Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA sequencing reveals a complete but an unconventional type of dosage compensation in the domestic silkworm Bombyx mori

Sex chromosomal dose difference between sexes is often normalized by a gene regulatory mechanism called dosage compensation (DC). Studies indicate that DC mechanisms are generally effective in XY rather than ZW systems. However, DC studies in lepidopterans (ZW system) gave bewildering results. In Manduca sexta, DC was complete and in Plodia interpunctella, it was incomplete. In Heliconius species, dosage was found to be partly incomplete. In domesticated silkmoth Bombyx mori, DC studies have yielded contradictory results thus far, showing incomplete DC based on microarray data and a possible existence of DC based on recent reanalysis of same data. In this study, analysis of B. mori sexed embryos (78, 96 and 120 h) and larval heads using RNA sequencing suggest an onset of DC at 120 h. The average Z-linked expression is substantially less than autosomes, and the male-biased Z-linked expression observed at initial stages (78 and 96 h) gets almost compensated at 120 h embryonic stage and perfectly compensated in heads. Based on these findings, we suggest a complete but an unconventional type of DC, which may be achieved by reduced Z-linked expression in males (ZZ). To our knowledge, this is the first next-generation sequencing report showing DC in B. mori, clarifying the previous contradictions.
Chlamydia trachomatis in pregnant women

contains an immuno-dominant region with repetitive epitopes. Eur. J. Immunol. 15:747-749. 5. Santoro, F. , D. Afchain, R. Pierce, J. Y. Cesbron, G. Ovlaque, and A. Capron. 1985. Serodiagnosis of toxoplasma infection using a purified parasite protein (P30). Clin. Exp. Immunol. 62:262-269. 6. Slizewicz, B. , J. Y. Cesbron, A. Capron, and J. F. Delagneau. 1985. Diagnostic de la toxoplasmose: utilisation d'un anticorps monoclonal anti-P30 K dans un test ELISA de dépistage des IgM sériques par immunocapture. Ann. Biol. Clin. 43:585-617.
Adaptive parameter estimation with guaranteed prescribed performance

This paper presents a novel adaptive parameter estimation framework for linearly parameterized nonlinear systems, which can guarantee the prescribed error convergence performance (e.g. overshoot, convergence rate). By introducing appropriate filter operations, an explicit expression of parameter estimation error is obtained. Then a prescribed performance function (PPF) and the associate transform are proposed, such that parameter estimation can be reduced as a regulation problem of the transformed system by designing an adaptive law. To this end, a novel adaptive law based on the obtained parameter estimation error is developed, such that the error convergence can be guaranteed to be within the prescribed bound. The parameter estimation is obtained without using the measurement of the state derivatives and is independent of any observer/predictor design. Simulation results illustrate that the proposed methods can achieve faster transient and better steady-state performance than some available results.
Trapping zones: The effect of fracture roughness on the directional anisotropy of fluid flow and colloid transport in a single fracture

In this paper we quantify the influence of geometry and distribution of surface roughness to the directional anisotropy of fluid flow and transport properties of a single fracture. Roughness of fractures appears to have first order control on how they behave mechanically and hydraulically. We directly quantified the surface roughness of a single fracture using high‐resolution laser scanning confocal microscopy. This roughness was input into directly coupled numerical models of fluid flow and transport. We simulated the transport of colloids (microspheres) through the fracture. We found tailing in the breakthrough and sensitivity of the breakthrough to flow direction in the fracture. Microspheres were observed to be trapped in low velocity zones on the lee side of fracture walls. This was not observed in smooth or sinusoidal varying fracture wall geometries. These observations have significant implications for quantifying the transport of dissolved and solid phase materials (colloids) through fractured rock.
Full abstraction for nondeterministic dataflow networks

