Miracle-dz/UniFAR-FTUs huggingface dataset:
A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation

Whole genome duplication has shaped eukaryotic evolutionary history and has been associated with drastic environmental change and species radiation. While the most common fate of WGD duplicates is a return to single copy, retained duplicates have been found enriched for highly interacting genes. This pattern has been explained by a neutral process of subfunctionalization and more recently, dosage balance selection. However, much about the relationship between environmental change, WGD and adaptation remains unknown. Here, we study the duplicate retention pattern postWGD, by letting virtual cells adapt to environmental changes. The virtual cells have structured genomes that encode a regulatory network and simple metabolism. Populations are under selection for homeostasis and evolve by point mutations, small indels and WGD. After populations had initially adapted fully to fluctuating resource conditions re-adaptation to a broad range of novel environments was studied by tracking mutations in the line of descent. WGD was established in a minority (≈30%) of lineages, yet, these were significantly more successful at re-adaptation. Unexpectedly, WGD lineages conserved more seemingly redundant genes, yet had higher per gene mutation rates. While WGD duplicates of all functional classes were significantly over-retained compared to a model of neutral losses, duplicate retention was clearly biased towards highly connected TFs. Importantly, no subfunctionalization occurred in conserved pairs, strongly suggesting that dosage balance shaped retention. Meanwhile, singles diverged significantly. WGD, therefore, is a powerful mechanism to cope with environmental change, allowing conservation of a core machinery, while adapting the peripheral network to accommodate change.
Dual hypothermic oxygenated machine perfusion in liver transplants donated after circulatory death

Experimental studies have suggested that end‐ischaemic dual hypothermic oxygenated machine perfusion (DHOPE) may restore hepatocellular energy status and reduce reperfusion injury in donation after circulatory death (DCD) liver grafts. The aim of this prospective case–control study was to assess the safety and feasibility of DHOPE in DCD liver transplantation.
Possible Pathogenesis of Painful Intervertebral Disc Degeneration

Study Design. We collected the specimens of lumbar intervertebral disc (i.e., the symptomatic degenerative disc) from patients with discogenic low back pain to study the histopathologic features and growth factor expressions. Objectives. To study the pathogenesis of disc degeneration, meanwhile discriminating between common disc degeneration (aging disc) (i.e., black asymptomatic disc, not clinically relevant) and painful disc degeneration (i.e., symptomatic disc, clinically relevant). Summary of Background Data. The pathogenesis of intervertebral disc degeneration is poorly understood, mainly because of the difficulty to establish the experimental model with good reproducibility. Recently, the popularity of spinal fusion leads to more opportunities to obtain disc specimens, which could be applied to explore the pathogenesis of disc degeneration with modern biologic techniques. Methods. There were 21 specimens of lumbar intervertebral discs from 15 patients with discogenic low back pain during posterior lumbar interbody fusion, 16 aging discs from patients without low back pain, and 10 normal discs as control collected for the study of their histopathologic features, as well as the expressions of basic fibroblast growth factor (bFGF) and its receptor (Flg), transforming growth factor-&bgr;1 (TGF-&bgr;1) and its receptor (TGF-&bgr;RI) by immunohistochemistry. The distribution of macrophages and mast cells was also noted. Proliferating cell nuclear antigen was assessed to evaluate proliferating activities of disc cells. Results. The distinct histologic characteristic of the disc from the patient with discogenic low back pain was the ingrowth of vascularized granulation tissue along torn fissures, extending from the external layer of the anulus fibrosus into the nucleus pulposus. The immunohistochemical staining showed that there were strong expressions of bFGF and TGF-&bgr;1 and their receptors, as well as a strong expression of proliferating cell nuclear antigen in the zones of granulation tissue in the painful discs. However, there were only weak expressions in the nongranulation tissue zones in the painful discs and aging discs, and no expression in the control discs. In addition, abundant macrophages and mast cells were found in the granulation tissue zones of painful discs but absent in the nongranulation tissue zones of painful discs or aging discs and the normal control discs. Conclusions. The findings indicated that degeneration of the painful disc might originate from the injury and subsequent repair of anulus fibrosus. Growth factors, such as bFGF and TGF-&bgr;1, macrophages and mast cells might play a key role in the repair of the injured anulus fibrosus and subsequent disc degeneration.
Characterization of human melanoma cell lines according to their migratory properties in vitro

