Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunohistochemical Ki67 after short-term hormone therapy identifies low-risk breast cancers as reliably as genomic markers

Background The purpose of this study was to test whether immunohistochemical (IHC) Ki67 levels after short-term preoperative hormone therapy (post-Ki67) predict similar numbers of patients with favorable prognoses as genomic markers. Results Thirty paired cases (60 samples) were enrolled in this study. Post-Ki67 levels were significantly lower than pre-treatment Ki67 levels (P < 0.001). Post-Ki67 predicted more low-risk cases (83.3%, 25/30) than pre-genomic surrogate signature(GSS) (66.7%: 20/30), but the difference in predictive power was not significant (P = 0.233). Proliferation (MKI67, STK15, Survivin, CCNB1, and MYBL2) and estrogen (ER, PGR, BCL2, and SCUBE2) related signatures were significantly downregulated after therapy (P < 0.001 and 0.041, respectively). Materials and Methods Core needle biopsy specimens of primary breast cancer were collected at Okayama University Hospital from hormone receptor-positive and human epidermal growth factor 2-negative patients that subsequently received two weeks of neoadjuvant hormone therapy. Paired post-treatment specimens from surgical samples were also collected. IHC Ki67 levels and GSS were compared between pre- and post-hormone treatment samples. Changes of gene expression pattern in short-term hormone therapy were also assessed. Conclusions IHC based post-Ki67 levels may have distinct predictive power compared with the naïve IHC Ki67. Future studies with larger cohorts and longer follow-up periods may be needed to validate our results.
Cytological study on the regulation of lymphocyte homing in the chicken spleen during LPS stimulation

The immune function of the chicken spleen depends on its different compartments of red and white pulps, but little is known about the mechanism underlying lymphocyte homing towards the different compartments. In the present study, the role of lymphocyte homing in the chicken spleen was investigated during lipopolysaccharide (LPS) stimulation. Morphological analysis demonstrated the cuboidal endothelial cells of the splenic sheathed capillary facilitated the passage of lymphocyte homing to the chicken spleen. The tissue-specific adhesion molecules- vascular cell adhesion molecule-1 (VCAM-1) and mucosal addressin cell adhesion molecule-1 (MADCAM-1) expressed on the sheathed capillary, which suggested the high endothelial venule (HEV)-like vessels of the chicken spleen. Electron microscope analysis showed LPS activated the endothelium of the sheathed capillary and recruited lymphocytes to the chicken spleen. Transferring of 5, 6- carboxyfluorescein diacetate, succinimidyl ester (CFSE) labeled lymphocytes depicted the rout of lymphocyte homing to the compartments of the chicken spleen was from the white pulp to the red pulp. Furthermore, the mRNA and protein levels of adhesion molecular integrin β1 and VCAM-1 increased after LPS stimulation. The mechanism underlying the integrin β1 and VCAM-1 during LPS stimulation might be associated with the integrin linked kinase (ILK)- dependent regulation of protein kinase B (PKB/AKT). This study firstly shows lymphocyte homing in the chicken spleen after LPS-induced inflammation. These results contribute to our knowledge of comparative immunology and provide a better means for investigating the pharmacological strategies concerning the possible role of lymphocyte homing in inflammation and immunological reactions in infectious disease.
Analysis of Asymptotically Optimal Sampling-based Motion Planning Algorithms for Lipschitz Continuous Dynamical Systems

Over the last 20 years significant effort has been dedicated to the development of sampling-based motion planning algorithms such as the Rapidly-exploring Random Trees (RRT) and its asymptotically optimal version (e.g. RRT*). However, asymptotic optimality for RRT* only holds for linear and fully actuated systems or for a small number of non-linear systems (e.g. Dubin's car) for which a steering function is available. The purpose of this paper is to show that asymptotically optimal motion planning for dynamical systems with differential constraints can be achieved without the use of a steering function. We develop a novel analysis on sampling-based planning algorithms that sample the control space. This analysis demonstrated that asymptotically optimal path planning for any Lipschitz continuous dynamical system can be achieved by sampling the control space directly. We also determine theoretical bounds on the convergence rates for this class of algorithms. As the number of iterations increases, the trajectory generated by these algorithms, approaches the optimal control trajectory, with probability one. Simulation results are promising.
A model study of the vertically integrated transport variability through the Yucatan Channel: Role of Loop Current evolution and flow compensation around Cuba

