huntingtin (Htt72Q), similarly, results in no or low induction of the HSR. In contrast, expression of a non-pathogenic but aggregation-prone form of firefly luciferase (Fluc) did induce an HSR in a significantly greater proportion of cells. Finally, we show that HSR induction is dependent on the intracellular levels of the aggregation-prone proteins, but the pathogenic proteins (SOD1G93Aand Htt72Q) elicit a significantly lower HSR compared to the non-pathogenic proteins (Fluc). These results suggest that pathogenic proteins either evade detection or impair induction of the HSR in neuronal-like cells. Therefore, defective HSR induction may facilitate the initiation of protein aggregation leading to inclusion formation in neurodegenerative diseases.
Depletion of the AD risk geneSORL1selectively impairs neuronal endosomal traffic independent of amyloidogenic APP processing
Authors: Knupp Allison , Mishra Swati , Martinez Refugio , Braggin Jacquelyn E. , Szabo Marcell , Hailey Dale W. , Small Scott A. , Jayadev Suman , Young Jessica E.
Published: January 2020

TheSORL1gene encodes for the protein SorLA, a sorting receptor involved in retromer-related endosomal traffic. ManySORL1genetic variants increase Alzheimer’s disease (AD) risk, and rare loss-of-function truncation mutations have been found to be causal of late-onset AD.SORL1is expressed in neurons and glia of the central nervous system and loss ofSORL1has been reported in AD tissue. To model the causal loss-of-function mutations, we used CRISPR/Cas9 technology to depleteSORL1in human induced pluripotent stem cells (hiPSCs) to test the hypothesis that loss ofSORL1contributes to AD pathogenesis by leading to endosome dysfunction. We report that loss ofSORL1in hiPSC-derived neurons leads to early endosome enlargement, a cellular phenotype that is indicative of ‘traffic jams’ and is now considered a hallmark cytopathology AD. We validate defects in neuronal endosomal traffic by showing decreased localization of amyloid-precursor protein (APP) in the trans-Golgi network (TGN), and increased localization of APP in early endosomes, a site of APP cleavage by the β secretase BACE1. Microglia, immune cells of the CNS, which play a role in AD pathology also expressSORL1. We therefore tested and found no effect ofSORL1depletion on endosome size or morphology in hiPSC-derived microglia, suggesting a selective effect on neuronal endosomal trafficking. Finally, because BACE1 dependent APP fragments can cause endosome enlargement, we treatedSORL1deficient hiPSC-derived neurons with BACE1 inhibitors and demonstrate that endosome enlargement occurs independent of amyloidogenic APP fragments. Collectively, these findings clarify where and howSORL1links to AD. Moreover, our data, together with recent findings, underscores how sporadic AD pathways that regulate endosomal trafficking, and autosomal-dominant AD pathways that regulate APP cleavage, independently converge on the defining cytopathology of AD.
Density-functional-theory-predicted symmetry lowering from cubic to tetragonal in nickel hexacyanoferrate
Authors: Ghazisaeed Seyedayat , Minuddin Md , Nakotte Heinz , Kiefer Boris
Published: January 2020

Density-functional-theory (DFT) computations on a Prussian blue analogue (PBA), nickel hexacyanoferrate, Ni2+
3[Fe3+(CN)6]2·nH2O, predict the existence of a tetragonal (P
4
m2) crystal structure that is energetically degenerate with the previously reported cubic (F
43m) structure for this PBA. The proposed tetragonal structure satisfies observations, such as X-ray diffraction and magnetic measurements, that have been reported previously. A van der Waals corrected exchange-correlation functional is used in the DFT+U computations for an improved description of hydrogen bonding. The results provide strong support for a revised and simplified crystallographic description of Ni2+
3[Fe3+(CN)6]2·nH2O, and show how H2O molecules stabilize the crystal structure and affect its magnetic and electronic properties. The symmetry lowering in nickel hexacyanoferrate is attributed to the hydration shell of the interstitial nickel cation. Calculations strongly suggest a maximum of n = 7 interstitial H2O molecules per formula unit for nickel hexacyanoferrate at room temperature, and a higher water content at temperatures below T ≃ 200 K. Since the symmetry lowering relies on the presence of interstitial H2O molecules, this revised crystallographic description may be applicable more generally to the large class of F
43m-structured PBAs.
Toward the optimized crowdsourcing strategy for OCR post-correction
Authors: Suissa Omri , Elmalech Avshalom , Zhitomirsky-Geffet Maayan
Published: January 2020

Purpose

Digitization of historical documents is a challenging task in many digital humanities projects. A popular approach for digitization is to scan the documents into images, and then convert images into text using optical character recognition (OCR) algorithms. However, the outcome of OCR processing of historical documents is usually inaccurate and requires post-processing error correction. The purpose of this paper is to investigate how crowdsourcing can be utilized to correct OCR errors in historical text collections, and which crowdsourcing methodology is the most effective in different scenarios and for various research objectives.

Design/methodology/approach

A series of experiments with different micro-task’s structures and text lengths were conducted with 753 workers on the Amazon’s Mechanical Turk platform. The workers had to fix OCR errors in a selected historical text. To analyze the results, new accuracy and efficiency measures were devised.

