Miracle-dz/UniFAR-FTUs huggingface dataset:
A tale of two CT studies: the combined impact of multiple human body composition projects in cancer

In this month ’ s JCSM , we see the publication of two excellent studies assessing the relationship between CT body composition (BC) analysis, systemic in ﬂ ammation (SI), and survival in patients with colorectal cancer. Both studies identify markers of worsened BC and SI as independent, and potentially additive, determinants of patient prognosis, over and above standard clinical prognostic measures of tumour staging. This editorial will describe additional lessons that may be gleaned by comparing the epidemiology, methodology, and interpretation of these two studies and other human BC projects in cancer. Moreover, it will highlight the emerging importance of host phenotyping in the delivery of modern oncological care. The authors of our papers this month and integrity the the two papers research histories
Indications for a vertical transmission pathway of piscine myocarditis virus in Atlantic salmon (Salmo salar L.)

Abstract Losses due to cardiomyopathy syndrome (CMS) keep increasing in salmon‐producing countries in the North‐Atlantic. Recently, Piscine myocarditis virus (PMCV) has been detected in post‐smolts shortly after sea‐transfer, indicating a possible carry‐over from the hatcheries. In addition, there are reports of prevalences of PMCV as high as 70%–90% in certain groups of broodfish, and a recent outbreak of CMS in the Faroe Islands has been linked to the importation of eggs from a CMS‐endemic area. Thus, there is a need to investigate whether PMCV can be transmitted vertically from infected broodstock to their progeny. In the present study, samples from eggs, larvae, fingerlings and presmolt originating from PMCV‐positive broodstock from two commercial Atlantic salmon producers were tested for PMCV. The prevalence of PMCV in the broodstock was 98% in the hearts, 69% in the roe and 59% in the milt. Piscine myocarditis virus was detected in all stages of the progeny until and including the 40 g stage. Piscine myocarditis virus was also detected in presmolt sampled for tissue tropism. This provides farmers with several options for minimizing the risk of transfer of PMCV from broodstock to progeny, including screening of broodstock and aiming to use only those that are negative for PMCV or have low levels of virus.
Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species.

The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non-contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV-4. Differently from HRTV-4, HFTV1 encodes host-derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp. , albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes.
Higher Insulin Resistance and Adiposity in Postmenopausal Women With Breast Cancer Treated With Aromatase Inhibitors

Abstract Context Aromatase deficiency causes obesity and insulin resistance in aromatase knockout mice and humans with rare mutations of the aromatase gene (CYP19). Aromatase inhibitors are a commonly prescribed therapy for postmenopausal breast cancer. Objective We hypothesized that aromatase inhibitors induce obesity and insulin resistance when used in treatment of breast cancer. Design Case-control study. Setting University teaching hospital. Participants Patients with postmenopausal breast cancer (n = 20) treated with aromatase inhibitors and 20 age-matched control subjects. Main outcome measures The primary outcome measure was insulin sensitivity index – Matsuda, derived from a 75-g oral glucose tolerance test. Body composition was assessed by dual energy x-ray absorptiometry and biopsy specimens of subcutaneous adipose tissue obtained for assessment of mRNA transcript levels. Data are reported as mean ± SEM (patients receiving inhibitors vs control group, respectively). Results Aromatase inhibitor therapy was associated with significantly lower insulin sensitivity (5.15 ± 0.45 vs 6.80 ± 0.64; P = 0.041), higher peak insulin concentration after oral glucose tolerance test (693.4 ± 78.6 vs 527.6 ± 85.5 pmol/L; P = 0.035), greater percentage of body fat (38.4% ± 1.0% vs 34.6% ± 1.3%; P = 0.026), and higher plasma leptin concentration (23.5 ± 2.8 vs 15.5 ± 2.3 ng/mL; P = 0.035). Conclusion Women who received aromatase inhibitors for postmenopausal breast cancer had greater percentage body fat and insulin resistance compared with control subjects with no history of breast cancer.
Disentangling the effects of empathy components on Internet gaming disorder: A study of vulnerable youth in China

