bluuebunny/crossref_metadata_2025 huggingface dataset:
ngsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language
Authors: Mas-Sandoval Alex , Jin Chenyu , Fracassetti Marco , Fumagalli Matteo
Published: January 2022

A sound analysis of DNA sequencing data is important to extract meaningful information and infer quantities of interest. Sequencing and mapping errors coupled with low and variable coverage hamper the identification of genotypes and variants and the estimation of population genetic parameters. Methods and implementations to estimate population genetic parameters from sequencing data available nowadays either are suitable for the analysis of genomes from model

organisms only, require moderate sequencing coverage, or are not easily adaptable to specific applications. To address these issues, we introduce ngsJulia, a collection of templates and functions in Julia language to process short-read

sequencing data for population genetic analysis. We further describe two implementations, ngsPool and ngsPloidy, for the analysis of pooled sequencing data and polyploid genomes, respectively. Through simulations, we illustrate the performance of estimating various population genetic parameters using these implementations, using both established and novel statistical methods. These results inform on optimal experimental design and demonstrate the applicabil-

ity of methods in ngsJulia to estimate parameters of interest even from low coverage sequencing data. ngsJulia provide users with a flexible and efficient framework for ad hoc analysis of sequencing data.ngsJulia is available from: https://github.com/mfumagalli/ngsJulia
Axiomatization of BLRI Determined by Limited Positive Relational Properties
Authors: Jarmużek Tomasz , Klonowski Mateusz
Published: January 2022

In the paper a generalised method for obtaining an adequate axiomatic system for any relating logic expressed in the language with Boolean connectives and relating implication (BLRI), determined by the limited positive relational properties is studied. The method of defining axiomatic systems for logics of a given type is called an algorithm since the analysis allows for any logic determined by the limited positive relational properties to define the adequate axiomatic system automatically, step-by-step. We prove in the paper that the algorithm really works and we show how it can be applied to BLRI.
El sesgo economicista o social como evidencia del Curriculum Oculto en los grados de Finanzas y Contabilidad y Relaciones laborales y Recursos Humanos de la Universidad de Sevilla.
Authors: Serrano Domínguez Francisco , Aguilar del Castillo Mª Carmen
Published: January 2022

Generalmente, el curriculum oculto pretende representar un trasfondo de normas, valores y reglas latentes en el proceso formativo, que los estudiantes han de asumir y adoptar para desempeñar convincentemente un papel social. Durante la etapa de formación primaria y secundaria, el curriculum oculto se centra, principalmente, en iniciar a los estudiantes en el desarrollo de determinadas competencias transversales Muchas de ellas se continúan potenciando en los estudios superiores. El trabajo que presentamos surge como consecuencia de la aparición en el grado de Finanzas y Contabilidad y del grado de Relaciones Laborales y Recursos Humanos de sendas asignaturas optativas especialmente singulares pues son impartidas por distintas áreas de conocimiento (Contabilidad y Derecho del Trabajo) en las que, desde sus inicios se ha observado la influencia del curriculum oculto, transmitido a los estudiantes durante su paso por la titulación, lo que se demuestra en la diferente respuesta que dan los alumnos a la resolución de problemas idénticos cuando disponen, aunque con distintos niveles de intensidad, de la misma información y formación. Se observa un claro corte economicista para los estudiantes de Finanzas y Contabilidad, en el que prima la eficacia, la eficiencia y la maximización del beneficio mientras que los estudiantes del Grado de Relaciones Laborales muestran una visión más social donde las relaciones laborales y su defensa cobran un especial protagonismo
The Analytics of Bed Shortages: Coherent Metric, Prediction, and Optimization
Authors: Xie Jingui , Loke Gar Goei , Sim Melvyn , Lam Shao Wei
Published: January 2022

This study proposes a risk-adjusted version of bed occupancy rates (BORs) that can be used for patient admission control and bed capacity planning in hospitals. Simulations indicate a potential increase of 11% in elective patient admissions by planning using the proposed bed shortage index (BSI) as opposed to the traditional BOR. The BSI is also illustrated for purposes of bed capacity allocation between departments and across acute and nonacute hospitals.
Hyperbush Algorithm for Strategy-Based Equilibrium Traffic Assignment Problems
Authors: Xu Zhandong , Xie Jun , Liu Xiaobo , Nie Yu (Marco)
Published: January 2022

Strategy-based equilibrium traffic assignment (SETA) problems define travel choice broadly as a strategy rather than a simple path. Travelers navigating through a network based on a strategy end up following a hyperpath. SETA is well suited to represent a rich set of travel choices that take place en route at nodes, such as transit passengers’ transfer decisions, truckers’ bidding decisions, and taxi drivers’ reposition decisions. This paper recognizes and highlights the commonalities among classical and emerging SETA problems and proposes to unify them within the same modeling framework, built on the concept of a hypergraph. A generic hyperbush algorithm (HBA) is developed by decomposing a hypergraph into destination-based hyperbushes. By constructing hyperbushes and limiting traffic assignments to them, HBA promises to obtain more precise solutions to larger instances of SETA problems at a lower computational cost, both in terms of CPU time and memory consumption. To demonstrate its generality and efficiency, we tailor HBA to solve two SETA problems. The results confirm that HBA consistently outperforms the benchmark algorithms in the literature, including two state-of-the-art hyperpath-based algorithms. To obtain high-quality equilibrium solutions for SETA instances of practical size, HBA runs up to five times faster than the best competitor with a fraction of its memory consumption.
Dynamic Panel Data Analysis of Capital Structure Determinants: Evidence from Iraqi Banks
Authors: Mohsin Jadah Hamid , Faez Hasan Mohammed , Mohammed Al-Husainy Noor Hashim
Published: January 2022

