Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancer action in trans is permitted throughout the Drosophila genome

Interactions between paired homologous genes can lead to changes in gene expression. Such trans-regulatory effects exemplify transvection and are displayed by many genes in Drosophila, in which homologous chromosomes are paired somatically. Transvection involving the yellow cuticle pigmentation gene can occur by at least two mechanisms, one involving the trans-action of enhancers on a paired promoter and a second involving pairing-mediated bypass of a chromatin insulator. A system was developed to evaluate whether the action of the yellow enhancers in trans could be reconstituted outside of the natural near telomeric location of the yellow gene. To this end, transgenic flies were generated that carried a yellow gene modified by the inclusion of strategically placed recognition sites for the Cre and FLP recombinases. Independent action of the recombinases produced a pair of derivative alleles, one enhancerless and the other promoterless, at each transgene location. Transvection between the derivatives was assessed by the degree of interallelic complementation. Complementation was observed at all eight sites tested. These studies demonstrate that yellow transvection can occur at multiple genomic locations and indicate that the Drosophila genome generally is permissive to enhancer action in trans.
Verbal and Nonverbal Correlates for Depression: A Review

Depression covers a substantial part of mental health problems worldwide. Currently, the occurrence of symptoms listed in DSM-IV is based on its diagnosis. However, there are also additional behavioral features distinguishing between depressed and healthy individuals that do not yet have the official status of symptoms. This article aims to provide a comprehensive literature overview of the distinctive characteristics of verbal and nonverbal behavior of depressed patients. Clinical psychology and psychiatry may benefit from the availability of better, more objective indicators of verbal and nonverbal functioning, which may be useful for diagnosis, prognosis, and treatment evaluation.
Muscle Tensing During Standing: Effects on Cerebral Tissue Oxygenation and Cerebral Artery Blood Velocity

Background and Purpose— When standing up causes dizziness, tensing of the leg muscles may alleviate the symptoms. We tested the hypothesis that leg tensing improves orthostatic tolerance via enhanced cerebral perfusion and oxygenation. Methods— In 10 healthy young adults, the effects of leg tensing on transcranial Doppler–determined middle cerebral artery (MCA) mean blood velocity (Vmean) and the near-infrared spectroscopy–determined frontal oxygenation (O2Hb) were assessed together with central circulatory variables and an arterial pressure low-frequency (LF) (0.07 to 0.15 Hz) domain evaluation of sympathetic activity. Results— Standing up reduced central venous pressure by (mean±SEM) 4.3±2.6 mm Hg, stroke volume by 49±7 mL, cardiac output by 1.9±0.4 L/min, and mean arterial pressure at MCA level by 9±4 mm Hg, whereas it increased heart rate by 30±4 beats per minute (P <0.05). MCA Vmean declined from 67±4 to 56±3 cm/s, O2Hb decreased by 7±2.8%, and LF spectral power increased (P <0.05). Leg tensing increased central venous pressure by 1.4±2.7 mm Hg and cardiac output by 1.8±0.4 L/min with no significant effect on blood pressure, whereas heart rate decreased by 11±3 beats per minute (P <0.05). MCA Vmean increased to 63±3 cm/s and O2Hb increased by 2.1±2.6%, whereas LF power declined (P <0.05). Within 2 minutes after leg tensing, these effects had disappeared. Conclusions— During standing, tensing of the leg muscles attenuates a reduction in cerebral perfusion and oxygenation as it stabilizes central circulatory variables and reduces sympathetic activity.
Multiplex PCR testing for nine different sexually transmitted infections