Findings

The analysis suggests that in terms of accuracy, the optimal text length is medium (paragraph-size) and the optimal structure of the experiment is two phase with a scanned image. In terms of efficiency, the best results were obtained when using longer text in the single-stage structure with no image.

Practical implications

The study provides practical recommendations to researchers on how to build the optimal crowdsourcing task for OCR post-correction. The developed methodology can also be utilized to create golden standard historical texts for automatic OCR post-correction.

Originality/value

This is the first attempt to systematically investigate the influence of various factors on crowdsourcing-based OCR post-correction and propose an optimal strategy for this process.
Improved analytical approach for studying the effect of diode power detector modelling on six-port communication receiver performance
Authors: Hazer Sahlabadi Mehran , Abdipour Abdolali , Mohammadi Abbas
Published: January 2020

Purpose

The purpose of this paper is to study the effect of diode power detector modelling on six-port communication receiver performance.

Design/methodology/approach

Based on proposed and conventional squared diode model, six-port receiver’s demodulation and its error vector magnitude (EVM) performance due to hardware impairments are studied. Through considering both the models, the accuracy of proposed power detector model is compared to the squared model, and then both results are validated with envelope simulation (ENV) in advanced design system (ADS).

Findings

Comparing the numerical results with envelope simulation results proved that the proposed model is much more accurate than the conventional squared model for a wide range of input power levels.

Originality/value

Studying the receiver’s performance numerically, by considering the new proposed analytical approach for diode power detectors which is more accurate than the conventional squared model.
Design tools for electromagnetic-driven multi-physics systems using high performance computing
Authors: Lowther David , Ghorbanian Vahid , Mohammadi Mohammad Hossain , Ibrahim Issah
Published: January 2020

Purpose

The design of electromagnetic systems for a variety of applications such as induction heating, electrical machines, actuators and transformers requires the solution of a multi-physics problem often involving thermal, structural and mechanical coupling to the electromagnetic system. This results in a complex analysis system embedded within an optimization process. The appearance of high-performance computing systems over the past few years has made coupled simulations feasible for the design engineer. When coupled with surrogate modelling techniques, it is possible to significantly reduce the wall clock time for generating a complete design while including the impact of the multi-physics performance on the device.

Design/methodology/approach

An architecture is proposed for linking multiple singe physics analysis tools through the material models and a controller which schedules the execution of the various software tools. The combination of tools is implemented on a series of computational nodes operating in parallel and creating a “super node” cluster within a collection of interconnected processors.

Findings

The proposed architecture and job scheduling system can allow a parallel exploration of the design space for a device.

Originality/value

The originality of the work derives from the organization of the parallel computing system into a series of “super nodes” and the creation of a materials database suitable for multi-physics interactions.
From principal cognitive complexity to teacher intent to leave
Authors: Da’as Rima’a , Schechter Chen , Qadach Mowafaq
Published: January 2020

Purpose

The purpose of this paper is to test an innovative model for exploring the direct and indirect relationships between principals’ cognitive complexity (CC), schools’ absorptive capacity (ACAP), a teacher’s affective commitment and a teacher’s intent to leave.

Design/methodology/approach

Data were collected from a survey of 1,664 teachers at 107 Arab elementary schools, randomly selected from the database of the Israeli educational system. To test the proposed model, multilevel structural equation modeling was conducted.

Findings

The analysis confirmed that schools’ ACAP and a teacher’s affective commitment are prominent mediators between principals’ CC and a teacher’s intent to leave.

Practical implications

Understanding the factors that contribute to a teacher’s intent to leave could help school principals and policy makers retain effective teachers in today’s schools.

Originality/value

This study adds to the body of research directed at identifying school principals’ characteristics, as well as work-related factors, which may decrease a teacher’s intent to leave and are amenable to leadership intervention.
“Wag the Dog” initiatives and the corporate immune system
Authors: Schweizer Roger , Lagerström Katarina
Published: January 2020

Purpose

This paper aims to contribute to the subsidiary initiative literature by studying the interaction between a headquarters and its subsidiary during an initiative process that has the potential to “wag the corporate dog” that is, for the global corporation’s promising subsidiary initiative in a strategically important emerging market to question the corporation’s prevailing schemata.

Design/methodology/approach

The longitudinal single case study draws on evidence from the Indian subsidiary of Swedish Volvo Bus and its efforts to introduce a value product in India.

Findings

The study argues that wag the dog initiatives provoke the corporate immune system independent of the initiative’s potential and the subsidiary’s autonomy and legitimacy. If the idea behind the wag the dog initiative is perceived as strategically important for the multinational corporation, then the corporate immune system tries to engulf – most likely unsuccessfully – the idea within the prevailing schemata. Failed attempts to engulf the initiative weaken the corporate immune system temporarily, thereby opening the organization to revitalization of the original initiative. Resistance, even though weakened, from the corporate immune system continues to exist.

Practical implications

Subsidiary managers need to avoid having their headquarters perceive an initiative as a wag the dog initiative by balancing their need to sell persistently the initiative with avoiding negative attention.