[1] In the paper “A model study of the vertically integrated transport variability through the Yucatan Channel: Role of Loop Current evolution and flow compensation around Cuba” by Lin et al. (Journal of Geophysical Research, 114, C08003, doi:10.1029/2008JC005199, 2009), in the last sentence of paragraph 31, the word “westward” in “drives enhanced westward” should be “eastward. ”
Objective quality assessment for video retargeting based on spatio-temporal distortion analysis

This paper proposes a novel objective quality metric for video retargeting based on spatio-temporal distortion analysis. The proposed metric combines three indices: one spatial distortion index taking into account perceptual geometric distortion and spatial information loss, and two temporal distortion indices including temporal inconsistency distortion and temporal saliency similarity. Subjective tests are conducted to evaluate the performance of the proposed metric. Our experimental results show the good consistency between the proposed objective metric and the subjective rankings.
Muscle Force-Velocity Relationships Observed in Four Different Functional Tests

Abstract The aims of the present study were to investigate the shape and strength of the force-velocity relationships observed in different functional movement tests and explore the parameters depicting force, velocity and power producing capacities of the tested muscles. Twelve subjects were tested on maximum performance in vertical jumps, cycling, bench press throws, and bench pulls performed against different loads. Thereafter, both the averaged and maximum force and velocity variables recorded from individual trials were used for force–velocity relationship modeling. The observed individual force-velocity relationships were exceptionally strong (median correlation coefficients ranged from r = 0.930 to r = 0.995) and approximately linear independently of the test and variable type. Most of the relationship parameters observed from the averaged and maximum force and velocity variable types were strongly related in all tests (r = 0.789-0.991), except for those in vertical jumps (r = 0.485-0.930). However, the generalizability of the force-velocity relationship parameters depicting maximum force, velocity and power of the tested muscles across different tests was inconsistent and on average moderate. We concluded that the linear force-velocity relationship model based on either maximum or averaged force-velocity data could provide the outcomes depicting force, velocity and power generating capacity of the tested muscles, although such outcomes can only be partially generalized across different muscles.
Real-time Business Process Intelligence. Comparison of different architectural approaches using the example of the order-to-cash process

Business operations are becoming more and more integrated with the real- time intelligence. Core business activities are being carried out through OLTP systems that provide limited monitoring capabilities of the running process instances. The arti- cle shows how to turn the gap between the classic transactional system and the process- centric approach into an organization that provides more accurate and faster decisions on the strategic and operational management levels. This study aims at determination of what kind of information can be retrieved during the process execution and it tries to identify the need for the real-time process intelligence on the example of the order-to- cash process. Furthermore, we compare two architectural approaches of the real-time process intelligence monitoring system. The proposed frameworks retrieve process data from the ERP system in order to record crucial performance indicators on a real-time basis with the use of the in-memory technology.
Identification, Characterization, and Application of the Replicon Region of the Halophilic Temperate Sphaerolipovirus SNJ1