Current sexually transmitted infection (STI) testing is not optimal due to delays in reporting or missed diagnoses due to a lack of comprehensive testing. The FilmArray® (BioFire Diagnostics, LLC, Salt Lake City, Utah) is a user-friendly, fully automated, multiplex PCR system that is being developed for rapid point-of-care use. A research-use-only STI panel including multiple PCR primer sets for each organism was designed to detect Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, Trichomonas vaginalis, Mycoplasma genitalium, Ureaplasma urealyticum, Haemophilus ducreyi, and herpes simplex virus (HSV) types 1 and 2. Standard clinical testing included Gram stain, nucleic acid amplification, wet mount examination, herpes simplex virus culture, and syphilis IgG. Standard clinical tests were not available for all the organisms tested by the FilmArray STI panel. Two hundred and ninety-five clinical specimens from 190 subjects were directly compared to standard testing. Urine (n = 146), urethral/cervical swabs (31), oral swabs (60), rectal swabs (43), and ulcer swabs (15) were tested. Among the tested samples, FilmArray detected C. trachomatis in 39 (13%), N. gonorrhoeae in 20 (7%), T. vaginalis in nine (3%), HSV 1 in five (2%), HSV 2 in five (2%), U. urealyticum in 36 (12%), M. genitalium in eight (3%), and T. pallidum in 11 (4%). Concordance between the FilmArray STI panel and standard nucleic acid amplification testing for C. trachomatis was 98% and for N. gonorrhoeae was 97%. Multiplex PCR STI testing has the potential to improve public health by providing rapid, sensitive, and reliable results within the clinic or nearby laboratory.
Attitudes about Death, Dying, and Terminal Care: Differences among Groups at a University Teaching Hospital

Attitudes of eight hospital groups on several aspects of terminal care were studied by means of a questionnaire responded to by 1080 people at a university teaching hospital. The questionnaire contained statements about terminally ill patients, settings for their care, terminally ill children, discussing death and terminal care, and meeting the emotional needs of patients. Responses of the groups, which included physicians, residents, nurses, aides, and orderlies, did not differ on general statements about terminal care. On more specific statements, responses from some groups differed significantly from other groups' responses. A suggested interpretation was that perception of personal involvement in the activity implied by the statements influenced responses by some groups. Compared to other groups, physicians responded conservatively to statements about terminal care. Differences in attitudes among hospital groups require further investigation, particularly with respect to their effect on coordination of patients' care. In addition, the consistency of attitudes across various aspects of terminal care needs systematic study.
Control in Multinational Corporations (MNCs): The Case of Korean Manufacturing Subsidiaries

Using both agency theory and comparative national culture frameworks, this study investigated factors determining the degree and type of control used by American and Japanese MNCs on their Korean subsidiaries. Two characteristics of MNCs affected the control they exerted—the degree of MNCs’ ownership, which affected the amount of control, and the nationality of the MNC’s headquarters, which affected the type of control exerted. As predicted, the size of the subsidiary relative to the MNC, moderated the relationship between the degree of ownership and amount of output control the MNC exerted. Overall, the study supported the usefulness of agency theory in explaining the degree of management control exerted, while national culture accounted for the type of control exerted.
Safety critical systems based on formal models

The Ravenscar profile for high integrity systems using Ada 95 is well defined in all real-time aspects. The complexity of the run-time system has been reduced to allow full utilization of formal methods for applications using the Ravenscar profile. In the Mana project a tool set is being developed including a formal model of a Ravenscar compliant run-time system, a gnat compatible run-time system, and an ASIS based tool to allow for the verification of a system including both COTS and code that is reused.
The organization of the motoneurons innervating the axial musculature of vertebrates. I. Goldfish (Carassius auratus) and mudpuppies (Necturus maculosus)