This study investigates if the choice of capital structure of Iraqi banks could be interpreting through factors which have been studied by prior studies, which represented by determinants of capital structure choice (i.e., bank size, bank profitability, bank growth, tangibility, bank age). Using dynamic panel GMM for the period 2005 to 2019, this study maintains the explore on the determinants of capital structure of Iraq banks "developing country" that has circumstances likely to be quite different from those in developed and other major developing countries, particularly in terms of it deteriorating economic environment. The findings indicate that the bank size, bank profitability, bank age have a dominant role in explaining the variation in the long-term debt ratios of Iraqi banks. Meanwhile, only bank size, bank profitability, bank growth, bank age has a leading role in interpreting the variation of short-term debt ratios in the Iraqi banks. The current study has initiated some basis to discover the capital structure determinants of Iraqi banks upon which a more detailed evaluation could be based. Moreover, the experimental results can help Iraqi banks directors to choose the optimum structure of capital.
Osteofibrous dysplasia of the tibia
Authors: Dala-Ali Benan , Donnan Leo , Masterton Gary , Briggs Lydia , Kauiers Cyrus , O’Sullivan Mark , Calder Peter , Eastwood Deborah M.
Published: January 2022

Aims

Osteofibrous dysplasia (OFD) is a rare benign lesion predominantly affecting the tibia in children. Its potential link to adamantinoma has influenced management. This international case series reviews the presentation of OFD and management approaches to improve our understanding of OFD.

Methods

A retrospective review at three paediatric tertiary centres identified 101 cases of tibial OFD in 99 patients. The clinical records, radiological images, and histology were analyzed.

Results

Mean age at presentation was 13.5 years (SD 12.4), and mean follow-up was 5.65 years (SD 5.51). At latest review, 62 lesions (61.4%) were in skeletally mature patients. The most common site of the tibial lesion was the anterior (76 lesions, 75.2%) cortex (63 lesions, 62.4%) of the middle third (52 lesions, 51.5%). Pain, swelling, and fracture were common presentations. Overall, 41 lesions (40.6%) presented with radiological deformity (> 10°): apex anterior in 97.6%. A total of 41 lesions (40.6%) were treated conservatively. Anterior bowing < 10° at presentation was found to be related to successful conservative management of OFD (p = 0.013, multivariable logistic regression). Intralesional excision was performed in 43 lesions (42.6%) and a wide excision of the lesion in 19 (18.8%). A high complication rate and surgical burden was found in those that underwent a wide excision regardless of technique employed. There was progression/recurrence in nine lesions (8.9%) but statistical analysis found no predictive factors. No OFD lesion transformed to adamantinoma.

Conclusion

This study confirms OFD to be a benign bone condition with low rates of local progression and without malignant transformation. It is important to distinguish OFD from adamantinoma by a histological diagnosis. Focus should be on angular deformity, monitored with full-length tibial radiographs. Surgery is indicated in symptomatic patients and predicted by the severity of the initial angular deformity. Surgery should focus more on the deformity rather than the lesion. Cite this article: Bone Joint J 2022;104-B(2):302–308.
The lifetime risk of revision following total knee arthroplasty
Authors: Stone Bradley , Nugent Mary , Young Simon W. , Frampton Christopher , Hooper Gary J.
Published: January 2022

Aims

The success of total knee arthroplasty (TKA) is usually measured using functional outcome scores and revision-free survivorship. However, reporting the lifetime risk of revision may be more meaningful to patients when gauging risks, especially in younger patients. We aimed to assess the lifetime risk of revision for patients in different age categories at the time of undergoing primary TKA.

Methods

The New Zealand Joint Registry database was used to obtain revision rates, mortality, and the indications for revision for all primary TKAs performed during an 18-year period between January 1999 and December 2016. Patients were stratified into age groups at the time of the initial TKA, and the lifetime risk of revision was calculated according to age, sex, and the American Society of Anesthesiologists (ASA) grade. The most common indications for revision were also analyzed for each age group.

Results

The overall ten-year survival rate was 95.6%. This was lowest in the youngest age group (between 46 and 50 years) and increased sequentially with increasing age. The lifetime risk of requiring revision was 22.4% in those aged between 46 and 50 years at the time of the initial surgery, and decreased linearly with increasing age to 1.15% in those aged between 90 and 95 years at the time of surgery. Higher ASA grades were associated with increased lifetime risk of revision in all age groups. The three commonest indications for revision were aseptic loosening, infection, and unexplained pain. Young males, aged between 46 and 50 years, had the highest lifetime risk of revision (25.2%).