Originality/value

This study is a pioneer in explaining how the corporate immune system reacts towards wag the dog initiatives taken from subsidiaries in large emerging markets.
Chronic prurigo: A retrospective study of 168 cases
Authors: Inui Keiko , Ugajin Tsukasa , Namiki Takeshi , Yokozeki Hiroo
Published: January 2020

Chronic prurigo is classified into two clinical subtypes: prurigo nodularis (PN) and prurigo chronica multiformis (PCM) in Japan. In this study, we retrospectively investigated the clinical features of 168 patients with chronic prurigo (103 with PN and 65 with PCM) diagnosed at the Tokyo Medical and Dental University, and compared age, sex, prevalence of comorbidities, blood test results, histology and treatment efficacy in both groups. We found that patients with PCM were significantly older than those with PN. Males were more frequently diagnosed with PCM than females; however, both sexes were similarly affected by PN. Chronic infection was more prevalent in PN, whereas diabetes was more common in PCM. For both subtypes, serum immunoglobulin E levels were elevated above the normal range. However, serum thymus and activation‐regulated chemokine/CCL17 levels and the number of blood eosinophils were significantly higher in patients with PCM than in those with PN. Histologically, much higher numbers of CD4+cells than CD8+cells were distributed in the lesions of both subtypes. Eosinophils were distributed predominantly in intracollagenous lesions in PCM but were observed mainly in perivascular lesions in PN. There were no differences in basophil and mast cell distributions in the lesions of the two groups. Treatment efficacy was also similar in both subtypes. Together, both subtypes exhibit inflammation patterns predominantly driven by T‐helper 2 cells. With respect to PCM, elevated numbers of blood eosinophils and the recruitment of these cells into intracollagenous areas may be important for pathogenesis.
Successful treatment of psoriatic arthritis and comorbid annular atrophic lichen planus with etanercept
Authors: Niebel Dennis , Wilsmann‐Theis Dagmar , Wenzel Joerg
Published: January 2020

Psoriasis vulgaris and lichen planus are distinct T‐cell‐driven inflammatory skin diseases. Both present in a variety of clinical subtypes. Mucosal or nail involvement may be present. Here, we report the rare concomitant clinical presentation of psoriatic arthritis and annular atrophic lichen planus on the trunk of a 52‐year‐old male patient. Treatment with sulfasalazine failed to control inflammatory activity; methotrexate and leflunomide were ceased due to side‐effects. After confirmation of both diagnoses, we initiated a tumor necrosis factor (TNF)‐α‐directed therapy with the fusion protein etanercept resulting in significant improvement of both conditions. This case report aims to highlight the rare colocalization of psoriasis and lichen planus, the rare entity of annular atrophic lichen planus, and to discuss a possible beneficial impact of certain TNF‐α inhibitors on subtypes of lichen planus.
Mediterranean marine protected areas have higher biodiversity via increased evenness, not abundance
Authors: Blowes Shane A. , Chase Jonathan M. , Di Franco Antonio , Frid Ori , Gotelli Nicholas J. , Guidetti Paolo , Knight Tiffany M. , May Felix , McGlinn Daniel J. , Micheli Fiorenza , Sala Enric , Belmaker Jonathan
Published: January 2020

Protected areas are central to biodiversity conservation. For marine fish, marine protected areas (MPAs) often harbour more individuals, especially of species targeted by fisheries. But precise pathways of biodiversity change remain unclear. For example, how local‐scale responses combine to affect regional biodiversity, important for managing spatial networks of MPAs, is not well known. Protection potentially influences three components of fish assemblages that determine how species accumulate with sampling effort and spatial scale: the total number of individuals, the relative abundance of species and within‐species aggregation. Here, we examined the contributions of each component to species richness changes inside MPAs as a function of spatial scale.

Using standardized underwater visual survey data, we measured the abundance and species richness of reef fishes in 43 protected and 41 fished sites in the Mediterranean Sea.

At both local and regional scales, increased species evenness caused by added common species in MPAs compared to fished sites was the most important proximate driver of higher diversity.

Site‐to‐site variation in the composition (i.e. β‐diversity) of common species was also higher among protected sites, and depended on sensitivity to exploitation. There were more abundant exploited species at regional scales than at local scales, reflecting a tendency for different protected sites to harbour different exploited species. In contrast, fewer abundant unexploited species were found at the regional scale than at the local scale, meaning that relative abundances at the regional scale were less even than at the local scale.