Background and aims Previous research shows that empathy can be one of the potential protective factors for Internet gaming disorder (IGD), yet the complex relationships between multidimensional factors of empathy and IGD remain understudied. Thus, a major question moving forward is to resolve the mixed empirical data by examining the specific contributions of empathy components. In this study, we disentangle the effects of cognitive component (i.e., perspective taking) and affective component (i.e., empathic concern and personal distress) on IGD symptoms and propose affect-oriented mediation pathways between them. Methods We surveyed a large sample (N = 3,348) of Chinese vocational school students, one of the most vulnerable groups to online gaming addiction. Results Our structural equation modeling results revealed that only personal distress, but not empathic concern or perspective taking, positively predicted IGD symptoms. However, empathic concern and personal distress were negatively and positively predicted gaming motive of escape from reality, respectively, which in turn predicted IGD symptoms. Furthermore, we found an indirect effect of perspective taking on IGD through empathic concern and then gaming motive of escape from reality. Discussion and conclusion The findings underscore the importance of separating the affective and cognitive components to understand the complex relationships between the empathy and IGD, and support our theorizing of the affect-oriented mediation mechanism.
Numerical Investigation into Gas-Particle Inter-Phase Combustion and Reduction in the Flash Ironmaking Process

Despite the dominance of the blast furnace ironmaking process, more attention is being paid to the new technologies with lower energy consumption and carbon dioxide emissions. A novel flash ironmaking technology using pulverized coals and iron concentrates as raw materials, which is different from flash ironmaking with the reductive gas as the reducing agent, is studied. In order to obtain the flow patterns, temperature, and gas composition distribution, as well as particle trajectories in the reaction shaft of the flash ironmaking furnace, the Euler–Lagrangian model with a custom user defined function (UDF) code is used to simulate the processes of the fluid flow, heat and mass transfer, and chemical reactions, including the combustion reaction of pulverized coals and reduction reaction of iron concentrates. The results indicate that the flow patterns, temperature, and gas composition distributions present symmetrical distribution characteristics. The central oxygen expands rapidly after entering the reaction shaft and its distribution is approximately bell-shaped. The temperature distribution in the reaction shaft is wing-shaped. The maximum temperature, 2615 K, is reached at 5 m below the roof of the reaction shaft. The O2 is quickly consumed after entering the reaction shaft. At 6 m below the roof of the reaction shaft, the oxygen concentration becomes almost zero, with the CO concentration reaching the highest. The Fe2O3 and FeO in the iron concentrates are mostly reduced to Fe at 9 m below the roof of the reaction shaft, and more than 95 wt% iron particles could be obtained within 1.2–7.7 s.
The role of protein-protein interactions in the biosynthesis of ribosomally synthesized and post-translationally modified peptides.

Covering: up to 02/2019This review covers the role of protein-protein complexes in the biosynthesis of selected ribosomally synthesized and post-translationally modified peptide (RiPP) classes. The genomic organization of RiPP systems usually allows the expression of each biosynthetic enzyme as an individual unit, which is in stark contrast to the giant assembly lines found in non-ribosomal peptide and polyketide synthesis systems. Evidence is mounting however that the formation of multi-enzyme complexes is critical for efficient RiPPs biosynthesis and that these complexes may be involved in substrate channeling or conformational sampling. In some pathways, polyfunctional enzymes have evolved, which can be viewed as perpetual protein complexes. We summarize what is currently known on enzyme complexes in RiPP systems for lasso peptides, cyanobactins, linear azolic peptides, thiopeptides, and lanthipeptides.
Upskilling and distributional changes in the electronics global value chain

The electronics industry has one of the most complex global production chains in the international economy. Using data from the World Input–Output Database for the period 2000– 14, this article traces individual contributions to the value chain in order to observe how financial turmoil has affected its evolution over timeand to map international interactions. The authors point to a rise in offshoring until the outbreak of the global financial crisis of 2007–08, as China and other Eastern Asian economies became an essential node of value creation. They also detect a deep transformation of production technologies, accompanied by a process of upskilling.
Relationship Between Bone Mineral Density T‐Score and Nonvertebral Fracture Risk Over 10 Years of Denosumab Treatment

Although treat‐to‐target strategies are being discussed in osteoporosis, there is little evidence of what the target should be to reduce fracture risk maximally. We investigated the relationship between total hip BMD T‐score and the incidence of nonvertebral fracture in women who received up to 10 years of continued denosumab therapy in the FREEDOM (3 years) study and its long‐term Extension (up to 7 years) study. We report the percentages of women who achieved a range of T‐scores at the total hip or femoral neck over 10 years of denosumab treatment (1343 women completed 10 years of treatment). The incidence of nonvertebral fractures was lower with higher total hip T‐score. This relationship plateaued at a T‐score between ‐2.0 and ‐1.5 and was independent of age and prevalent vertebral fractures, similar to observations in treatment‐naïve subjects. Reaching a specific T‐score during denosumab treatment was dependent on the baseline T‐score, with higher T‐scores at baseline more likely to result in higher T‐scores at each time point during the study. Our findings highlight the importance of follow‐up BMD measurements in patients receiving denosumab therapy because BMD remains a robust indicator of fracture risk. These data support the notion of a specific T‐score threshold as a practical target for therapy in osteoporosis. © 2019 The Authors Journal of Bone and Mineral Research published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research (ASBMR)
Expression analysis of selected miR‐206 targets from the transforming growth factor‐β signaling pathway in breast cancer