ABSTRACT The temperate haloarchaeal virus SNJ1 displays lytic and lysogenic life cycles. During the lysogenic cycle, the virus resides in its host, Natrinema sp. strain J7-1, in the form of an extrachromosomal circular plasmid, pHH205. In this study, a 3.9-kb region containing seven predicted genes organized in two operons was identified as the minimal replicon of SNJ1. Only RepA, encoded by open reading frame 11-12 (ORF11-12), was found to be essential for replication, and its expression increased during the lytic cycle. Sequence analysis suggested that RepA is a distant homolog of HUH endonucleases, a superfamily that includes rolling-circle replication initiation proteins from various viruses and plasmids. In addition to RepA, two genetic elements located within both termini of the 3.9-kb replicon were also required for SNJ1 replication. SNJ1 genome and SNJ1 replicon-based shuttle vectors were present at 1 to 3 copies per chromosome. However, the deletion of ORF4 significantly increased the SNJ1 copy number, suggesting that the product of ORF4 is a negative regulator of SNJ1 abundance. Shuttle vectors based on the SNJ1 replicon were constructed and validated for stable expression of heterologous proteins, both in J7 derivatives and in Natrinema pallidum JCM 8980T, suggesting their broad applicability as genetic tools for Natrinema species. IMPORTANCE Archaeal viruses exhibit striking morphological diversity and unique gene content. In this study, the minimal replicon of the temperate haloarchaeal virus SNJ1 was identified. A number of ORFs and genetic elements controlling virus genome replication, maintenance, and copy number were characterized. In addition, based on the replicon, a novel expression shuttle vector has been constructed and validated for protein expression and purification in Natrinema sp. CJ7 and Natrinema pallidum JCM 8980T. This study not only provided mechanistic and functional insights into SNJ1 replication but also led to the development of useful genetic tools to investigate SNJ1 and other viruses infecting Natrinema species as well as their hosts.
The Relationship between Lifestyle Factors and Body Compositionin Young Adults

Background: Little is known of how lifestyle factors might influence on body composition parameters in young adults from Croatia. The main purpose of the present study was to investigate the relationship between the lifestyle factors and body composition in young adults. Methods: In this cross-sectional study, participants were 271 university students (59.0% of women). Body composition was measured by using bioelectric impendance analysis (BIA). Blood pressure and heart rate were measured according to standardized protocol and Mediterranean diet adherence (MD), physical activity (PA) and psychological distress (PD) were assessed with validated questionnaires. Results: Self-rated health (SRH) and PA were inversely associated with weight, body-mass index (BMI), fat-mass percentage and blood pressure in men and with weight, BMI, fat-mass percentage and heart rate in women. Higher levels of SRH and PA were positively associated with fat-free mass percentage in both men and women. Smoking was positively associatedwith BMI and fat-mass percentage in women and with heart rate in men. Alcohol consumption was positively associated with weight and BMI in women and fat-mass percentage and heart rate in men, yet inversely associated with fat-free mass percentage only in men. PD was positively associated with weight and blood pressure in men and with BMI, fat-mass percentage and blood pressure in women. Conclusions: Our study shows that higher levels of SRH, MD and PA are related with healthy body composition parameters in young adults. Special interventions and policies that enhance PA and MD and decrease substance use and misuse (SUM) and PD should be implemented within the university school systems.
The Primary Role of Fibrinogen-Related Proteins in Invertebrates Is Defense, Not Coagulation

In vertebrates, the conversion of fibrinogen into fibrin is an essential process that underlies the establishment of the supporting protein framework required for coagulation. In invertebrates, fibrinogen-domain-containing proteins play a role in the defense response generated against pathogens; however, they do not function in coagulation, suggesting that this role has been recently acquired. Molecules containing fibrinogen motifs have been identified in numerous invertebrate organisms, and most of these molecules known to date have been linked to defense. Moreover, recent genome projects of invertebrate animals have revealed surprisingly high numbers of fibrinogen-like loci in their genomes, suggesting important and perhaps diverse functions of fibrinogen-like proteins in invertebrates. The ancestral role of molecules containing fibrinogen-related domains (FReDs) with immunity is the focus of this review, with emphasis on specific FReDs called fibrinogen-related proteins (FREPs) identified from the schistosome-transmitting mollusc Biomphalaria glabrata. Herein, we outline the range of invertebrate organisms FREPs can be found in, and detail the roles these molecules play in defense and protection against infection.
Characterization of Thyroid Abnormalities in a Large Cohort of Children with Down Syndrome 