The problem of finding fully abstract semantic models for nondeterministic dataflow networks is discussed. The author presents a result indicating that there exist nondeterministic networks using only bounded choice for which the input-output relation is not compositional. It is shown that the trace semantics is fully abstract for all nondeterministic as well as deterministic networks. <<ETX>>
Seasonal occurrence of Aphis glycines and physiological responses of soybean plants to its feeding

The soybean aphid Aphis glycines Matsumura (Hemiptera: Aphididae) is an important pest of soybean in China. To monitor and manage this pest effectively it is necessary to understand its population dynamics and demographics, as well as the physiological responses of soybean plants to its feeding. In this study, using field surveying and suction‐trap monitoring, we investigated the population dynamics of the soybean aphid in Xiuyan County, Liaoning Province in northeastern China during 2009–2012. The results indicated that the population dynamics of the soybean aphid followed a unimodal curve distribution, with the insect generally colonizing soybean fields from the middle of June to early July and the population reaching a peak between early July and early August. On the whole, soybean aphids occurred in suction‐traps at least 2 weeks earlier than they were found in field surveys. A total of 72 alates were collected by suction‐trapping over the 4 years, with the earliest alate captures occurring on 28 May in 2009, 2011, 2012 and 4 June in 2010. The life table parameters clearly showed that this aphid had a short doubling time (4.73 ± 0.21 days), and 7.36 ± 0.98 nymphs were produced by a soybean aphid adult during its lifetime (13.57 ± 0.30 days). Finally, biochemical assays indicated that the amount of malondialdehyde and the activities of four defense‐related enzymes in soybean leaves significantly changed between 0 day and 7 days of aphid infestation. Polyphenol oxidase (PPO) and catalase (CAT) activities increased more dramatically after 1 day of aphid feeding. In addition, significantly higher levels of superoxide dismutase and CAT were found after aphid feeding for 7 days, whereas there was no significant change in the activities of peroxidase and PPO. Consequently, this study will be beneficial in determining the seasonal occurrence of the soybean aphid and selecting insect‐resistant soybean varieties, and thus in developing a theoretical framework for appropriate management strategies.
Design and simulation of RFID tag with artificial magnetic conductor at 0.92 GHz for green projects

Radio Frequency Identification (RFID) tag and sensor combination has become increasingly popular in green projects. Artificial Magnetic Conductor (AMC) is commonly used to enhance the performance of an antenna. In this paper, a new dipole AMC is proposed for 0.92 GHz Radio Frequency Identification tag application. The new square AMC structure optimized with multiple slots produced a bandwidth of 2.31 % using FR4 substrate. The combination of dipole antenna with AMC 2×1 array has further enhanced the performance of the antenna with return loss = -23.01 dB, directivity = 6.01 dBi and gain = 4.53 dB.
Fast repetitive control Scheme for shunt active power filter in Synchronous Rotational Frame

This paper proposes a fast repetitive control (FRC) scheme for the shunt active power filter (SAPF) in the three-phase three-wire system, which can improve the dynamic response performance of the SAPF compared with the conventional RC strategy (CRC). The FRC is designed in the synchronous rotational frame (SRF) which can reduce the repetitive period to one-sixth of the fundamental cycle. A fractional delay (FD) filter is employed to eliminate the tracking error due to the grid frequency variations. To improve the performance of the SAPF in weak grid situation, this paper also proposed a close loop harmonic detection scheme so that the reference value can track the varied harmonic currents rapidly. Compared with the conventional open loop detection scheme, the compensation performance is highly improved. Simulations and experiments verified the proposed scheme.
Unconventional RORγt+ T Cells Drive Hepatic Ischemia Reperfusion Injury