Conclusion

Lifetime risk of revision may be a more meaningful measure of outcome than implant survival at defined time periods when counselling patients prior to TKA. This study highlights the considerably higher lifetime risk of revision surgery for all indications, including infection, in younger male patients. Cite this article: Bone Joint J 2022;104-B(2):235–241.
Should patient age thresholds dictate fixation strategy in total hip arthroplasty?
Authors: Bloch Benjamin V. , White Jonathan J. E. , Matar Hosam E. , Berber Reshid , Manktelow Andrew R. J.
Published: January 2022

Aims

Total hip arthroplasty (THA) is a very successful and cost-effective operation, yet debate continues about the optimum fixation philosophy in different age groups. The concept of the 'cementless paradox' and the UK 'Getting it Right First Time' initiative encourage increased use of cemented fixation due to purported lower revision rates, especially in elderly patients, and decreased cost.

Methods

In a high-volume, tertiary referral centre, we identified 10,112 THAs from a prospectively collected database, including 1,699 cemented THAs, 5,782 hybrid THAs, and 2,631 cementless THAs. The endpoint was revision for any reason. Secondary analysis included examination of implant survivorship in patients aged over 70 years, over 75 years, and over 80 years at primary THA.

Results

Cemented fixation had the lowest implant survival in all age groups, with a total ten-year survivorship of 97.0% (95% confidence interval (CI) 95.8 to 97.8) in the cemented group, 97.6% (95% CI 96.9 to 98.1) in the hybrid group, and 97.9% (95% CI 96.9 to 98.6) in the cementless group. This was not statistically significant (p = 0.092). There was no age group where cemented fixation outperformed hybrid or cementless fixation.

Conclusion

While all fixation techniques performed well at long-term follow-up, cemented fixation was associated with the lowest implant survival in all age groups, including in more elderly patients. We recommend that surgeons should carefully monitor their own outcomes and use fixation techniques that they are familiar with, and deliver the best outcomes in their own hands. Cite this article: Bone Joint J 2022;104-B(2):206–211.
Intraoperative monitoring of the femoral nerve using free electromyography during total hip arthroplasty via the direct anterior approach
Authors: Wang Qiuru , Wang Haoyang , A Ge , Xiao Tingting , Kang Pengde
Published: January 2022

Aims

This study aimed to use intraoperative free electromyography to examine how the placement of a retractor at different positions along the anterior acetabular wall may affect the femoral nerve during total hip arthroplasty (THA) when undertaken using the direct anterior approach (THA-DAA).

Methods

Intraoperative free electromyography was performed during primary THA-DAA in 82 patients (94 hips). The highest position of the anterior acetabular wall was defined as the “12 o’clock” position (middle position) when the patient was in supine position. After exposure of the acetabulum, a retractor was sequentially placed at the ten, 11, 12, one, and two o’clock positions (right hip; from superior to inferior positions). Action potentials in the femoral nerve were monitored with each placement, and the incidence of positive reactions (defined as explosive, frequent, or continuous action potentials, indicating that the nerve was being compressed) were recorded as the primary outcome. Secondary outcomes included the incidence of positive reactions caused by removing the femoral head, and by placing a retractor during femoral exposure; and the incidence of femoral nerve palsy, as detected using manual testing of the strength of the quadriceps muscle.

Results

Positive reactions were significantly less frequent when the retractor was placed at the ten (15/94; 16.0%), 11 (12/94; 12.8%), or 12 o’clock positions (19/94; 20.2%), than at the one (37/94; 39.4%) or two o’clock positions (39/94; 41.5%) (p < 0.050). Positive reactions also occurred when the femoral head was removed (28/94; 29.8%), and when a retractor was placed around the proximal femur (34/94; 36.2%) or medial femur (27/94; 28.7%) during femoral exposure. After surgery, no patient had reduced strength in the quadriceps muscle.

Conclusion

Placing the anterior acetabular retractor at the one or two o’clock positions (right hip; inferior positions) during THA-DAA can increase the rate of electromyographic signal changes in the femoral nerve. Thus, placing a retractor in these positions may increased the risk of the development of a femoral nerve palsy. Cite this article: Bone Joint J 2022;104-B(2):193–199.
A dramatic interpretation of the fragilities of the FGM narrative: a reply to ‘The prosecution of Dawoodi Bohra women’ by Richard Shweder
Authors: Rozin Seth B.
Published: January 2022

Inspired by Richard Shweder’s paper, What about ‘Female Genital Mutilation?’ And Why Understanding Culture Matters in the First Place (MIT Press, 2000), I wrote the play Human Rites seeking to challenge audiences’ assumptions about the practice of circumcision among women, known colloquially as ‘female genital mutilation’ (FGM). Throughout the development of Human Rites, which involved research and extensive interaction with Shweder and Fuambai Sia Ahmadu (both of whom served as bases for characters in the play), I experienced anticipated and unanticipated pushback on the controversial perspectives voiced in the play, as well as the appropriateness of a Caucasian man authoring a play about black and brown women’s bodies. The two productions of Human Rites went on to generate highly engaged dialogue among audiences, as they grappled with their own, mostly unexamined pre-conceptions about FGM, the disparity in moral attitudes toward male and female circumcision, and the inherent moral authority Westerners often hold with regard to ‘primitive’ practices in other countries and cultures. Shweder’s subsequent paper ‘The prosecution of Dawoodi Bohra women: some reasonable doubts,’ has inspired a kind of sequel to Human Rites, that will interrogate the widely accepted practice of circumcision among infant boys in Western Jewish and Christian communities.
Males and females have different anatomy: is this relevant to circumcision? A reply to ‘The prosecution of Dawoodi Bohra women’ by Richard Shweder
Authors: Jacobs Allan J.
Published: January 2022

