Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization and Analysis of a Model of the Mammalian Circadian Clock

Circadian rhythms are found in plants, animals, fungi, and bacteria and are responsible for the regulation of many biological, physiological, behavioral, and metabolic activities. In mammals, the “master” clock is embedded in the suprachiasmatic nuclei (SCN) of the anterior hypothalamus. It is composed of thousands of cells signaling each other to synchronize and produce a unified rhythm. It is hypothesized that this communication enables the clock to rescue rhythms in gene knockout experiments that destroy oscillations at the single cell level. Henry Mirsky developed a model of this gene regulatory network within a single cell in 2009, but the published model is unable to accurately predict some knockout phenotypes in tissue. We determined that binary ‘arrhythmic’ and ‘rhythmic’ classifications were unsuitable for describing cellular behavior, so we utilized a novel ‘damped’ classification to describe cellular phenotype. We then used a genetic algorithm optimization technique to fit the model’s parameters to better mimic damped Cry1 single-cell knockout behavior. This optimization produced a parameter set that is able to correctly predict all single-cell knockout phenotypes as well as accurately predict the oscillatory phenotypes for two additional SCN tissue knockouts not previously demonstrated. The rescue of oscillations was confirmed by simulating SCN tissue—a process that involves reproduction of intercellular signaling and normal variation of unique cellular parameter sets. Further work seeks to explain the causes for the ability of this new parameter set to rescue oscillations in tissue simulations where the published parameter set was unsuccessful.
An Interactive Sketching Modeling System: Sketch3D

An interactive incremental sketching design system for rapidly constructing 3D solid models has been implemented. The system, dubbed Sketch3D, provides a calligraphic interface on which users can freely create feature-based solid models by sketching feature strokes with a pen or a mouse. Our method is very simple and efficient. Once the user finishes sketching the profile section and trajectory path of the feature, the system can automatically capture userpsilas design intention, and recognizes and beautifies the sketching strokes, then constructs the suitable sweeping feature-based model according to the location relationship between the profile section stroke and the trajectory path stroke. This method overcomes some deficiencies of traditional CAD systems to create conceptual models and some disadvantages of current sketch-based modeling systems. Some examples show that the sketching feature-based modeling method is suitable for rapidly expressing designerspsila creativity in the stage of conceptual design.
Optimal MAC state switching for cdma2000 networks

This paper deals with the performance modeling of the various MAC states as defined by the cdma2000 protocol. Our method uses a composite performance metric which has the capability of proportionally combining three basic parameters: channel utilization, waiting time and the saving in the signalling overhead. The scheduler at the base station is not only responsible for admitting new services into the system but also for switching the MAC states of a service depending on its activity. Since the true nature of the wireless data traffic is yet unknown, we use a mix of Poisson-distributed voice packets and Pareto-distributed data packets. We derive analytical expressions and also conduct simulation experiments to study the nature of the performance curve and thus compute the optimal values of expiration timers at which the MAC states should be switched such that the system performance is maximized. We show how our model can be made suitable for different systems by tuning the scaling functions (or weights) for each of the three performance parameters considered.
Five ways to hack and cheat with bring-your-own-device electronic examinations

Bring-your-own-device electronic examinations (BYOD e-exams) are a relatively new type of assessment where students sit an in-person exam under invigilated conditions with their own laptop. Special software restricts student access to prohibited computer functions and files, and provides access to any resources or software the examiner approves. In this study, the decades-old computer security principle that ‘software security depends on hardware security’ is applied to a range of BYOD e-exam tools. Five potential hacks are examined, four of which are confirmed to work against at least one BYOD e-exam tool. The consequences of these hacks are significant, ranging from removal of the exam paper from the venue through to receiving live assistance from an outside expert. Potential mitigation strategies are proposed; however, these are unlikely to completely protect the integrity of BYOD e-exams. Educational institutions are urged to balance the additional affordances of BYOD e-exams for examiners against the potential affordances for cheaters.
The Nature, Extent, and Consequences of Genetic Variation in the opa Repeats of Notch in Drosophila