Synthesis and applications. Although marine protected areas (MPAs) are known to strongly influence fish community abundance and biomass, we found that changes to the relative abundance of species (i.e. increased evenness) dominated the biodiversity response to protection. MPAs had more relatively common species, which in turn led to higher diversity for a given sampling effort. Moreover, higher β‐diversity of common species meant that local‐scale responses were magnified at the regional scale due to site‐to‐site variation inside protected areas for exploited species. Regional conservation efforts can be strengthened by examining how multiple components of biodiversity respond to protection across spatial scales.
GQ‐130, a novel analogue of thiazolidinedione, improves obesity‐induced metabolic alterations in rats: Evidence for the involvement of PPARβ/δ pathway
Authors: Silva Odair Alves , Ribeiro‐Filho Helder Veras , Avelino Thayna Mendonca , Tittanegro Thais Helena , Figueira Ana Carolina Migliorini , Rabelo Luiza Antas , Pitta Ivan da Rocha , Lahlou Saad , Duarte Glória Pinto
Published: January 2020

The present investigation aimed to characterize the effect of a short‐time treatment with a new thiazolidinedione (TZD) derivative, GQ‐130, on metabolic alterations in rats fed a high‐fat diet (HFD). We investigated whether metabolic alterations induced by GQ‐130 were mediated though a mechanism that involves PPARβ/δ transactivation. Potential binding and transactivation of PPARα, PPARβ/δ or PPARγ by GQ‐130 were examined through cell transactivation, 8‐anilino‐1‐naphthalenesulfonic acid (ANS) fluorescence quenching assays and thermal shift assay. For in vivo experiments, male 8‐week‐old Wistar rats were divided into three groups fed for 6 weeks with: (a) a standard rat chow (14% fat) (control group), (b) a HFD (57.8% fat) alone (HFD group), or (c) a HFD associated with an oral treatment with GQ‐130 (10 mg/kg/d) during the last week (HFD‐GQ group). In 293T cells, unlike rosiglitazone, GQ‐130 did not cause significant transactivation of PPARγ but was able to activate PPARβ/δ by 153.9 folds in comparison with control values (DMSO). Surprisingly, ANS fluorescence quenching assay reveals that GQ‐130 does not bind directly to PPARβ/δ binding site, a finding that was further corroborated by thermal shift assay which evaluates the thermal stability of PPARβ/δ in the presence of GQ‐130. Compared to the control group, rats of the HFD group showed obesity, increased systolic blood pressure (SBP), insulin resistance, impaired glucose intolerance, hyperglycaemia, and dyslipidaemia. GQ‐130 treatment abolished the increased SBP and improved all metabolic dysfunctions observed in the HFD group. Oral treatment with GQ‐130 was effective in improving HFD‐induced metabolic alterations probably through a mechanism that involves PPARβ/δ activation.
Deciphering proteolysis pathways for the error‐prone DNA polymerase in cyanobacteria
Authors: Jin Haojie , Kim Rick , Bhaya Devaki
Published: January 2020

Protein quality control pathways require AAA+ proteases, such as Clp and Lon. Lon protease maintains UmuD, an important component of the error‐prone DNA repair polymerase (Pol V), at very low levels in E. coli. Most members of the phylum Cyanobacteria lack Lon (including the model cyanobacterium, Synechocystis sp. PCC6803), so maintenance of UmuD at low levels must employ different proteases. We demonstrate that the first 19 residues from the N‐terminus of UmuD (Sug1‐19) fused to a reporter protein are adequate to trigger complete proteolysis and that mutation of a single leucine residue (L6) to aspartic acid inhibits proteolysis. This process appears to follow the N‐end rule and is mediated by ClpA/P protease and the ClpS adaptor. Additionally, mutations of arginine residues in the Sug1‐19 tag suggest that the ClpX/P pathway also plays a role in proteolysis. We propose that there is a dual degron at the N‐terminus of the UmuD protein in Synechocystis sp. PCC6803, which is distinct from the degron required for degradation of UmuD in E. coli. The use of two proteolysis pathways to tune levels of UmuD might reflect how a photosynthetic organism responds to multiple environmental stressors.
Discovery of Two New Peculiar Subgenera and Two New Species of Tipula Linnaeus, 1758 (Diptera, Tipulidae) from Baltic Amber
Authors: KRZEMIŃSKI Wiesław , KANIA Iwona , JORDAN‐STASIłO Wiktoria , DE JONG Herman , KRZEMIŃSKA Ewa , SKIBIŃSKA Kornelia
Published: January 2020

Two new fossil subgenera and two new fossil species of the genus Tipula Linnaeus, 1758, Tipula (Succinica) berendti subgen. and sp. n. and Tipula (Gedanica) adamowiczi subgen. and sp. n., are described from Baltic amber and compared with other species of Tipula known from the Eocene. The two new subgenera and species described herein are an excellent bridge between recent specimens and those preserved in sedimentary rocks, and thus enrich knowledge on the evolution of the family.
On the Validity and Evolution of Assilina Species during the Ypresian–Lutetian: Example from Bir Dakhl, Eastern Desert, Egypt
Authors: AL MENOUFY Safia , BOUKHARY Mohamed
Published: January 2020