Procedural safety is one of the determinants of whether parents ought to be able to authorise ritual circumcision (foreskin removal) for their minor children. The penis and clitoris differ greatly in anatomy. Their homology is irrelevant to whether boys and girls should be treated differently regarding circumcision. The infantile male foreskin is easily separable from the penile head for safe removal. It is large enough that circumcision is technically easy but small enough not to be highly vascularised. In contrast, the prepubertal clitoris is tightly bound to the clitoral hood, and both are tightly bound to adjacent non-clitoral tissue. This, and the tiny size of the clitoris, make infantile circumcision dangerous. Circumcision increases in safety with age in girls, for whom the procedure is probably safest after sexual maturation. The opposite is true in boys. Circumcision is safest in infancy but becomes more dangerous as the penis enlarges and its blood supply increases. I argue that religion has sufficiently powerful positive effects within a society, and is sufficiently important to its adherents, as to warrant some deference by the state. In a liberal society, rituals should be prohibited only if likely to create serious physical and psychological harm. Male infant circumcision fails to meet this bar; however, it is uncertain whether this is the case for prepubertal female circumcision.
Dual-update data-driven control of deformable mirrors using Walsh basis functions
Authors: Haber Aleksandar , Bifano Thomas
Published: January 2022

We develop a novel data-driven method for deformable mirror (DM)
control. The developed method updates both the DM model and DM control
actions that produce desired mirror surface shapes. The novel method
explicitly takes into account actuator constraints and couples a
feedback-control algorithm with an algorithm for recursive estimation
of DM influence function models. We also explore the possibility of
using Walsh basis functions for DM control. By expressing the desired
and observed mirror surface shapes as sums of Walsh pattern matrices,
we formulate the control problem in the 2D Walsh basis domain. We
thoroughly experimentally verify the developed approach on a
140-actuator MEMS DM, developed by Boston Micromachines. Our results
show that the novel method produces the root-mean-square surface error
in the 14–40 nanometer range. These results can additionally be
improved by tuning the control and estimation parameters. The
developed approach is also applicable to other DM types such as
segmented DMs.
Far-field position-tunable trapping of dielectric particles using a graphene-based plasmonic lens
Authors: Hemayat Saeed , Darbari Sara
Published: January 2022

In this report, a graphene-based plasmonic lens is designed for far-field position-tunable trapping of dielectric particles at a wavelength of 1550 nm, in which target particles can be floated at a variable z-position, using a variable gate voltage applied to the graphene ribbons. Preventing proximity of the trapped particle and the metallic lens structure, we can diminish general thermal issues in plasmonic tweezers, while realizing higher degrees of freedom in studying target characteristics of the particles by achieving position-tunable 3D trapping. These advantageous aspects are impossible in conventional plasmonic tweezers, because of the highly evanescent nature of the plasmonic field at the metal interface. The proposed structure is comprised of two concentric circular slit-sets (S1, S2), each capable of sending a directive beam, which can lead to a constructive interference, and forming a subwavelength focal spot in the far-field. Taking advantage of the epsilon-near-zero (ENZ) behavior of graphene, each of the radiating slit-sets can be switched ON/OFF, with a radiation switching ratio of about 49, by applying a small electric pulse of 80 meV to change the Fermi energy of the corresponding graphene ribbon from 0.535 eV to 0.615 eV. Hence, inverting the radiation state of the designed lens, from (S1:ON, S2:OFF) to (S1:OFF, S2:ON), we can change the z-position of the focal trapping site from 5000 nm to 9800 nm. This configuration can be proposed as a new generation of long-range, electrostatically tunable 3D plasmonic tweezing, without the need for any external bulky optomechanical equipment.
Multipass spectral broadening and compression in the green spectral range
Authors: Hariton Victor , Bin Wahid Ammar , Figueira Gonçalo , Fritsch Kilian , Pronin Oleg
Published: January 2022

Multipass spectral broadening and compression around 515 nm are experimentally demonstrated. A nonlinear multipass cell with a bulk medium is used to compress 250-fs pulses down to 38 fs. The same input pulses create a sufficient bandwidth for sub-20-fs pulse generation in a multipass cell with gaseous media. In both cases, the efficiency exceeds 85%. Dispersion management by reduction of the cell size and the thickness of the nonlinear medium allows an efficient generation of ultrashort pulses in the visible range and establishes a pathway for ultraviolet spectral broadening by means of multipass cells.
Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods
Authors: Jiang Richard , Singh Prashant , Wrede Fredrik , Hellander Andreas , Petzold Linda
Published: January 2022

Identifying the reactions that govern a dynamical biological system is a crucial but challenging task in systems biology. In this work, we present a data-driven method to infer the underlying biochemical reaction system governing a set of observed species concentrations over time. We formulate the problem as a regression over a large, but limited, mass-action constrained reaction space and utilize sparse Bayesian inference via the regularized horseshoe prior to produce robust, interpretable biochemical reaction networks, along with uncertainty estimates of parameters. The resulting systems of chemical reactions and posteriors inform the biologist of potentially several reaction systems that can be further investigated. We demonstrate the method on two examples of recovering the dynamics of an unknown reaction system, to illustrate the benefits of improved accuracy and information obtained.
Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types
Authors: Wen Jia , Lagler Taylor M. , Sun Quan , Yang Yuchen , Chen Jiawen , Harigaya Yuriko , Sankaran Vijay G. , Hu Ming , Reiner Alexander P. , Raffield Laura M. , Li Yun
Published: January 2022