An emerging body of evidence suggests a pivotal role of CD3+ T cells in mediating early ischemia reperfusion injury (IRI). However, the precise phenotype of T cells involved and the mechanisms underlying such T cell–mediated immune responses in IRI, as well as their clinical relevance, are poorly understood. In this study, we investigated early immunological events in a model of partial warm hepatic IRI in genetically targeted mice to study the precise pathomechanistic role of RORγt+ T cells. We found that unconventional CD27−γδTCR+ and CD4−CD8− double-negative T cells are the major RORγt-expressing effector cells in hepatic IRI that play a mechanistic role by being the main source of IRI-mediating IL-17A. We further show that unconventional IRI-mediating T cells are contingent on RORγt, as highlighted by the fact that a genetic deficiency for RORγt, or its therapeutic antagonization via digoxin, is protective against hepatic IRI. Therefore, identification of CD27−γδTCR+ and CD4−CD8− double-negative T cells as the major source of IL-17A via RORγt in hepatic IRI opens new therapeutic options to improve liver transplantation outcomes.
Hamstring shortening in healthy adults.

Hamstring shortening (HS) causes changes in the posture and walking ability in spastic children, however, there are no studies defining the abnormalities in patellar alignment in individuals with HS.Twenty-five patients with a primary complaint of anterior knee pain, having HS detected at physical examination, and 11 healthy individuals without any HS or knee discomfort as a control group are included in this study. Serial x-rays of the spine, pelvis and knee are taken and knee x-rays are evaluated for the position of the patella in both groups.In patients with Knee Extension Deficit (KED) ≥ 60°, the Blackburne-Peel ratio is lower and the Insall-Salvati ratio is higher than the other groups, denoting a cephalic location of the patella (p < 0.05). There are no changes in the congruency and sulcus angles between the HS and control groups. Vertebral and pelvic changes correlate well with the literature, confirming that significant alterations occur after 60° of KED in adults.The extensor mechanism of the knee is affected and patella is located higher than normal in patients with severe HS, which may be a cause for knee discomfort. In the light of these findings, a routine knee extension deficit examination can be suggested in the initial evaluation of knee discomfort.
Does intra‐uterine growth discordance predict differential risk for adult psychiatric disorder in a population‐based sample of monozygotic twins?

&NA; The study of discordant monozygotic twins may identify important developmental risk factors for adult psychiatric disorder. Differential experience in utero is one candidate environmental risk factor that may distinguish monozygotic twins. In this report, we examine whether intra‐pair differences in birth weight predicts discordance for adult psychiatric disorders in 527 female monozygotic twin pairs from a population‐based twin registry. Twins were personally interviewed about their lifetime history of DSM‐III‐R alcoholism, anorexia nervosa, bulimia nervosa, generalized anxiety disorder, major depression, panic disorder, social phobia and simple phobia. Birth weight was estimated from birth certificates, or from retrospective maternal, paternal and self‐reports. Conditional logistic regression is used to characterize the association between intra‐pair differences in birth weight and discordance for psychiatric disorder in monozygotic twins. The twin with the heavier birth weight in discordant pairs is (insignificantly) more likely to have a history of alcoholism or bulimia. The twin with the lighter birth weight in discordant pairs is (insignificantly) more likely to have a history of major depression, simple phobia, panic disorder, anorexia nervosa, social phobia or generalized anxiety disorder. For all psychiatric disorders examined, the lighter (or heavier) co‐twin at birth is not systematically the affected twin within discordant pairs.
The predictability study of channel state duration based on Hurst index

Spectrum prediction is one key enabling method for cognitive radio to improve spectrum utilization. Different from the traditional methods which predict the spectrum state slot-by-slot, in this paper we investigate the issue of prediction analysis of channel state duration (CSD). Specifically, we first introduce the concept of Hurst index to characterize the predictability between different scales of historical data and use the method of R/S (rescaled range) analysis the Hurst index of three different kinds of Large-Scale data and validate if we can obtain best prediction result from high predictability. Then, we introduce a pattern matching approach to validate the practical prediction performance. Furthermore, we focus on the predictability in small-scale data and find sometimes it performs even better than using large-scale data. Moreover, real world spectrum measurements are used to show that selecting historical data based on the predictability theory in this paper, we can smartly improve the predictive efficiency and enhance the prediction accuracy.
Isomorphic but not lower base-isomorphic cylindric set algebras