The genus Assilina is a taxon within the Nummulitacea that appeared early in the Ypresian (Early Eocene) and continued until the end of the Lutetian (Middle Eocene). Thus, this taxon could be useful for the chronostratigraphy of this time interval. Lower Eocene rocks in southern Galala, Egypt are exposed at Bir Dakhl. This section includes marl sediments with debris flow shallow‐marine facies deposits laid down during early Eocene times and includes fossils of large foraminifera: Assilina placentula Deshayes, 1838 and Nummulites burdigalensis de la Harpe, 1926. These are systematically treated, described and illustrated. Nummulites burdigalensis belongs to the N. burdigalensis group, and Assilina placentula belongs to the group of Assilina exponens. This assumption is based on qualitative morphology and quantitative measurements. Both species, together with Operculina libyca Schwager, 1883, enable the assignment of the Bir Dakhl (D5‐40 Section) to the Early Eocene, Ypresian (SBZ10 of Serra‐ Kiel et al., 1998) supporting an earlier opinion that Assilina placentula belongs to that zone in the calibrated larger foraminiferal biostratigraphic zonation.
Prevalence of and factors associated with depression and anxiety in patients with rheumatoid arthritis: A multicenter prospective cross‐sectional study
Authors: Katchamart Wanruchada , Narongroeknawin Pongthorn , Chanapai Wanwisa , Thaweeratthakul Phakhamon , Srisomnuek Ananya
Published: January 2020

Aim

To investigate the prevalence of and factors associated with depression and anxiety in patients with rheumatoid arthritis (RA).

Methods

This prospective cross‐sectional study included patients who were consecutively enrolled in the Siriraj Rheumatoid Arthritis Registry or the Thai Army Rheumatoid Arthritis Cohort during the September 2016 to March 2018 study period. Demographic data and clinical variables, including disease activity, functional status, health‐related quality of life, and cognitive function, were collected. Depression and anxiety were assessed using the Thai version of the Hospital Anxiety and Depression Scale (Thai HADS).

Results

Four hundred and sixty‐four patients were included. Mean age was 59 years, median disease duration was 9.9 years, and 85% of patients were female. Based on the Thai HADS cutoff value of 8 or higher, 12.5% and 14.5% of patients had some degree of depression and anxiety, respectively. Multivariate analysis revealed global health score (risk ratio [RR]: 0.98, P = .001) to be the only factor independently negatively associated with depression. Regarding anxiety, functional disability (RR: 2.46, P = .004) and married status (RR: 2.43, P = .009) were significantly associated with increased risk, whereas disease duration of 10 years or more (RR: 0.45, P = .007) and global health score (RR: 0.97, P < .001) were significantly associated with decreased risk of developing anxiety.

Conclusion

Depression and anxiety are common in patients with RA. Patients' perceptions of their current health are significantly related to mood disorders. Therefore, mental health status, especially mood disturbances, should be addressed in routine practice to improve quality of life in RA.
Genome‐enable prediction for health traits using high‐density SNP panel in US Holstein cattle
Authors: Lopes F. , Rosa G. , Pinedo P. , Santos J. E. P , Chebel R. C. , Galvao K. N. , Schuenemann G. M. , Bicalho R. C. , Gilbert R. O. , Rodrigez‐Zas S. , Seabury C. M. , Thatcher W.
Published: January 2020

The objective of this study was to compare accuracies of different Bayesian regression models in predicting molecular breeding values for health traits in Holstein cattle. The dataset was composed of 2505 records reporting the occurrence of retained fetal membranes (RFM), metritis (MET), mastitis (MAST), displaced abomasum (DA), lameness (LS), clinical endometritis (CE), respiratory disease (RD), dystocia (DYST) and subclinical ketosis (SCK) in Holstein cows, collected between 2012 and 2014 in 16 dairies located across the US. Cows were genotyped with the Illumina BovineHD (HD, 777K). The quality controls for SNP genotypes were HWEP‐value of at least 1 × 10−10; MAF greater than 0.01 and call rate greater than 0.95. TheFImputeprogram was used for imputation of missing SNP markers. The effect of each SNP was estimated using the Bayesian Ridge Regression (BRR), Bayes A, Bayes B and Bayes Cπ methods. The prediction quality was assessed by the area under the curve, the prediction mean square error and the correlation between genomic breeding value and the observed phenotype, using a leave‐one‐out cross‐validation technique that avoids iterative cross‐validation. The highest accuracies of predictions achieved were: RFM [Bayes B (0.34)], MET [BRR (0.36)], MAST [Bayes B (0.55), DA [Bayes Cπ (0.26)], LS [Bayes A (0.12)], CE [Bayes A (0.32)], RD [Bayes Cπ (0.23)], DYST [Bayes A (0.35)] and SCK [Bayes Cπ (0.38)] models. Except for DA, LS and RD, the predictive abilities were similar between the methods. A strong relationship between the predictive ability and the heritability of the trait was observed, where traits with higher heritability achieved higher accuracy and lower bias when compared with those with low heritability. Overall, it has been shown that a high‐density SNP panel can be used successfully to predict genomic breeding values of health traits in Holstein cattle and that the model of choice will depend mostly on the genetic architecture of the trait.
Timing and flow pattern of the Orta Glacier (European Alps) during the Last Glacial Maximum
Authors: Braakhekke Jochem , Ivy‐Ochs Susan , Monegato Giovanni , Gianotti Franco , Martin Silvana , Casale Stefano , Christl Marcus
Published: January 2020