Existing studies of chromatin conformation have primarily focused on potential enhancers interacting with gene promoters. By contrast, the interactivity of promoters per se, while equally critical to understanding transcriptional control, has been largely unexplored, particularly in a cell type-specific manner for blood lineage cell types. In this study, we leverage promoter capture Hi-C data across a compendium of blood lineage cell types to identify and characterize cell type-specific super-interactive promoters (SIPs). Notably, promoter-interacting regions (PIRs) of SIPs are more likely to overlap with cell type-specific ATAC-seq peaks and GWAS variants for relevant blood cell traits than PIRs of non-SIPs. Moreover, PIRs of cell-type-specific SIPs show enriched heritability of relevant blood cell trait (s), and are more enriched with GWAS variants associated with blood cell traits compared to PIRs of non-SIPs. Further, SIP genes tend to express at a higher level in the corresponding cell type. Importantly, SIP subnetworks incorporating cell-type-specific SIPs and ATAC-seq peaks help interpret GWAS variants. Examples include GWAS variants associated with platelet count near the megakaryocyte SIP gene EPHB3 and variants associated lymphocyte count near the native CD4 T-Cell SIP gene ETS1. Interestingly, around 25.7% ~ 39.6% blood cell traits GWAS variants residing in SIP PIR regions disrupt transcription factor binding motifs. Importantly, our analysis shows the potential of using promoter-centric analyses of chromatin spatial organization data to identify biologically important genes and their regulatory regions.
Assessment of independent comorbidities and comorbidity measures in predicting healthcare facility-onset Clostridioides difficile infection in Kenya
Authors: Mutai Winnie C. , Mureithi Marianne , Anzala Omu , Kullin Brian , Ofwete Robert , Kyany’ a Cecilia , Odoyo Erick , Musila Lillian , Revathi Gunturu
Published: January 2022

Introduction

Clostridioides difficile is primarily associated with hospital-acquired diarrhoea. The disease burden is aggravated in patients with comorbidities due to increased likelihood of polypharmacy, extended hospital stays and compromised immunity. The study aimed to investigate comorbidity predictors of healthcare facility-onset C. difficile infection (HO-CDI) in hospitalized patients.

Methodology

We performed a cross sectional study of 333 patients who developed diarrhoea during hospitalization. The patients were tested for CDI. Data on demographics, admission information, medication exposure and comorbidities were collected. The comorbidities were also categorised according to Charlson Comorbidity Index (CCI) and Elixhauser Comorbidity Index (ECI). Comorbidity predictors of HO-CDI were identified using multiple logistic regression analysis.

Results

Overall, 230/333 (69%) patients had comorbidities, with the highest proportion being in patients aged over 60 years. Among the patients diagnosed with HO-CDI, 63/71(88.7%) reported comorbidities. Pairwise comparison between HO-CDI patients and comparison group revealed significant differences in hypertension, anemia, tuberculosis, diabetes, chronic kidney disease and chronic obstructive pulmonary disease. In the multiple logistic regression model significant predictors were chronic obstructive pulmonary disease (odds ratio [OR], 9.51; 95% confidence interval [CI], 1.8–50.1), diabetes (OR, 3.56; 95% CI, 1.11–11.38), chronic kidney disease (OR, 3.88; 95% CI, 1.57–9.62), anemia (OR, 3.67; 95% CI, 1.61–8.34) and hypertension (OR, 2.47; 95% CI, 1.–6.07). Among the comorbidity scores, CCI score of 2 (OR 6.67; 95% CI, 2.07–21.48), and ECI scores of 1 (OR, 4.07; 95% CI, 1.72–9.65), 2 (OR 2.86; 95% CI, 1.03–7.89), and ≥ 3 (OR, 4.87; 95% CI, 1.40–16.92) were significantly associated with higher odds of developing HO-CDI.

Conclusion

Chronic obstructive pulmonary disease, chronic kidney disease, anemia, diabetes, and hypertension were associated with an increased risk of developing HO-CDI. Besides, ECI proved to be a better predictor for HO-CDI. Therefore, it is imperative that hospitals should capitalize on targeted preventive approaches in patients with these underlying conditions to reduce the risk of developing HO-CDI and limit potential exposure to other patients.
Cryptosporidiosis outbreak in Amazonia, French Guiana, 2018
Authors: Menu Estelle , Mosnier Emilie , Cotrel Arnaud , Favennec Loic , Razakandrainibe Romy , Valot Stéphane , Blanchet Denis , Dalle Frédéric , Costa Damien , Gaillet Mélanie , Demar Magalie , de Laval Franck
Published: January 2022

Background

Cryptosporidiosis outbreaks in South America are poorly documented. In March 2018, 51 cases of cryptosporidiosis were reported in Maripasoula, a village located in a remote forest area along the border between Surinam and French Guiana.

Method

To identify the origin of the epidemic, we performed epidemiological, microbiological, and environmental investigations. Only the cases involving diarrhoea and Cryptosporidium-positive stool were considered as bona fide, while cases involving diarrhoea and close contact with a confirmed case were classified as “possible”.