The motoneurons innervating different regions of the myomeres in goldfish and mudpuppies were examined by applying HRP to the musculature or to branches of spinal nerves. In goldfish, the populations of motoneurons innervating epaxial or hypaxial muscle occupied similar positions in the motor column and had similar size distributions. There was no relationship between the size or location of a motoneuron in the motor column and the dorsoventral location of the muscle it innervated in the myomeres. Instead, different populations of motoneurons innervated the functionally different red and white musculature. The red muscle was innervated only by small motoneurons that occupied the ventral portion of the motor column. Their small axons passed lateral to the Mauthner axon in the cord, and most of them traveled in a separate branch of each spinal nerve that ran in the horizontal septum to the red muscle. The white muscle was innervated by a population of motoneurons that did not innervate red. They were large and they occupied a characteristic position in the extreme dorsal part of the motor column. Their large axons traveled medial to the Mauthner axon in the cord and entered branches of spinal nerves running deep in the epaxial or hypaxial muscle. The white muscle was probably also innervated by some smaller motoneurons similar to those innervating red; however, these may have been motoneurons whose axons ran through white muscle to reach other muscle. The large motoneurons innervating only white muscle are similar to the primary motoneurons identified in developmental studies in teleosts (Myers: Soc. Neurosci. Abstr. 9:848, '83); the smaller ones, innervating both red and white, are like secondary motoneurons. Therefore, in goldfish, motoneurons having different morphology and developmental history also innervate different regions in the myomeres.
HISTOPATHOLOGICAL CHANGES IN LIVER AND GILL EPITHELIUM OF NILE TILAPIA, OREOCHROMIS NILOTICUS, EXPOSED TO WATERBORNE COPPER

Nile tilapia, Oreochromis niloticus, of both sexes were reared in freshwater and exposed to 0.5, 1.0 and 2.5mg L-1 of waterborne copper for a period of 21 days. Liver and gill samples were collected after 21 days of exposure to copper and lesions were analyzed by light microscopy. The main histopathological changes observed in gills exposed to the highest concentration were edema, lifting of lamellar epithelia and an intense vasodilatation of the lamellar vascular axis. Although less frequent, lamellar fusion caused by the filamentar epithelium proliferation and some lamellar aneurisms were also found. The liver of control group exhibited a quite normal architecture, while the fish exposed to copper showed vacuolation and necrosis. These hepatic alterations were more evident in fish exposed to 1.0 and 2.5mg L-1 copper concentrations. The number of hepatocytes nucleus per mm2 of hepatic tissue decreased with the increase of copper concentration. In contrast, the hepatic somatic index was high in fish exposed at 2.5mg L-1 of copper. In short, this work advance new knowledge as influence of copper in the gill and liver histology of O. niloticus and demonstrated that their effects could be observed at different concentrations.
The psychology of gratitude

A hala gyakorta atelt tarsas erzelmeink egyike. Jellemzően olyan helyzetekhez kotődik, amelyekben azt eszleljuk, hogy a masik szemely (szandekos) cselekvese rank nezve pozitiv kovetkezmennyel jar, vagyis szamunkra valamilyen modon hasznos. A hala megjelenhet vallasi kontextusba agyazottan vagy attol fuggetlenul, egy olyan altalanosabb eletszemlelet reszekent is, amely az eletunk pozitiv aspektusainak felismeresevel es fokozott ertekelesevel fugg ossze. A ketezres evektől kezdve (dontően a pozitiv pszichologia ternyeresehez kapcsolodoan) ugrasszerűen megnőtt a halaval kapcsolatos tudomanyos publikaciok, azon belul is főkent a hala es egyes szemelyisegvonasok, a jollet, a pszichopatologiak, a tarsas kapcsolatok es a megkuzdes osszefuggeseit feltaro empirikus kutatasok szama. A jelen tanulmany celja egyfelől annak bemutatasa, hogyan gondolkodik a pszichologia tudomanya a hala termeszeteről, milyen modon konceptualizalja es teszi merhetőve azt; masreszt azoknak a kutatasi eredmenyeknek az attekintese, amelyek.
A conical laser light-sectioning method for navigation of Autonomous Underwater Vehicles for internal inspection of pipelines