Knowledge of the glacial chronologies for the Last Glacial Maximum (LGM) helps in understanding the interactions between climate, topography and glacier development. In this sense, the investigation of the Lake Orta moraine amphitheatre (Alpine foreland, northern Italy) allowed spatial and temporal reconstruction of the Orta Glacier. The end‐moraine system was investigated by means of geomorphological field surveys, analysis of 13 rock samples for cosmogenic 10Be and 36Cl concentrations, and remote sensing analysis. The dating results indicate that the age of the outer moraine belt is concordant with the LGM culmination at 26.5–23 ka, as found in other amphitheatres in the Alps. This new age estimate of the outermost moraines shows that the maximum extent of the Orta Glacier during the LGM was significantly bigger than recently suggested. A younger stabilization phase of the glacier front at about 19 ka indicates that the onset of the withdrawal of glaciers from the lower Alpine valleys started later. Provenance analysis of the boulders shows that the greatest contribution of ice to the Orta Glacier came from the Anzasca Valley rather than the major Ossola Valley. This reflects the closeness (about 45 km) to the foreland of the high‐elevated accumulation area of the Monte Rosa massif (4634 m a.s.l.), whose eastern glacier seems to have reached the lower valley faster than the trunk Toce Glacier. This fact underlines the key role played by high‐elevation accumulation areas that are located close to the foreland in controlling the path and geometry of major glaciers in the Alps.
Is neoadjuvant chemoradiotherapy sufficient in patients with advanced rectal malignancy and positive extra‐mesorectal lateral lymph nodes?
Authors: Ahmadi N. , Brown K. G. M. , Lee P. , Quinn M. , Austin K. K. S. , Solomon M. J.
Published: January 2020

Aim

There is current debate about the optimal management of lateral pelvic lymph nodes (LPLNs) in rectal cancer between Western and Eastern centres. This paper aims to report the rate of histologically proven positive LPLNs in a group of patients undergoing the conventional Western approach to primary and recurrent rectal cancer.

Method

A retrospective cohort review of all patients who underwent LPLN dissection at Royal Prince Alfred Hospital in Sydney, Australia. This included patients who underwent pelvic exenteration who had LPLNs excised either en bloc for laterally invasive or recurrent tumours or as part of selective node dissection for suspicious lymph nodes on preoperative imaging. Histopathological results for these patients were compared with node status at preoperative imaging.

Results

Seventy‐one patients satisfied the inclusion criteria. Of those patients with positive nodes on histology, 27% (9/33) with radiologically positive LPLNs were treated with preoperative radiotherapy and 75% (9/12) with radiologically positive LPLNs were not treated with preoperative radiotherapy (P = 0.004). None of the 12 patients with radiologically negative nodes treated with radiotherapy had positive nodes; 25% (3/12) of the patients with radiologically negative nodes who were not treated with radiotherapy had positive nodes. Fifty‐three per cent of patients developed postoperative complications.

Conclusion

Our study suggests that in patients with radiologically positive LPLNs chemoradiotherapy may not be enough to sterilize these extra‐mesorectal lymph nodes as a large proportion (27%) will have residual viable adenocarcinoma cells. In patients with radiologically negative LPLNs, however, the addition of chemoradiotherapy may serve to adequately sterilize these lymph nodes without the need for prophylactic LPLN dissection.
Surgery with and without adjuvant radiotherapy is associated with similar survival in T4 colon cancer
Authors: Sebastian N. T. , Tan Y. , Miller E. D. , Williams T. M. , Diaz D. A.
Published: January 2020

Aim

There is little evidence regarding the role of adjuvant radiotherapy for colon cancer. Despite this, national consensus guidelines recommend consideration of radiation for patients with T4 colon cancer. Large comparative studies may be beneficial in clarifying the potential benefit of postoperative radiation for this cohort.

Method

We compared the overall survival between patients treated with surgery with and without adjuvant radiation using the National Cancer Database (NCDB) and the Surveillance, Epidemiology, and End Results Program (SEER), as well as disease‐specific survival using SEER. Cox proportional hazards models and propensity score matching were used to adjust for relevant confounders.

Results

There were a total of 18 776 patients in the NCDB cohort and 9926 patients in the SEER cohort. After propensity score matching, there was no statistically significant difference in overall mortality between surgery with and without radiation in the NCDB [hazard ratio (HR) 1.11; 95% CI 0.93–1.31; P = 0.25] or in SEER (HR 1.20; 95% CI 0.84–1.72; P = 0.32). Additionally, using SEER, we found no statistically significant difference in disease‐specific mortality between these two groups (HR 1.13; 95% CI 0.76–1.67; P = 0.54).

Conclusion

Using the NCDB and SEER, we found no statistically significant difference in overall survival or disease‐specific survival between patients treated with and without adjuvant radiation. Further studies should evaluate the impact of adjuvant radiotherapy on local control and prevention of recurrence‐related morbidity in patients with T4 colon cancer.
How 25 years of psychosocial research has contributed to a better understanding of the links between depression and diabetes
Authors: Pouwer F. , Schram M. T. , Iversen M. M. , Nouwen A. , Holt R. I. G.
Published: January 2020