Results

We identified 16 confirmed cases and 35 possible ones. Confirmed cases comprised nine children (median age of 18 months, range: 6–21), one immunocompromised adult and six soldiers. One child required a hospitalisation for rehydration. All 16 Cryptosporidium stools were PCR positive, and sequencing of the gp60 gene confirmed only one Cryptosporidium hominis subtype IbA10G2. Tap water consumption was the only common risk factor identified. Contamination of the water network with Cryptosporidium parvum subtype IIdA19G2 was found.

Conclusion

Water quality is a major public health issue in Amazonian French Guiana, especially for population at risk (children, people with comorbidity, travelers). For them, alternative water supply or treatment should be implemented.
Transplantation of adipose-derived stem cells ameliorates Echinococcus multilocularis-induced liver fibrosis in mice
Authors: Yang Ning , Ma Wenmei , Ke Ying , Liu Hui , Chu Jin , Sun Li , Lü Guodong , Bi Xiaojuan , Lin Renyong
Published: January 2022

Background

Alveolar echinococcosis (AE) can cause severe liver fibrosis and could be fatal if left untreated. Currently, there are no effective therapeutic options for AE-induced liver fibrosis. In view of the therapeutic potential of adipose-derived stem cells (ADSCs), we investigated whether ADSCs transplantation has the ability to control or reverse fibrosis progression in the liver ofEchinococcus multilocularis(E.multilocularis) infected mice.

Methodology/Principal findings

C57BL/6 mice infected withE.multilocularisthrough portal vein inoculation were intravenously injected with ADSCs isolated from inguinal adipose tissues of 6–8 weeks old mice. Histopathological analysis including heamatoxylin & eosin staining as well as Masson’s trichrome staining, and Sirius red staining were performed to access the degree of liver fibrosis. Histopathological examination 30 days after ADSCs transplantation revealed that ADSCs significantly decreased the degree of liver fibrosis inE.multilocularisinfected mice by inhibiting the expressions of α-SMA and type 1 collagen deposition. In addition, compared to the non-transplanted group, ADSCs transplantation reduced fibrotic areas inE.multilocularisinfected mice. We also found that ADSCs transplantation significantly down-regulated TGF-β1 and TGF-βR expressions, while up-regulating Smad7 expression in the TGF-β/Smad signaling pathway.

Conclusions

ADSCs can alleviateEchinococcus multilocularisinfection-induced liver fibrosis by modulating the activity level of the TGF-β/Smad7 signaling pathway and provide a potential therapeutic approach forE.multilocularis-induced fibrosis.
Firing discrimination: Selective labor market responses of firms during the COVID-19 economic crisis
Authors: Auer Daniel
Published: January 2022

The speed of the economic downturn in the wake of the COVID-19 pandemic has been exceptional, causing mass layoffs—in Germany up to 30% of the workforce in some industries. Economic rationale suggests that the decision on which workers are fired should depend on productivity-related individual factors. However, from hiring situations we know that discrimination—i.e., decisions driven by characteristics unrelated to productivity—is widespread in Western labor markets. Drawing on representative survey data on forced layoffs and short-time work collected in Germany between April and December 2020, this study highlights that discrimination against immigrants is also present in firing situations. The analysis shows that employees with a migration background are significantly more likely to lose their job than native workers when otherwise healthy firms are unexpectedly forced to let go of part of their workforce, while firms make more efforts to substitute firing with short-time working schemes for their native workers. Adjusting for detailed job-related characteristics shows that the findings are unlikely to be driven by systematic differences in productivity between migrants and natives. Moreover, using industry-specific variation in the extent of the economic downturn, I demonstrate that layoff probabilities hardly differ across the less affected industries, but that the gap between migrants and natives increases with the magnitude of the shock. In the hardest-hit industries, job loss probability among migrants is three times higher than among natives. This confirms the hypothesis that firing discrimination puts additional pressure on the immigrant workforce in times of crisis.
Cleaner wrasse Labroides dimidiatus perform above chance in a “matching-to-sample” experiment
Authors: Aellen Mélisande , Siebeck Ulrike E. , Bshary Redouan
Published: January 2022

Concept learning have been studied widely in non-human animal species within or not an ecological context. Here we tested whether cleaner fishLabroides dimidiatus, which show generalised rule learning in an ecologically relevant context; they generalise that any predator may provide protection from being chased by other fish; can also learn a general concept when presented with abstract cues. We tested for this ability in the matching-to-sample task. In this task, a sample is shown first, and then the subject needs to choose the matching sample over a simultaneously presented different one in order to obtain a food reward. We used the most general form of the task, using each stimulus only once in a total of 200 trials. As a group, the six subjects performed above chance, and four individuals eventually reached learning criteria. However, individual performance was rather unstable, yielding overall only 57% correct choices. These results add to the growing literature that ectotherms show the ability of abstract concept learning, though the lack of stable high performance may indicate quantitative performance differences to endotherms.
Comparison of seven SNP calling pipelines for the next-generation sequencing data of chickens
Authors: Liu Jing , Shen Qingmiao , Bao Haigang
Published: January 2022