Breast cancer as a molecularly heterogeneous malignancy is associated with dysregulation of several signaling pathways, including transforming growth factor‐β (TGF‐β) signaling. On the other hand, several recent studies have demonstrated the role of microRNAs (miRNAs) in breast cancer pathogenesis. In the current study, we performed a computerized search to find miR‐206 target genes that are functionally linked to the TGF‐β signaling pathway. We selected LEF1, Smad2, and Snail2 genes to assess their expression in 65 breast cancer samples and their adjacent noncancerous tissues (ANCTs) in correlation with expression levels of miR‐206 as well as clinicopathological characteristics of patients. miR‐206 was significantly downregulated in (Estrogen receptor) ER‐positive breast cancer samples compared with their corresponding ANCTs. Association analysis between expression levels of genes and demographic features of patients showed significant association between expressions of SMAD2 and LEF1 genes and body mass index ( P values of 0.03 and 0.02, respectively). miR‐206 low‐expression levels were associated with TNM stage, mitotic rate, and lymph node involvement ( P values of 0.02, 0.01, and 0.01 respectively). In addition, SMAD2 high‐expression levels were associated with HER2 status ( P = 0.02). Consequently, our data highlight the role of TGF‐β signaling dysregulation in the pathogenesis of breast cancer and warrant further evaluation of miRNAs and messenger RNA coding genes in this pathway to facilitate detection of cancer biomarkers and therapeutic targets.
Human T‐cell receptor V gene segment of alpha and beta families: A revised primer design strategy

The application of human TCR in cancer immunotherapy has gained momentum with developments in tumor killing strategies using endogenous adaptive immune responses. The successful coverage of a diverse TCR repertoire is mainly attributed to the primer design of the human TCR V genes. Here, we present a refined primer design strategy of the human TCR V gene by clustering V gene sequence homolog for degenerate primer design based on the data from IMGT. The primers designed were analyzed and the PCR efficiency of each primer set was optimized. A total of 112 alpha and 160 beta sequences were aligned and clustered using a phylogram yielding 32 and 27 V gene primers for the alpha and beta family. The new primer set was able to provide 93.75% and 95.63% coverage for the alpha and beta family, respectively. A semi‐qualitative approach using the designed primer set was able to provide a relative view of the TCR V gene diversity in different populations. Taken together, the new primers provide a more comprehensive coverage of the TCR gene diversity for improved TCR library generation and TCR V gene analysis studies.
Influence of a delamination on Lamb wave excitation by a nearby piezoelectric transducer

This article presents the results of theoretical and experimental investigations of characteristic changes of Lamb wave excitation and scattering by a strip-like horizontal delamination in a layered elastic waveguide for Lamb waves induced by a piezoelectric wafer active sensor. The boundary integral equation method is used to describe wave propagation in an infinite layered waveguide with a delamination, while the frequency domain spectral element method is employed to model the dynamic behaviour of the piezoelectric wafer active sensor, which allows to simulate debonding between the piezoelectric wafer active sensor and the waveguide. Experimental investigations of the dynamic interaction of the piezoelectric wafer active sensor with a layered plate containing a horizontal delamination is conducted for several damage scenarios, showing a good agreement with the results obtained using the developed mathematical model. The obtained mathematical model is employed to analyse alteration of the piezo-induced Lamb waves including modes’ decomposition due to delamination. The conversion and/or conservation of the Lamb waves on account of a delamination is investigated. The electro-mechanical impedance of the piezoelectric transducer and the stress intensity factors of a delamination are analysed in dependence on the delamination location.
Addressing engineering threshold concepts in an African university of technology

Learning new skills isn’t only for the benefit of passing the exam but being able to apply those skills in a productive way. One cannot learn before one understands which is why student understanding is a priority for facilitators. This becomes especially important in threshold concepts where a student will be unable to progress to the next stage before the threshold concept is mastered, but facilitators do not focus on pedagogy as they rely on the support of instructional designers. This explorative paper looks at student perceptions of their understanding of the threshold concept in electrical engineering, logic gates, after completing a lesson designed using the proposed ten-step activity plan. The activity plan is derived from the learning theories of Gagne, Biggs, Vygotsky and Gibson. A sample of 18 students completed an online survey that focused on their acquiring of skills relating to logic gates, truth tables and Boolean algebra. Results showed a positive experience with 88.89% of participants indicating that they left the lesson with a good understanding of the threshold concept. This ten-step activity plan can assist to close the gap between instructional designer and facilitator to design threshold concept lessons based on sound learning theory.
The Effect of Anxiety on Regional Brain Volumes in the National Alzheimer’s Coordinating Center Uniform Data Set