SummaryThe migratory responses of four human melanoma cell lines (A-2058, DEMEL, HTB-63, and HTB-72), using chemotaxis (CTX) and haptotaxis (HPTX) assays, were studied. The attractants were three extracellular matrix components (EMCs), fibronectin, laminin, and collagen type IV. The conditioned media (CM) of each cell line were used to study autocrine and paracrine responses. A screening and sensitive CTX assay was performed, using pertussis toxin (PTX)—treated A-2058 as responder cells; the other melanoma cells and normal cells were used as secretory cells. Autotaxin (ATX), a purified autocrine motility factor, was also used as a chemoattractant. Reverse transcriptase-polymerase chain reaction was used to detect the expression of ATX by all cell lines. The secretion of ATX was determined by Western blot. The invasive capacity of the cell lines was evaluated using Matrigel and ATX as attractant. Chemotaxis responses to EMCs varied. Except for the A-2058 cells, HPTX migration was low. Autocrine and paracrine responses also varied. The migration of PTX-treated A-2058 cells to ATX and to their own CM was abolished. All the melanoma cells expressed ATX, and except for the HTB-72 and normal cells, all secreted ATX. Matrigel was invaded by all the melanoma cell lines except the HTB-72 and normal cells. The migratory properties of human melanoma cells in vitro suggest that they could correlate to their metastatic potential in vivo.
Integrating MOOC and Flipped Classroom Practice in a Traditional Undergraduate Course: Students' Experience and Perceptions

The purpose of this experimental study was to redesign a traditional undergraduate course by integrating MOOC content and flipped classroom practice and to see its effectiveness through students’ experience and perceptions. The course named “Internet and Distance Education” was taught in Winter Semester, 2013 at the Zhejiang University in Hangzhou, China to 15 undergraduate students majoring in education. E-learner satisfaction surveys found that students were generally satisfied with many aspects of the redesigned course, including instructor response timeliness, instructor attitude toward the technology, e-learning course flexibility, technology quality, Internet quality, perceived usefulness, perceived ease of use, and perceived e-learner satisfaction, while learner perceived interaction with others was not so satisfactory. Based on the findings, several suggestions to improve the course design are offered.
Population Genetic Structure and Phylogeography of Masu Salmon (Oncorhynchus Masou Masou) Inferred from Mitochondrial and Microsatellite DNA Analyses

The population genetic structure and phylogeography of masu salmon were investigated by using variation in the mitochondrial NADH dehydrogenase subunit 5 gene (ND5) and six polymorphic microsatellite loci among a total of 895 fish representing 18 populations collected from Japan (9), Russia (7), and Korea (2) from 2000 to 2008. An analysis of ND5 nucleotide sequences revealed 22 variable sites in about 560 bp in the 5′ half of the gene, which defined 20 haplotypes, including some associated with geographical regions. Haplotype and nucleotide diversities were greater in the populations in Japan and Korea than in those in Russia, indicating greater genetic diversity in the Japanese and Korean populations than in the Russian populations. All the microsatellite loci examined showed a high level of variation, but the expected heterozygosity indicated a similar level of genetic diversity among the populations of the three regions, contrary to the results for ND5. However, AMOVA and pairwise population F ST estimates for both ND5 and the microsatellite markers indicated a similar pattern of moderate genetic differentiation among populations of the three regions, and large population groups on the coasts of the Sea of Japan, Sea of Okhotsk, and Pacific Ocean in the Far East. From a mismatch distribution analysis and neutrality test, the observed genetic structure appears to have been influenced primarily by bottlenecks during glacial periods and population expansions during interglacial periods in the late Pleistocene.
Characterization of the cell wall of the sheathed methanogen Methanospirillum hungatei GP1 as an S layer