Single nucleotide polymorphisms (SNPs) are widely used in genome-wide association studies and population genetics analyses. Next-generation sequencing (NGS) has become convenient, and many SNP-calling pipelines have been developed for human NGS data. We took advantage of a gap knowledge in selecting the appropriated SNP calling pipeline to handle with high-throughput NGS data. To fill this gap, we studied and compared seven SNP calling pipelines, which include 16GT, genome analysis toolkit (GATK), Bcftools-single (Bcftools single sample mode), Bcftools-multiple (Bcftools multiple sample mode), VarScan2-single (VarScan2 single sample mode), VarScan2-multiple (VarScan2 multiple sample mode) and Freebayes pipelines, using 96 NGS data with the different depth gradients of approximately 5X, 10X, 20X, 30X, 40X, and 50X coverage from 16 Rhode Island Red chickens. The sixteen chickens were also genotyped with a 50K SNP array, and the sensitivity and specificity of each pipeline were assessed by comparison to the results of SNP arrays. For each pipeline, except Freebayes, the number of detected SNPs increased as the input read depth increased. In comparison with other pipelines, 16GT, followed by Bcftools-multiple, obtained the most SNPs when the input coverage exceeded 10X, and Bcftools-multiple obtained the most when the input was 5X and 10X. The sensitivity and specificity of each pipeline increased with increasing input. Bcftools-multiple had the highest sensitivity numerically when the input ranged from 5X to 30X, and 16GT showed the highest sensitivity when the input was 40X and 50X. Bcftools-multiple also had the highest specificity, followed by GATK, at almost all input levels. For most calling pipelines, there were no obvious changes in SNP numbers, sensitivities or specificities beyond 20X. In conclusion, (1) if only SNPs were detected, the sequencing depth did not need to exceed 20X; (2) the Bcftools-multiple may be the best choice for detecting SNPs from chicken NGS data, but for a single sample or sequencing depth greater than 20X, 16GT was recommended. Our findings provide a reference for researchers to select suitable pipelines to obtain SNPs from the NGS data of chickens or nonhuman animals.
Challenges and practices identification in complex outsourcing relationships: A systematic literature review
Authors: Khan Ghulam Murtaza , Khan Siffat Ullah , Khan Habib Ullah , Ilyas Muhammad
Published: January 2022

Complex IT outsourcing relationships aptitude several benefits such as increased cost likelihood and lowered costs, higher scalability and flexibility upon demand. However, by virtue of its complexity, the complex outsourcing typically necessitates the interactions among various stakeholders from diverse regions and cultures, making it significantly more challenging to manage than traditional outsourcing. Furthermore, when compared to other types of outsourcing, complex outsourcing is extremely difficult because it necessitates a variety of control and coordination mechanisms for project management, which proportionally increases the risk of project failure. In order to overcome the failure of projects in complex outsourcing relationships, there is a need of robust systematic research to identify the key challenges and practices in this area. Therefore, this research implements systematic literature review as a research method and works as a pioneer attempt to accomplish the aforementioned objectives. Upon furnishing the SLR results, the authors identified 11 major challenges with 67 practices in hand from a total of 85 papers. Based on these findings, the authors intend to construct a comprehensive framework in the future by incorporating robust methodologies such as AHP and fuzzy logic, among others.
Antibodies directed towards neuraminidase restrict influenza virus replication in primary human bronchial epithelial cells
Authors: Smet Anouk , Catani Joao Paulo Portela , Ysenbaert Tine , Gonçalves Amanda , Kleanthous Harry , Vogel Thorsten U. , Saelens Xavier , Job Emma R.
Published: January 2022

Influenza neuraminidase (NA) is implicated in various aspects of the virus replication cycle and therefore is an attractive target for vaccination and antiviral strategies. Here we investigated the potential for NA-specific antibodies to interfere with A(H1N1)pdm09 replication in primary human airway epithelial (HAE) cells. Mouse polyclonal anti-NA sera and a monoclonal antibody could block initial viral entry into HAE cells as well as egress from the cell surface. NA-specific polyclonal serum also reduced virus replication across multiple rounds of infection. Restriction of virus entry correlated with the ability of the serum or monoclonal antibody to mediate neuraminidase inhibition (NI). Finally, human sera with NI activity against the N1 of A(H1N1)pdm09 could decrease H6N1 virus infection of HAE cells, highlighting the potential contribution of anti-NA antibodies in the control of influenza virus infection in humans.
Assessing the performance of a serological point-of-care test in measuring detectable antibodies against SARS-CoV-2
Authors: Coyle Peter V. , El Kahlout Reham Awni , Dargham Soha R. , Chemaitelly Hiam , Kacem Mohamed Ali Ben Hadj , Al-Mawlawi Naema Hassan Abdulla , Gilliani Imtiaz , Younes Nourah , Al Kanaani Zaina , Al Khal Abdullatif , Al Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Rahim Hanan F. Abdul , Nasrallah Gheyath K. , Yassine Hadi M. , Al Kuwari Mohamed G. , Al Romaihi Hamad Eid , Tang Patrick , Bertollini Roberto , Al-Thani Mohamed H. , Abu-Raddad Laith J.
Published: January 2022