Abstract This paper belongs to cylindric-algebraic model theory understood in the sense of algebraic logic. We show the existence of isomorphic but not lower base-isomorphic cylindric set algebras. These algebras are regular and locally finite. This solves a problem raised in [N 83] which was implicitly present also in [HMTAN 81]. This result implies that a theorem of Vaught for prime models of countable languages does not continue to hold for languages of any greater power.
Breast Cancer and Symptom Clusters During Radiotherapy

Background: Symptom clusters assessment shifts the clinical focus from a specific symptom to the patient’s experience as a whole. Few studies have examined breast cancer symptom clusters during treatment, and fewer studies have addressed symptom clusters during radiation therapy (RT). The theoretical underpinning of this study is the Symptoms Experience Model. Research is needed to identify antecedents and consequences of cancer-related symptom clusters. Objective: The present study was intended to determine the clustering of symptoms during RT in women with breast cancer and significant correlations among the symptoms, individual characteristics, and mood. Methods: A secondary data analysis from a descriptive correlational study of 93 women at weeks 3 to 7 of RT from centers in the mid-Atlantic region of the United States, Symptom Distress Scale, the subscales of the Positive and Negative Affect Scale, Life Orientation Test, and Self-transcendence Scale were completed. Results: Confirmatory factor analysis revealed symptoms grouped into 3 distinct clusters: pain-insomnia-fatigue, cognitive disturbance-outlook, and gastrointestinal. The pain-insomnia-fatigue and cognitive disturbance-outlook clusters were associated with individual characteristics, optimism, self-transcendence, and positive and negative mood. The gastrointestinal cluster correlated significantly only with positive mood. Conclusions: This study provides insight into symptoms that group together and the relationship of symptom clusters to antecedents and mood. Implications for Practice: These findings underscore the need to define and standardize the measurement of symptom clusters and understand variability in concurrent symptoms. Attention to symptom clusters shifts the clinical focus from a specific symptom to the patient’s experience as a whole and helps identify the most effective interventions.
The expression of alpha‐haemolysin is required for Staphylococcus aureus phagosomal escape after internalization in CFT‐1 cells

Staphylococcus aureus colonizes the lungs of cystic fibrosis patients and treatment with antibiotics usually results in recurrent and relapsing infections. We have shown that S. aureus can invade and replicate within a cystic fibrosis epithelial cell line (CFT‐1), and that these internalized bacteria subsequently escape from the endocytic vesicle. The accessory gene regulator, agr, in S. aureus has been shown to control the expression of a large number of secreted toxins involved in virulence. Here we show that an agr mutant of S. aureus strain RN6390 was unable to escape from the endocytic vesicle after invasion of the CFT‐1 cells using markers of vesicular trafficking (LAMP‐1 and 2, LysoTracker and Vacuolar‐ATPase). Trafficking analysis of live S. aureus which did not express alpha‐haemolysin, a specific agr regulated toxin, revealed a defect in vesicular escape that was undistinguishable from the trafficking defect exhibited by the agr mutant. Furthermore, overexpression of alpha‐haemolysin under an inducible promoter in an agr mutant of S. aureus partially restored the phagosome‐escaping phenotype of an agr mutant. These results demonstrate that the expression of agr is required for vesicular escape, and that biologically active alpha‐haemolysin is required for S. aureus escape from the endocytic vesicle into the cytosol of CFT‐1 cells.
Correcting Inversion and Synchronization Errors Using Binary Neural Networks

A binary neural network is applied to the problem of error correction. The neural network will be implemented to correct both inversion and synchronization errors. Neural networks have been used before to correct inversion and synchronization errors, however, additional redundancy in the form of markers or watermarks were added to aid synchronization recovery. It is shown in this paper that it is not necessary to add markers or watermarks to the transmitted sequence in order to correct synchronization errors. A combination of inversion and synchronization errors can also be corrected. A moment balanced Low Density Parity Check (LDPC) code will be used as a codebook.
Fitness Modeling With Markov Networks