Purpose: The present study examined the feasibility of internet-based cognitive behavioral therapy (iCBT) for home care older adults. Method: A feasibility open trial was conducted with 26 recipients of nonmedical home care with depressive symptoms. When possible, home care workers (HCWs) of older adults (n = 13) were recruited to provide external support for iCBT usage. Results: The mean therapy sessions completed was 4.7 out of 8, and 86% would recommend the program to others with depressed mood. Participants’ depressive symptoms and anxiety symptoms decreased, whereas their quality of life ratings improved. Discussion: iCBT is a feasible and acceptable treatment modality for home care older adults with depressive symptoms and is potentially effective. Future studies are warranted to refine the existing treatment platform to achieve a better fit between the demands of the program and the needs and capabilities of homebound older adults and to examine treatment effectiveness as a function of HCW support.
PEMODELAN TIGA DIMENSI (3D) BANGUNAN CAGAR BUDAYA MENGGUNAKAN DATA POINT CLOUD

Indonesia adalah negara yang kaya akan warisan budaya sebagai daya tarik wisata seperti bangunan cagar budaya. Arsip bangunan budaya belum dikelola dengan baik. Sebagian besar dari bangunan cagar budaya hanya berisi informasi atribut (nama, alamat, dan sejarah), aspek geospasial seperti alamat ter- geocoding dan peta struktural belum menjadi prioritas. Metode yang paling populer terkait dengan struktur bangunan adalah Building Information Modeling (BIM). BIM telah digunakan secara luas dalam perencanaan bangunan baru dan manajemen aset. Dalam beberapa tahun terakhir, BIM mulai digunakan dalam dokumentasi bangunan budaya. Teknik ini dikenal sebagai Heritage Building Information Modeling (HBIM). Tujuan HBIM adalah untuk melestarikan dan memantau bangunan warisan melalui model 3D. Model tersebut memuat unsur arsitektur bangunan cagar budaya dengan informasi semantiknya. Kompleksitas elemen bangunan dapat mempengaruhi Level of Detail (LoD) dari suatu model. LoD model berkorelasi dengan metode perolehan data. Makalah ini bertujuan untuk membuat model 3D bangunan budaya dan menguji LoD model 3D yang berasal dari point cloud bangunan budaya di Yogyakarta. Point cloud untuk membuat model 3D diperoleh dari survei topografi dan survey laser scanner . Atribut informasi diperoleh dengan melakukan dokumen dan penelitian lapangan.
Beyond sigmoids: How to obtain well-calibrated probabilities from binary classifiers with beta calibration

: For optimal decision making under variable class distributions and misclassiﬁcation costs a classiﬁer needs to produce well-calibrated estimates of the posterior probability. Isotonic calibration is a powerful non-parametric method that is however prone to overﬁtting on smaller datasets; hence a parametric method based on the logistic sigmoidal curve is commonly used. While logistic calibration is designed for normally distributed per-class scores, we demonstrate experimentally that many classiﬁers including Naive Bayes and Adaboost suﬀer from a particular distortion where these score distributions are heavily skewed. In such cases logistic calibration can easily yield probability estimates that are worse than the original scores. Moreover, the logistic curve family does not include the identity function, and hence logistic calibration can easily uncalibrate a perfectly calibrated classiﬁer. In this paper we solve all these problems with a richer class of parametric calibration maps based on the beta distribution. We derive the method from ﬁrst principles and show that ﬁtting it is as easy as ﬁtting a logistic curve. Extensive experiments show that beta calibration is superior to logistic calibration for a wide range of classiﬁers: Naive Bayes, Adaboost, random forest, logistic regression, support vector machine and multi-layer perceptron. If the original classiﬁer is already calibrated, then beta calibration learns a function close to the identity. On this we build a statistical test to recognise if the model deviates from being well-calibrated.
Identification of staphylococci by 16 S internal transcribed spacer rRNA gene restriction fragment length polymorphism

The capacity of 16S internal transcribed spacer (16S-ITS) rRNA gene RFLP to differentiate 16 type strains and nine clinical isolates of staphylococci was evaluated. The 16S rRNA gene was amplified together with the ITS region and the amplification products were digested with TaqI restriction enzyme. Analysis of the 16S-ITS rRNA gene RFLP profiles differentiated each of the 16 type strains into distinct RFLP haplotypes.