The cell wall of Methanospirillum hungatei GP1 is a labile structure that has been difficult to isolate and characterize because the cells which it encases are contained within a sheath. Cell-sized fragments, 560 nm wide by several micrometers long, of cell wall were extracted by a novel method involving the gradual drying of the filaments in 2% (wt/vol) sodium dodecyl sulfate and 10% (wt/vol) sucrose in 50 mM N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES) buffer containing 10 mM EDTA. The surface was a hexagonal array (a = b = 15.1 nm) possessing a helical superstructure with a ca. 2.5 degrees pitch angle. In shadowed relief, the smooth outer face was punctuated with deep pits, whereas the inner face was relatively featureless. Computer-based two-dimensional reconstructed views of the negatively stained layer demonstrated 4.0- and 2.0-nm-wide electron-dense regions on opposite sides of the layer likely corresponding to the openings of funnel-shaped channels. The face featuring the larger openings best corresponds to the outer face of the layer. The smaller opening was encircled by a stalk-like mass from which 2.2-nm-wide protrusions were resolved. The cell wall in situ was degraded at pH 9.6 at 56 degrees C but was unaffected at pH 7.4 at the same temperature. The cell wall was composed of two nonglycosylated polypeptides (114 and 110 kDa). The cell wall resembled an archaeal S layer and may function in regulating the passage of small (< 10-kDa) sheath precursor proteins.
Effect of the Arterial Input Function on the Measured Perfusion Values and Infarct Volumetric in Acute Cerebral Ischemia Evaluated by Perfusion Computed Tomography

Objectives:We sought to evaluate the accuracy of the perfusion computed tomography (PCT) deconvolution-based brain perfusion measurements and the lesions’ (infarct and penumbra) volumetric with regard to arterial input function (AIF) selection in patients with acute stroke. Materials and Methods:Eighteen consecutive patients with symptoms of acute stroke underwent PCT at admission. Follow-up magnetic resonance imaging was obtained in all patients after 3.6 ± 1.7 days (range, 1.5–6 days). PCT maps were generated focusing on the anterior cerebral artery (ACA) and branches of the middle cerebral artery (MCA) ipsilateral and contralateral to the ischemic lesion as AIFs. Infarct, penumbra, and total ischemic lesion were delineated on cerebral blood flow (CBF) maps. CBF, cerebral blood volume (CBV), and mean transit time (MTT) were calculated in the ischemic regions as provided by the 3 different AIFs, the normality test was applied for the obtained parameters, and the values were correlated (Pearson's correlation coefficient). Volumes of the ischemic regions (as obtained by the different AIFs) also were correlated and compared (paired t test) to the follow-up infarct volume. Results:The CBF and CBV values obtained by the different AIFs in the infarct, penumbra, and total ischemic lesion were significantly correlated (r = 0.94–0.96, P ≤ 0.01). Only in the infarct region calculated MTT values were correlated (r = 0.88–0.91, P < 0.05) between the different AIFs groups. High correlation coefficients (r = 0.79–0.91, P < 0.001) were observed between the admission PCT infarct and total ischemic volume and the MRI follow-up infarct volume. ACA as AIF provided the best correlations (r = 0.91, P = 0.0002) with the follow-up measurements. No statistically significant difference was found between the 3 different AIF-estimated admission total ischemic volumes and the follow-up infarct volume. Conclusions:The AIF selection in the ACA as well as in the ipsilateral (to the hypoperfused area) or contralateral branches of the MCA has no statistically significant impact on the calculation of the CBF, CBV values, and the volume estimation of the ischemic region in the acute stroke patients.
Self-calibration of metrics of Java methods