This narrative review of the literature provides a summary and discussion of 25 years of research into the complex links between depression and diabetes. Systematic reviews have shown that depression occurs more frequently in people with type 1 or type 2 diabetes compared with people without diabetes. Currently, it remains unclear whether depression is also more common in people with impaired glucose metabolism or undiagnosed type 2 diabetes compared with people without diabetes. More prospective epidemiological research into the course of depression and an exploration of mechanisms in individuals with diabetes are needed. Depression in diabetes is associated with less optimal self‐care behaviours, suboptimal glycaemic control, impaired quality of life, incident micro‐ and macrovascular diseases, and elevated mortality rates. Randomized controlled trails concluded that depression in diabetes can be treated with antidepressant medication, cognitive–behavioural therapy (individual, group‐based or web‐based), mindfulness‐based cognitive therapy and stepped care. Although big strides forward have been made in the past 25 years, scientific evidence about depression in diabetes remains incomplete. Future studies should investigate mechanisms that link both conditions and test new diabetes‐specific web‐ or app‐based interventions for depression in diabetes. It is important to determine whether treatment or prevention of depression prevents future diabetes complications and lowers mortality rates.
Advances in femtosecond laser processing of optical material for device applications
Authors: Choi Jiyeon , Schwarz Casey
Published: January 2020

Femtosecond laser induced changes and writing in optical materials have proven to be an excellent route to the production of high‐quality micro‐ and nanofabrication of functional devices. In this paper we present the latest advancements in femtosecond laser processing of optical materials for device applications. We look at femtosecond direct laser writing for photonic device fabrication in fused silica and active glasses. We also discuss femtosecond laser writing and wet chemical etching in fused silica, Foturan, and chalcogenide glasses with applications in microfluidics, optics, sensors, and photonic devices.
Expression of Th17‐ and Treg‐specific transcription factors in vitiligo patients
Authors: Bhardwaj Supriya , Rani Seema , Kumaran Muthu S. , Bhatia Alka , Parsad Davinder
Published: January 2020

Background

Vitiligo is mainly considered an autoimmune skin disease as the number of IL‐17 producing Th17 cells, involved in the development of autoimmune and inflammatory pathologies, increased in vitiligo skin. T regulatory cells (Tregs) seem to be altered during the disease. Thus, there must be some upstream molecular factors that regulate the cellular response to apoptotic and inflammatory stimuli.

Objectives

To investigate the expression of Th17‐ and Treg‐specific transcription factors in PBMCs and to evaluate the correlation between these transcription factors and cytokines in vitiligo patients.

Methods

We investigated 30 active NSV patients for Th17‐ and Treg‐specific transcription factors RORγt (retinoic acid‐related orphan receptor gamma t), FOXP3 (forkhead/winged helix), HELIOS, EOS, and IRF4 (Interferon Regulatory Factor 4) as well as apoptotic marker NALP1 (NACHT‐leucine‐rich‐repeat protein 1) in PBMCs with RT‐qPCR. Immunostaining was done for transcription factors and cytokines on skin sections.

Results

The mRNA level of FOXP3 was significantly lower in patients (0.76 fold, P < 0.001), whereas RORγt was slight but not significantly increased (0.76 fold, P = 0.06). Furthermore, NALP1 in lymphocytes was found to be increased in patients (0.69 fold, P < 0.01). The immunostaining results revealed increased expression of RORγ, IL‐17A, NALP1, and IL‐1β in vitiligo skin when compared to normal healthy skin.

Conclusion

Reduced FOXP3/RORγt mRNA ratio suggests thriving of the Th17 cell population in PBMCs of vitiligo patients. Increased NALP1 levels indicate the existence of an apoptotic phenomenon which correlates with the increased expression of IL‐1β in vitiligo pathogenesis.
Clinical profile, anatomical features and long‐term outcome of acute coronary syndromes in human immunodeficiency virus‐infected patients
Authors: Postigo Andrea , Díez‐Delhoyo Felipe , Devesa Carolina , Bruña Vanesa , Clavero‐Olmos Marta , Vicent Lourdes , Juárez Miriam , Sousa Iago , Fernández‐Avilés Francisco , Martínez‐Sellés Manuel
Published: January 2020

Background

Long‐term prognosis of acute coronary syndromes (ACS) in human immunodeficiency virus (HIV)‐infected patients is unknown.

Aims

To compare outcomes after ACS in HIV‐infected and uninfected patients.

Methods

Retrospective observational study. HIV cases were matched with two HIV‐uninfected controls for age, sex and type of ACS.

Results

In 92 HIV patients (mean age 51.3 ± 9.0 years, 7.6% women), the prevalence of cardiovascular risk factors was high (smoking 71.7%; hypertension 41.3%; diabetes 14.1%); dyslipidaemia was more frequent (53 (57.6%) vs 79 (42.9%), P = 0.02) and obesity less common (8 (8.7%) vs 41 (22.3%), P = 0.002) than in controls. Eighty‐seven (94.6%) HIV patients had undetectable viral load and 85 (92.4%) were under anti‐retroviral therapy. Multivessel disease was more common in HIV patients than in controls (44 (47.8%) vs 71 (39.1%); P = 0.05) as was Killip class 3–4 on admission (9 (9.8%) vs 6 (3.3%); P = 0.04). The rate of in‐hospital mortality was similar in both groups (2%), and there were no significant differences in 3‐year mortality (10.2% vs 5.7%; P = 0.27). Non‐cardiovascular readmissions at 3 years were more frequent in HIV patients than in controls (36.5% vs 7.4%; P < 0.001). Multivariate analysis identified previous coronary artery disease as the strongest predictor of mortality in HIV patients (hazard ratio 4.7, 95% confidence interval 1.4–15.7, P = 0.01), whereas HIV infection was not associated with prognosis.