Background/Aims: Thyroid disease is a common comorbidity in individuals with Down syndrome (DS), but historical studies have multiple limitations. We assessed thyroid abnormalities in a large cohort of children with DS. Methods: Retrospective records review from a single institution. Calculated prevalence of common thyroid abnormalities and associations with common comorbidities. Results: Among 508 patients, 120 (24%) had a thyroid-related diagnosis, the majority having elevated thyrotropin treated with levothyroxine. A Kaplan-Meier estimate projects that 50% have thyroid disorder by adulthood, with 20% of hypothyroidism diagnosed before the age of 6 months. When tested, approximately 50% had positive antithyroid antibodies, though this rate was 100% in overt hypothyroidism. There was no association between congenital or acquired hypothyroidism and common comorbidities. Conclusion: Thyroid disease in DS is more common and occurs earlier than in the general population, and is often transient. Thyroid disease is unrelated to gender, obesity, or other comorbidities. Apart from overt hypothyroidism, much of hypothyroidism in DS appears unrelated to autoimmunity; we recommend checking of antithyroid antibodies only in select cases. An additional screen for thyroid disease between the newborn screen and the 6-month well-child visit will detect early cases of hypothyroidism who passed their newborn screen.
The future of health behavior change research: What is needed to improve translation of research into health promotion practice?

Background: It is well documented that the results of most behavioral and health promotion studies have not been translated into practice.Purpose: In this article, reasons for this gap, focusing on study design characteristics as a central contributing barrier, are discussed.Methods: Four reviews of recent controlled studies in work sites, health care, school, and community settings are briefly discussed and summarized. Their implications for future research and for closing the gap between research and practice are then discussed.Results: These reviews come to consistent conclusions regarding key internal and external validity factors that have and have not been reported. It is very clear that moderating variables and generalization issues have not been included or reported in the majority of investigations, and that as a consequence little is known about the representatives or the robustness of results from current studies.Conclusions: To significantly improve the current state of affairs, substantial changes will be required on the part of researchers, funding agencies, and review and editorial boards. In conclusion, recommendations for each of these entities are provided.
Household point of care CD4 testing and isoniazid preventive therapy initiation in a household TB contact tracing programme in two districts of South Africa

Background In South Africa, TB household contact tracing provides an opportunity for increased TB and HIV case finding. We aimed to determine the effect of two new potential interventions for TB contact tracing programmes: Point of Care CD4 (PoC CD4) on HIV linkage to care and household Isoniazid Preventive Therapy (IPT) provision on uptake and retention of IPT. Methods A pragmatic, three-arm, cluster-randomized trial was undertaken. TB Household contacts were randomised to 3 arms: 1) Standard of Care TB and HIV testing (SOC); 2) SOC with POC CD4 for those testing HIV positive; 3) SOC with POC CD4 and IPT for eligible household members. Linkage to care within 90 days was assessed either through patient visits (at 10 weeks and 6 months) or via telephonic contact. Results 2,243 index TB patients and 3,012 contacts (64,3% female, median age 30 years) were enrolled. On self-report, 26(1.2%) were currently receiving TB treatment and 1816 (60.3%) reported a prior HIV test. HIV testing uptake was 34.7% in the SoC arm, 40.2% in the PoC CD4 arm (RR1.16, CI 0.99–1.36, p-value = 0.060) and 39.9% in the PoC CD4 + HH-IPT arm (RR = 1.15, CI 0.99–1.35, p-value = 0.075). Linkage to care within 3 months was 30.8% in the SoC arm and 42.1% in the POC CD4 arms (RR 1.37; CI: 0.68–2.76, p-value = 0.382). 20/21 contacts (95.2%) initiated IPT in the PoC CD4 + HH-IPT arm, compared to 3/20 (15.0%) in the PoC CD4 arm (p = 0.004; p-value from Fisher’s exact test < 0.001). Among 3,008 contacts screened for tuberculosis, 15 (3.4%) had bacteriologically confirmed TB with an overall yield of TB of 0.5% (95% CI: 0.3%, 0.8%). Conclusions Household PoC CD4 testing and IPT initiation is feasible. There was only weak evidence that PoCCD4 led to a small increase in HCT uptake and no evidence for an increase in linkage-to-care. IPT initiation and completion was increased by the household intervention. Although feasible, these interventions had low impact due to the low uptake of HIV testing in households.
Spontaneous Reversions of an Evolutionary Trait Loss Reveal Regulators of a Small RNA That Controls Multicellular Development in Myxobacteria