Self-calibration is a new technique for the study of internal product metrics, sometimes called "observations" and calibrating these against their frequency, or probability of occurring in common programming practice (CPP). Data gathering and analysis of the distribution of observations is an important prerequisite for predicting external qualities, and in particular software complexity. The main virtue of our technique is that it eliminates the use of absolute values in decision-making, and allows gauging local values in comparison with a scale computed from a standard and global database. Method profiles are introduced as a visual means to compare individual projects or categories of methods against the CPP. Although the techniques are general and could in principle be applied to traditional programming languages, the focus of the paper is on object oriented languages using Java. The techniques are employed in a suite of 17 metrics in a body of circa thirty thousand Java methods.
Guidelines of The Korean Association of Urogenital Tract Infection and Inflammation : Recurrent Urinary Tract Infection

Seung-Ju Lee, Hyun-Sop Choe, Yong Gil Na, Ki Ho Kim, Jae Heon Kim, Hong Chung, Jae Min Chung, Jae Hung Jung, Hoon Choi, Sun-Ju Lee, Yong-Hyun Cho Department of Urology, College of Medicine, The Catholic University of Korea, Seoul, Department of Urology, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Department of Urology, Dongguk University Gyeongju Hospital, Gyeongju, Department of Urology, Soonchunhyang University Seoul Hospital, Sonchunhyang University College of Medicine, Seoul, Department of Urology, Konkuk University School of Medicine, Chungju, Department of Urology, Pusan National University School of Medicine, Yangsan, Department of Urology, Yonsei University Wonju College of Medicine, Wonju, Department of Urology, Korea University Ansan Hospital, Korea University College of Medicine, Ansan, Department of Urology, Kyung Hee University School of Medicine, Seoul, Korea
Recognition and treatment of autonomic disturbances in Parkinson’s disease

Symptoms of dysautonomia are common in Parkinson’s disease (PD), and almost all the functional autonomic subsystems can be involved in PD. However, they are still under-recognized in everyday clinical practice. Autonomic dysfunction can be observed in the early stages of PD, affect a substantial proportion of patients, impact quality of life and can also help in differential diagnosis. This review aims to provide an overview of the pathophysiology, clinical manifestations, relevant examination and treatment of cardiovascular, gastrointestinal, urogenital, thermoregulatory and pupil autonomic dysfunctions in Parkinson’s disease.
Latency and Resource Utilization Analysis for V2X Communication over LTE MBSFN Transmission

In this paper, we investigate the performance of LTE Multicast-Broadcast Single-Frequency Networks (MBSFN). LTE-MBSFN is viewed as one of the most promising candidates for vehicular communications which can enhance reliability of vehicular application traffic. This is achieved due to the possibility to efficiently support message exchange in-between vehicles by multicasting information to several vehicles in parallel (point-to-multipoint transmission) employing an Multimedia Broadcast/Multicast Service (MBMS). We investigate two metrics to gauge the performance of MBMS/MBSFN transmissions in comparison with standard unicast transmissions for vehicular communications: latency of packet delivery and overhead caused by vehicular traffic, i.e., network utilization. Additionally, we present technique of prediction of system behaviour and explore the influence of transmission bandwidth and transmission rate on mentioned metrics.
Application of near-infrared spectroscopy for the evaluation of placental oxygenation

Aims: As the utero-placental circulation have major impact on the fetus, and the placental function can be criti- cal for determining fetal conditions, the placental oxygenation status was investigated. Methods: Near-infrared spectroscopy (NIRS) is a non-invasive technique used for the evaluation of regional tissue oxy- genation in a number of organs. The trans-abdominal NIRS was developed as a non-invasive technique for monitoring placental oxygenation, which was evaluated by the ratio of oxygenated hemoglobin to total hemoglobin (%) (tissue oxy- genation index ,TOI) values. The near-infrared light was confirmed to reach the placenta using the NIRS probe with an in- ter-optode distance of 4.5 cm and the NIRO apparatus (Hamamatsu Photonics, Hamamatsu, Japan). Results: Placental TOI values in pregnant women with pregnancy-induced hypertension and intrauterine fetal growth re- striction were significantly higher than those of pregnant women without complications, although there were no differ- ences of TOI values between the women with threatened preterm delivery and those without complications. Conclusion: Non-invasive monitoring of placental tissue oxygenation assessed by NIRS for the study of utero-placental function may have a high potential for clinical application, particularly in prenatal management.
The Interplay between Maternal Nutrition and Stress during Pregnancy: Issues and Considerations