Polyglutamine (pQ) tracts are abundant in proteins co-interacting on DNA. The lengths of these pQ tracts can modulate their interaction strengths. However, pQ tracts >40 residues are pathologically prone to amyloidogenic self-assembly. Here, we assess the extent and consequences of variation in the pQ-encoding opa repeats of Notch in Drosophila melanogaster. We use Sanger sequencing to genotype opa sequences (5′-CAX repeats), which have resisted assembly using short sequence reads. While most sampled lines carry the major allele opa31 encoding Q13HQ17 or the opa32 allele encoding Q13HQ18, many lines carry rare alleles encoding pQ tracts >32 residues: opa33a (Q14HQ18), opa33b (Q15HQ17), opa34 (Q16HQ17), opa35a1/opa35a2 (Q13HQ21), opa36 (Q13HQ22), and opa37 (Q13HQ23). Only one rare allele encodes a tract <31 residues: opa23 (Q13–Q10). This opa23 allele shortens the pQ tract while simultaneously eliminating the interrupting histidine. We introgressed these opa variant alleles into common backgrounds and measured the frequency of Notch-type phenotypes. Homozygotes for the short and long opa alleles have defects in embryonic survival and sensory bristle organ patterning, and sometimes show wing notching. Consistent with functional differences between Notch opa variants, we find that a scute inversion carrying the rare opa33b allele suppresses the bristle patterning defect caused by achaete/scute insufficiency, while an equivalent scute inversion carrying opa31 manifests the patterning defect. Our results demonstrate the existence of potent pQ variants of Notch and the need for long read genotyping of key repeat variables underlying gene regulatory networks.
High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera: Parnassius apollo and Euphydryas aurinia

Microsatellite flanking regions have been compared in two butterfly species. Several microsatellite flanking regions showed high similarity to one another among different microsatellites within a same species, but very few similarities were found between species. This can be the consequence of either duplication/multiplication events involving large regions containing microsatellites or of microsatellites imbedded in minisatellite regions. The multiplication of microsatellites might also be linked to mobile elements. Furthermore, crossing over between nonhomologous microsatellites can lead to the exchange of the flanking regions between microsatellites. The same phenomenon was observed in both studied butterfly species but not in Aphis fabae (Hemiptera), which was screened at the same time using the same protocol. These findings might explain, at least partially, why microsatellite isolation in Lepidoptera has been relatively unsuccessful so far.
PRINCIPAR - An Efficient, Broad-coverage, Principle-based Parser

We present an efficient, broad-coverage, principle-based parser for English. The parser has been implemented in C++ and runs on SUN Sparcstations with X-windows. It contains a lexicon with over 90,000 entries, constructed automatically by applying a set of extraction and conversion rules to entries from machine readable dictionaries.
Rapid effects of statins: from prophylaxis to therapy for ischemic stroke.

Ischemic stroke is a leading cause of death and disability worldwide and is a major contributor to rising healthcare costs. It has been estimated that in the United States, an individual is afflicted with stroke every 53 seconds with fatality occurring about every 2 minutes. Despite recent advances in the treatment of cardiovascular diseases, the therapeutic options for acute ischemic stroke remain limited. For secondary prevention, antiplatelet therapy with aspirin was the only available treatment. However, recent randomized trials with 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors or statins have shown remarkable benefits in terms of reducing the incidence of stroke in patients with risks for cardiovascular disease.1 It is not clear from these studies, however, how much of the benefits were attributed to the reduction of atherosclerotic coronary artery disease because ischemic heart disease is a risk factor for stroke. Nevertheless, several ongoing trials with statins in patients without coronary artery disease should help clarify the extent of stroke protection. See page 322 Earlier this year, two randomized trials have added important clinical information. The Heart Protection Study (HPS) demonstrated reduction of stroke in a large number of patients irrespective of baseline cholesterol levels and in whom total cholesterol levels were as low as 135 mg/dL.2 Furthermore, the analysis of stroke as a predefined secondary endpoint of the Myocardial Ischemia Reduction With Aggressive Cholesterol Lowering (MIRACL) trial showed that early treatment of high-risk patients with acute coronary syndromes halved the incidence of stroke within 4 months.3 These trials demonstrate not only the rapidity of statin’s …
Improved face recognition result reranking based on shape contexts