This paper presents a novel sensing method for navigation of Autonomous Underwater Vehicles, AUVs, through pipelines to conduct autonomous internal inspection. Unlike remotely operated pipe inspection robots, AUVs do not have an umbilical cable and so they can easily maneuver through bent sections of pipelines and the distance they can cover is not restricted by the length of the cable. Presently pipe inspection robots come in contact with the walls of the pipe during their operation. However old and aged pipelines may have loose corroded materials or biological growth which may get detached and pollute the fluid or further damage pipe interior when the pipe inspections robots touch the walls. AUVs can operate without coming in contact with the pipe wall and so this technique is a non-contact measurement and inspection technique. The proposed navigation sensor makes use of computer vision techniques to estimate the relative position and orientation of the vehicle inside the pipe with 4 degrees of freedom, which will enable the AUV to swim through the center of the pipe. A conical laser is projected on the pipe wall and the image of the laser is acquired by a camera. The features of the image are extracted and matched with a feature database prepared apriori. The position and orientation of the matching feature record in the database gives the estimated position and orientation of the vehicle. Experiments were conducted in dry experimental pipelines to verify the performance of the proposed sensor and results are presented. Control Simulations were performed to verify the ability of the sensor to navigate an AUV. The results of these controls simulated are also presented in this paper.
In the Nick of Time: Proactive Prevention of Obligation Violations

We present a system model, an enforcement mechanism, and a policy language for the proactive enforcement of timed provisions and obligations. Our approach improves upon existing formalisms in two ways: (1) we exploit the target system's existing functionality to avert policy violations proactively, rather than compensate for them reactively, and, (2) instead of requiring the manual specification of remedial actions in the policy, we automatically deduce required actions directly from the policy. As a policy language, we employ timed dynamic condition response (DCR) processes. DCR primitives declaratively express timed provisions and obligations as causal relationships between events, and DCR states explicitly represent pending obligations. As key technical results, we show that enforceability of DCR policies is decidable, we give a sufficient polynomial time verifiable condition for a policy to be enforceable, and we give an algorithm for determining from a DCR state a sequence of actions that discharge impending obligations.
Continuous limit of a crowd motion and herding model: Analysis and numerical simulations

In this paper we study the continuum limit of a cellular automaton model used for simulating human crowds with herding behaviour. We derive a system of non-linear partial differential equations resembling the Keller-Segel model for chemotaxis, however with a non-monotone interaction. The latter has interesting consequences on the behaviour of the model's solutions, which we highlight in its analysis. In particular we study the possibility of stationary states, the formation of clusters and explore their connection to congestion. We also introduce an efficient numerical simulation approach based on an appropriate hybrid discontinuous Galerkin method, which in particular allows flexible treatment of complicated geometries. Extensive numerical studies also provide a better understanding of the strengths and shortcomings of the herding model, in particular we examine trapping effects of crowds behind non-convex obstacles.
Learning Explanation-Based Search Control Rules for Partial Order Planning

This paper presents SNLP+EBL, the first implementation of explanation based learning techniques for a partial order planner. We describe the basic learning framework of SNLP+EBL, including regression, explanation propagation and rule generation. We then concentrate on SNLP+EBL's ability to learn from failures and present a novel approach that uses stronger domain and planner specific consistency checks to detect, explain and learn from the failures of plans at depth limits. We will end with an empirical evaluation of the efficacy of this approach in improving planning performance.
Memory-Based Feedback Controls to Support Groupware Coordination

In this paper we first present an empirical study of groupware use illustrating problems that users faced with restricted feedback about others' activities. Awareness can aid users in learning interdependencies, and in forming conventions to regulate system use and information-sharing. As a solution to providing awareness, we integrate the framework of organizational memory with intelligent agent technology to provide a coordination mechanism that enables the structuring of awareness events and gives information about the users' feedback control. In the proposed model, feedback control relationships are captured into a multilayered model of organizational memory and transferred to users by agents-facilitators. The approach is based on a system dynamics approach to organizational learning.
Security Economics in the HTTPS Value Chain

Even though we increasingly rely on HTTPS to secure Internet communications, several landmark incidents in recent years have illustrated that its security is deeply flawed. We present an extensive multi-disciplinary analysis that examines how the systemic vulnerabilities of the HTTPS authentication model could be addressed. We conceptualize the security issues from the perspective of the HTTPS value chain. We then discuss the breaches at several Certificate Authorities (CAs). Next, we explore the security incentives of CAs via the empirical analysis of the market for SSL certificates, based on the SSL Observatory dataset. This uncovers a surprising pattern: there is no race to the bottom. Rather, we find a highly concentrated market with very large price differences among suppliers and limited price competition. We explain this pattern and explore what it tells us about the security incentives of CAs, including how market leaders seem to benefit from the status quo. In light of these findings, we look at regulatory and technical proposals to address the systemic vulnerabilities in the HTTPS value chain, in particular the EU eSignatures proposal that seeks to strictly regulate HTTPS communications.
Respiratory and behavioral dysfunction following loss of the GABAA receptor α4 subunit