Fitness modeling has received growing interest from the evolutionary computation community in recent years. With a fitness model, one can improve evolutionary algorithm efficiency by directly sampling new solutions, developing hybrid guided evolutionary operators or using the model as a surrogate for an expensive fitness function. This paper addresses several issues on fitness modeling of discrete functions, particularly how modeling quality and efficiency can be improved. We define the Markov network fitness model in terms of Walsh functions. We explore the relationship between the Markov network fitness model and fitness in a number of discrete problems, showing how the parameters of the fitness model can identify qualitative features of the fitness function. We define the fitness prediction correlation, a metric to measure fitness modeling capability of local and global fitness models. We use this metric to investigate the effects of population size and selection on the tradeoff between model quality and complexity for the Markov network fitness model.
Adsorption, penetration and uncoating of herpes simplex virus.

Summary The interaction of herpes virus particles with BSC1 cells was studied with purified virus particles labelled in the DNA and coat proteins. Intact virions adsorbed to the cell within 3 hr, a process not affected by inhibitors of nucleic acid and protein synthesis. Heparin, a negatively charged polysaccharide, interfered with the interaction of the virions with the cell membrane, and released virions attached to the cell surface. After entering the cytoplasm, some virus particles were associated with large structures. The virus particles were uncoated by existing cellular enzymes and naked viral DNA, but not the coat proteins, was gradually transported into the nuclei.
Evolutionary history shapes the association between developmental instability and population‐level genetic variation in three‐spined sticklebacks

Developmental instability (DI) is the sensitivity of a developing trait to random noise and can be measured by degrees of directionally random asymmetry [fluctuating asymmetry (FA)]. FA has been shown to increase with loss of genetic variation and inbreeding as measures of genetic stress, but associations vary among studies. Directional selection and evolutionary change of traits have been hypothesized to increase the average levels of FA of these traits and to increase the association strength between FA and population‐level genetic variation. We test these two hypotheses in three‐spined stickleback (Gasterosteus aculeatus L.) populations that recently colonized the freshwater habitat. Some traits, like lateral bone plates, length of the pelvic spine, frontal gill rakers and eye size, evolved in response to selection regimes during colonization. Other traits, like distal gill rakers and number of pelvic fin rays, did not show such phenotypic shifts. Contrary to a priori predictions, average FA did not systematically increase in traits that were under presumed directional selection, and the increases observed in a few traits were likely to be attributable to other factors. However, traits under directional selection did show a weak but significantly stronger negative association between FA and selectively neutral genetic variation at the population level compared with the traits that did not show an evolutionary change during colonization. These results support our second prediction, providing evidence that selection history can shape associations between DI and population‐level genetic variation at neutral markers, which potentially reflect genetic stress. We argue that this might explain at least some of the observed heterogeneities in the patterns of asymmetry.
Autopsy Proven Pulmonary Embolism in Hospital Patients: Are We Detecting Enough Deep Vein Thrombosis?

To investigate the present status of pulmonary embolism as a cause of death in a general hospital patient population, a 5-year retrospective study of all autopsy reports and associated hospital records was undertaken. Pulmonary embolism was thought to be the cause of death in 239 of 2388 autopsies performed (10%): 15% of these patients were aged less than 60 years and 68% did not have cancer. Of these patients, 83% had deep-vein thrombosis (DVT) in the legs at autopsy, of whom only 19% had symptoms of DVT before death. Only 3% of patients who had DVT at autopsy had undergone an investigation for such before death. Twenty-four per cent of patients who died from pulmonary embolism had undergone surgery a mean of 6.9 days before. Screening tests for DVT should be applied widely in the hospital population.