This study investigated the performance of a rapid point-of-care antibody test, the BioMedomics COVID-19 IgM/IgG Rapid Test, in comparison with a high-quality, validated, laboratory-based platform, the Roche Elecsys Anti-SARS-CoV-2 assay. Serological testing was conducted on 709 individuals. Concordance metrics were estimated. Logistic regression was used to assess associations with seropositivity. SARS-CoV-2 seroprevalence was 63.5% (450/709; 95% CI 59.8%-67.0%) using the BioMedomics assay and 71.9% (510/709; 95% CI 68.5%-75.2%) using the Elecsys assay. There were 60 discordant results between the two assays, all of which were seropositive in the Elecsys assay, but seronegative in the BioMedomics assay. Overall, positive, and negative percent agreements between the two assays were 91.5% (95% CI 89.2%-93.5%), 88.2% (95% CI 85.1%-90.9%), and 100% (95% CI 98.2%-100%), respectively, with a Cohen’s kappa of 0.81 (95% CI 0.78–0.84). Excluding specimens with lower (Elecsys) antibody titers, the agreement improved with overall, positive, and negative percent concordance of 94.4% (95% CI 92.3%-96.1%), 91.8% (95% CI 88.8%-94.3%), and 100% (95% CI 98.2%-100%), respectively, and a Cohen’s kappa of 0.88 (95% CI 0.85–0.90). Logistic regression confirmed better agreement with higher antibody titers. The BioMedomics COVID-19 IgM/IgG Rapid Test demonstrated good performance in measuring detectable antibodies against SARS-CoV-2, supporting the utility of such rapid point-of-care serological testing to guide the public health responses and vaccine prioritization.
A scoping review of measurement of violence against women and disability
Authors: Meyer Sarah R. , Stöckl Heidi , Vorfeld Cecilia , Kamenov Kaloyan , García-Moreno Claudia
Published: January 2022

Introduction

Existing evidence indicates that prevalence of violence against women with disability is elevated compared to women without disability. We conducted a scoping review with a focus on measurement to assess the forms of measurement and study design utilized to explore the intersection of violence against women with disabilities, and to identify strengths and limitations in current approaches to measuring violence against women with disabilities. This scoping review is designed to inform current debates and discussions regarding how to generate evidence concerning violence against women with disabilities.

Methods and results

We conducted systematic searches of the following databases: PubMed, PsycINFO, Embase, CINAHL, PILOTS, ERIC, Social Work Abstracts, International Bibliography of the Social Sciences, Social Services Abstracts, ProQuest Criminal Justice, and Dissertations & Theses Global, and conducted structured searches of national statistics and surveys and grey literature available on-line. We identified 174 manuscripts or reports for inclusion. n = 113 manuscripts or reports utilized acts-specific measurement of violence. In terms of measurement of disability, we found that amongst the included manuscripts and reports, n = 75 utilized measures of functioning limitations (n = 20 of these were Washington Group questions), n = 15 utilized a single question approach and n = 67 defined participants in the research as having a disability based on a diagnosis or self-report of a health condition or impairment.

Discussion

This scoping review provides a comprehensive overview of measurement of violence against women with disabilities and measurement of violence within disability-focused research. We identified several important gaps in the evidence, including lack of sex and disability disaggregation, limited evidence concerning adaptation of data collection methods to ensure accessibility of research activities for women with disabilities, and limited evidence concerning differential relationships between types of disability and violence exposure. This scoping review provides directions for sub-analyses of the included studies and further research to address gaps in evidence.
Is it possible to model the impact of calorie-reduction interventions on childhood obesity at a population level and across the range of deprivation: Evidence from the Avon Longitudinal Study of Parents and Children (ALSPAC)
Authors: Russell Simon J. , Hope Steven , Croker Helen , Packer Jessica , Viner Russell M.
Published: January 2022

Background

Simulated interventions using observational data have the potential to inform policy and public health interventions where randomised controlled trials are not feasible. National childhood obesity policy is one such area. Overweight and obesity are primarily caused by energy-rich and low-nutrient diets that contribute to a positive net energy imbalance. Using data from the Avon Longitudinal Study of Parents and Children (ALSPAC), we investigated whether causal modelling techniques could be applied to simulate the potential impact of policy-relevant calorie-reduction interventions on population prevalence and inequalities in obesity in childhood.

Methods

Predicted probabilities of obesity at age 11 (UK90 cut offs) were estimated from logistic marginal structural models (MSM) accounting for observed calorie consumption at age 7 and confounding, overall and by maternal occupational social class. A series of population intervention scenarios were modelled to simulate daily calorie-reduction interventions that differed in effectiveness, targeting mechanism and programme uptake level.

Results

The estimated effect of maternal social class on obesity after accounting for confounding and observed calorie intake was provided by the controlled direct effect (CDE), in which, 18.3% of children were living with obesity at age 11 years,. A universal simulation to lower median intake to the estimated average requirement (EAR) (a 6.1% reduction in daily calories) with 75% uptake reduced overall obesity prevalence by 0.6%; there was little impact on inequalities. A targeted intervention to limit consumption to the EAR for children with above average intake reduced population obesity prevalence at 11 years by 1.5% but inequalities remained broadly unchanged. A targeted intervention for children of low-income families reduced prevalence by 0.7% and was found to slightly reduce inequalities.

Conclusions

MSMs allow estimation of effects of simulated calorie-reduction interventions on childhood obesity prevalence and inequalities, although estimates are limited by the accuracy of reported calorie intake. Further work is needed to understand causal pathways and opportunities for intervention. Nevertheless, simulated intervention techniques have promise for informing national policy where experimental data are not available.