γ‐Aminobutyric acid type A (GABAA) receptor plasticity participates in mediating adaptation to environmental change. Previous studies in rats demonstrated that extrasynaptic GABAA receptor subunits and receptors in the pons, a brainstem region involved in respiratory control, are upregulated by exposure to sustained hypobaric hypoxia. In these animals, expression of the mRNA encoding the extrasynaptic α4 subunit rose after 3 days in sustained hypoxia, while those encoding the α6 and δ subunits increased dramatically by 2 weeks. However, the participation of extrasynaptic subunits in maintaining respiration in normoxic conditions remains unknown. To examine the importance of α4 in a normal environment, respiratory function, motor and anxiety‐like behaviors, and expression of other GABAA receptor subunit mRNAs were compared in wild‐type (WT) and α4 subunit‐deficient mice. Loss of the α4 subunit did not impact frequency, but did lead to reduced ventilatory pattern variability. In addition, mice lacking the subunit exhibited increased anxiety‐like behavior. Finally, α4 subunit loss resulted in reduced expression of other extrasynaptic (α6 and δ) subunit mRNAs in the pons without altering those encoding the most prominent synaptic subunits. These findings on subunit‐deficient mice maintained in normoxia, in conjunction with earlier findings on animals maintained in chronic hypoxia, suggest that the expression and regulation of extrasynaptic GABAA receptor subunits in the pons is interdependent and that their levels influence respiratory control as well as adaptation to stress.
Policy and practice in the anonymisation of linguistic data

What is anonymisation? This paper addresses this question, its relationship to linguistic data and its potential importance to corpus builders and users. It examines attitudes towards anonymisation such as hostility and disinterest and investigates relevant rights, responsibilities, and obligations. The paper then overviews and critiques methods of anonymisation and seeks to assess which items should be anonymised and which maintained. Finally, some troublesome and noteworthy cases are presented as evidence of the need for sensitive, realistic consideration of this issue. The paper was developed through consultation with researchers from the international community of corpus builders and users and, therefore, reflects the diversity of attittude and practice currently at large. It addresses this variability by finally proposing methods for systematic assessment of the need for anonymisation within individual corpora.
Vascular access and increased risk of death among hemodialysis patients.

BACKGROUND Hemodialysis with a venous catheter increases the risk of infection. The extent to which venous catheters are associated with an increased risk of death among hemodialysis patients has not been extensively studied. METHODS We conducted a retrospective cohort study of 7497 prevalent hemodialysis patients to assess the association between dialysis with a venous catheter and risk of death due to all causes and to infection. RESULTS A tunneled cuffed catheter was used for access in 12% of the patients and non-cuffed, not tunneled catheter in 2%. Younger age (P = 0.0005), black race (P = 0.0022), female gender (P = 0.0004), short duration since starting dialysis (P = 0.0003) and impaired functional status (P = 0.0001) were independently associated with increased use of catheter access. The proportion of patients who died was higher among those who were dialyzed with a non-cuffed (16.8%) or cuffed (15.2%) catheter compared to those dialyzed with either a graft (9.1%) or a fistula (7.3%; P < 0.001). The proportion of deaths due to infection was higher among patients dialyzed with a catheter (3.4%) compared to those dialyzed with either a graft (1.2%) or a fistula (0.8%; P < 0.001). The adjusted odds ratio (95% CI) for all-cause and infection-related death among patients dialyzed with a catheter was 1.4 (1.1, 1.9) and 3.0 (1.4, 6.6), respectively, compared to those with an arteriovenous (AV) fistula. CONCLUSION Venous catheters are associated with an increased risk of all-cause and infection-related mortality among hemodialysis patients.