ABSTRACT Lost traits can reevolve, but the probability of trait reversion depends partly on a trait's genetic complexity. Myxobacterial fruiting body development is a complex trait controlled by the small RNA (sRNA) Pxr, which blocks development under conditions of nutrient abundance. In developmentally proficient strains of Myxococcus xanthus, starvation relaxes the inhibition by Pxr, thereby allowing development to proceed. In contrast, the lab-evolved strain OC does not develop because it fails to relay an early starvation signal that alleviates inhibition by Pxr. A descendant of OC, strain PX, previously reevolved developmental proficiency via a mutation in pxr that inactivates its function. A single-colony screen was used to test whether reversion of OC to developmental proficiency occurs only by mutation of pxr or might also occur through alternative regulatory loci. Five spontaneous mutants of OC that exhibited restored development were isolated, and all five showed defects in Pxr synthesis, structure, or processing, including one that incurred an eight-nucleotide deletion in pxr. Two mutations occurred in the σ54 response regulator (RR) gene MXAN_1078 (named pxrR here), immediately upstream of pxr. PxrR was found to positively regulate pxr transcription, presumably via the σ54 promoter of pxr. Two other mutations were identified in a histidine kinase (HK) gene (MXAN_1077; named pxrK here) immediately upstream of pxrR. Evolutionarily, the rate of trait restoration documented in this study suggests that reversion of social defects in natural microbial populations may be common. Molecularly, these results suggest a mechanism by which the regulatory functions of an HK-RR two-component signaling system and an sRNA are integrated to control initiation of myxobacterial development. IMPORTANCE Many myxobacteria initiate a process of multicellular fruiting body development upon starvation, but key features of the regulatory network controlling the transition from growth to development remain obscure. Previous work with Myxococcus xanthus identified the first small RNA (sRNA) regulator (Pxr) known to serve as a gatekeeper in this life history transition, as it blocks development when nutrients are abundant. In the present study, a screen for spontaneous mutants of M. xanthus was developed that revealed a two-component system operon (encoding a histidine kinase and a σ54 response regulator) associated with the production and processing of Pxr sRNA. This discovery broadens our knowledge of early developmental gene regulation and also represents an evolutionary integration of two-component signaling and sRNA gene regulation to control a bacterial social trait.
How PHP Releases Are Adopted in the Wild?

This empirical paper examines the adoption of PHP releases in the the contemporary world wide web. Motivated by continuous software engineering practices and software traceability improvements for release engineering, the empirical analysis is based on big data collected by web crawling. According to the empirical results based on discrete time-homogeneous Markov chain (DTMC) analysis, (i) adoption of PHP releases has been relatively uniform across the domains observed, (ii) which tend to also adopt either old or new PHP releases relatively infrequently. Although there are outliers, (iii) downgrading of PHP releases is generally rare. To some extent, (iv) the results vary between the recent history from 2016 to early 2017 and the long-run evolution in the 2010s. In addition to these empirical results, the paper contributes to the software evolution and release engineering research traditions by elaborating the applied use of DTMCs for systematic empirical tracing of online software deployments.