Conclusion

HIV patients with ACS had more frequent multivessel disease and heart failure than matched controls. However, in‐hospital and long‐term mortality was similar in both groups. Non‐cardiovascular re‐hospitalisations were more common in HIV patients.
Use of a limited‐channel device for obstructive sleep apnoea diagnosis in a tertiary sleep disorders centre
Authors: Smith Dugal , Park Joanna , Hay Karen , Hoey Lynn , Leong Gemma , Leong Matthew , Downey Carl , Curtin Deanne , Tay George
Published: January 2020

Background

A major impediment to the provision of obstructive sleep apnoea (OSA) treatment is reliance on labour‐intensive and costly laboratory‐based polysomnography (PSG).

Aims

To investigate if measurement of oximetry and nasal flow through the ApneaLink device (AL) could identify patients with moderate–severe OSA among those referred for PSG to a tertiary sleep service.

Methods

New referrals to The Prince Charles Hospital Sleep Disorders Centre were assessed for suitability. Demographics, anthropometrics, Epworth Sleepiness and OSA50 scores were collected. Exclusion criteria included age <18 years, pregnancy, significant cognitive impairment, poorly controlled psychiatric disorder, domiciliary oxygen and prior OSA treatment. Participants underwent concurrent type 1 PSG and AL assessments.

Results

One hundred participants had a mean age of 55 years (standard deviation 17) and were 49% male. Forty‐eight (48%) had moderate–severe OSA on PSG. Composite variable AL 3% oxygen desaturation index ≥16 and AL apnoea–hypopnoea index (AHI) ≥15 had receiver operator characteristic area under the curve of 0.87, sensitivity of 80% and specificity of 94% for PSG AHI ≥15. The three false‐positives seen with this composite variable had PSG AHI 11–14 and Epworth Sleepiness Score 6–17. The various composites of AL, anthropometric and questionnaire variables did not improve the AUC or specificity but did improve sensitivity.

Conclusions

AL is useful in the diagnosis of moderate–severe OSA in patients referred to a tertiary sleep disorders centre. This could lessen reliance on PSG, expedite OSA care, lead to significant cost savings and make diagnosis of OSA more available in non‐urban areas.
‘I have anxiety, but I have values and preferences’ Experiences of users with generalized anxiety disorder: A qualitative study
Authors: Hurtado María M. , Villena Amelia , Vega Amanda , Amor Gisela , Gómez Clara , Morales‐Asencio José Miguel
Published: January 2020

To understand the experience and perceptions of people diagnosed with generalized anxiety disorder, along the whole process and their role through the decision‐making process for their treatment. A qualitative study through focus groups composed of people diagnosed with generalized anxiety disorder was carried out. Content analysis was carried out to explore the most representative issues. Five thematic categories were identified: onset of the disorder, symptoms and course; daily life with the disorder; coping with the disorder; demand of healthcare for anxiety, and treatment options and decision‐making. Most of the patients reported physical symptoms of anxiety. The majority of participants perceived little social support from their environment and occupational interferences. Coping seems to differ among participant that have recovered or not recovered. The involvement of users with generalized anxiety disorder was scarce, and pharmacological treatment was always the first option offered. There is scarce orientation to elicit preferences and values of patients across the process of care for people with generalized anxiety disorder. The consequence is a biased predisposition of the healthcare system to provide pharmacological treatment as the first option and ignore the perspective of patients on how to cope with their illness.
The origin of urban communities: From the regional species pool to community assemblages in city
Authors: Fournier Bertrand , Frey David , Moretti Marco
Published: January 2020

Aim

Cities worldwide are characterized by unique human stressors that filter species based on their traits, potentially leading to biodiversity loss. The knowledge of which species are filtered and at which scale is important to gain a more mechanistic understanding of urban community assembly and to develop strategies to manage human impact on urban ecosystems. We investigate the ecological mechanisms shaping urban community assembly, taking into account changes across scales, taxa and urban green space types.

Location

City of Zurich, Switzerland.

Taxon

Carabid beetles and wild bees.

Methods

We use a large species occurrence and trait dataset with a high spatial resolution to assess the filtering effect of a medium‐sized city on a regional pool of potential colonists. We then assess the filtering from the urban pool to five widely distributed types of urban green spaces.

Results

We found that our model city selects for functionally similar but taxonomically diverse bee and carabid beetle species from the regional species pool. Within the city, community assembly processes vary among green space types and taxa resulting in important changes in community taxonomic and functional composition.

Main conclusions

Our findings suggest that urban community assembly is a multi‐scale process dominated by the strong environmental filtering from a regional to an urban species pool. This leads to the selection of species pre‐adapted to urban conditions. Spatial habitat heterogeneity within and among UGS types can maintain an important taxonomic diversity within cities. However, increasing urban functional diversity would require stronger management efforts that consider regional ecological processes.