Background: Several studies about humans and animals have separately examined the effects of prenatal nutrition and stress on fetal development, pregnancy, and birth outcomes, and subsequent child health and disease risk. Although substantial evidence from non-pregnant literature supports the presence of bidirectional interactions between nutrition and stress at various psychological, behavioral, and physiological levels, such interaction effects have not yet been systematically examined in the context of pregnancy. Summary: This paper discusses the multifaceted and multilevel relationship between nutrition and stress. It then reviews the currently available observational and experimental evidence in animals and humans regarding the interplay between maternal psychosocial stress, dietary intake, and nutritional state during pregnancy, and implications for maternal and child health-related outcomes. Key Messages: During pregnancy, maternal psychosocial stress, dietary behavior, and nutritional state likely regulate and counter-regulate one another. Emerging evidence suggests that omega-3 fatty acids may attenuate maternal psychosocial stress, and that high maternal pre-pregnancy body mass index exacerbates unhealthy dietary behaviors under high-stress conditions. Longitudinal studies are warranted in order to understand the interplay between prenatal psychosocial stress, diet, and stress- and nutrition-related biomarkers to obtain further insight and inform the development and design of future, more effective intervention trials for improved maternal and child health outcomes.
Proteins induced by anaerobiosis in Escherichia coli

The contribution of protein induction and repression to the adaptation of cells to changes in oxygen supply is only poorly understood. We assessed this contribution by measuring the levels of 170 individual polypeptides produced by Escherichia coli K-12 in cells growing aerobically or anaerobically with and without nitrate. Eighteen reached their highest levels during anaerobic growth. These 18 polypeptides include at least 4 glycolytic enzymes and pyruvate formate-lyase (beta-subunit). Most of these proteins were found at significant levels during aerobic growth and appeared to undergo metabolic regulation by stimuli other than anaerobiosis. Anaerobic induction ratios ranged from 1.8- to 11-fold, and nitrate antagonized the anaerobic induction of all of the proteins except one. The time course of synthesis of the proteins after shifts in oxygen supply revealed at least three distinct temporal patterns. These results are discussed in light of known physiological alterations associated with changes in oxygen availability.
Quickest detection problems for Bessel processes

Consider the motion of a Brownian particle that initially takes place in a twodimensional plane and then after some random/unobservable time continues in the three-dimensional space. Given that only the distance of the particle to the origin is being observed, the problem is to detect the time at which the particle departs from the plane as accurately as possible. We solve this problem in the most uncertain scenario when the random/unobservable time is (i) exponentially distributed and (ii) independent from the initial motion of the particle in the plane. The solution is expressed in terms of a stopping time that minimises the probability of a false early detection and the expected delay of a missed late detection.
Image Deconvolution With Multi-Stage Convex Relaxation and Its Perceptual Evaluation

This paper proposes a new image deconvolution method using multi-stage convex relaxation, and presents a metric for perceptual evaluation of deconvolution results. Recent work in image deconvolution addresses the deconvolution problem via minimization with non-convex regularization. Since all regularization terms in the objective function are non-convex, this problem can be well modeled and solved by multi-stage convex relaxation. This method, adopted from machine learning, iteratively refines the convex relaxation formulation using concave duality. The newly proposed deconvolution method has outstanding performance in noise removal and artifact control. A new metric, transduced contrast-to-distortion ratio (TCDR), is proposed based on a human vision system (HVS) model that simulates human responses to visual contrasts. It is sensitive to ringing and boundary artifacts, and very efficient to compute. We conduct comprehensive perceptual evaluation of image deconvolution using visual signal-to-noise ratio (VSNR) and TCDR. Experimental results of both synthetic and real data demonstrate that our method indeed improves the visual quality of deconvolution results with low distortions and artifacts.