Automatic face recognition techniques applied on particular group or mass database introduces error cases. Error prevention is crucial for the court. Reranking of recognition results based on anthropology analysis can significant improve the accuracy of automatic methods. Previous studies focused on manual facial comparison. This paper proposed a weighted facial similarity computing method based on morphological analysis of components characteristics. Search sequence of face recognition reranked according to similarity, while the interference terms can be removed. Within this research project, standardized photographs, surveillance videos, 3D face images, identity card photographs of 241 male subjects from China were acquired. Sequencing results were modified by modeling selected individual features from the DMV altas. The improved method raises the accuracy of face recognition through anthroposophic or morphologic theory.
Access and Binding of Local Anesthetics in the Closed Sodium Channel

Local anesthetics (LAs) are known to bind Na+ channels in the closed, open, and inactivated states and reach their binding sites via extracellular and intracellular access pathways. Despite intensive studies, no atomic-scale theory is available to explain the diverse experimental data on the LA actions. Here we attempt to contribute to this theory by simulating access and binding of LAs in the KcsA-based homology model of the closed Na+ channel. We used Monte Carlo minimizations to model the channel with representative local anesthetics N-(2,6-dimethylphenylcarbamoylmethyl)triethylammonium (QX-314), cocaine, and tetracaine. We found the nucleophilic central cavity to be a common binding region for the ammonium group of LAs, whose aromatic group can extend either along the pore axis (vertical binding mode) or to the III/IV domain interface (horizontal binding mode). The vertical mode was earlier predicted for the open channel, but only the horizontal mode is consistent with mutational data on the closed-channel block. To explore hypothetical access pathways of the permanently charged QX-314, we pulled the ligand via the selectivity filter, the closed activation gate, and the III/IV domain interface. Only the last pathway, which leads to the horizontal binding mode, did not impose steric obstacles. The LA ammonium group mobility within the central cavity was more restricted in the vertical mode than in the horizontal mode. Therefore, occupation of the selectivity-filter DEKA locus by a Na+ ion destabilizes the vertical mode, thus favoring the horizontal mode. LA binding in the closed channel requires the resident Na+ ion to leave the nucleophilic central cavity through the selectivity filter, whereas the LA egress should be coupled with reoccupation of the cavity by Na+. This hypothesis on the coupled movement of Na+ and LA in the closed channel explains seemingly contradictory data on how the outer-pore mutations as well as tetrodotoxin and μ-conotoxin binding affect the ingress and egress of LAs.
Assessment of left ventricular long axis contraction can detect early myocardial dysfunction in asymptomatic patients with severe aortic regurgitation

OBJECTIVE To identify variables that could be applied at rest to diagnose subclinical ventricular dysfunction in asymptomatic patients with severe aortic regurgitation. DESIGN Cross sectional study. PATIENTS Left ventricular long axis contraction was studied using tissue Doppler and M mode echocardiography in 21 patients with no symptoms (New York Heart Association (NYHA) functional class ⩽ 2a) but severe aortic regurgitation (jet area/left ventricular outflow tract area > 40%). MAIN OUTCOME MEASURES Left ventricular ejection fraction (LVEF) at baseline and peak exercise (Weber protocol), cardiopulmonary function, and left ventricular long axis function at rest (peak systolic velocity and excursion of the mitral annulus). RESULTS In 11 patients, ejection fraction increased or did not change (from mean (SD) 55 (5)% to 58 (4)%, p < 0.05) (group I); in 10 patients it decreased by > 5% (from 54 (4)% to 42 (5)%, p < 0.001) (group II). Exercise ejection fraction was < 50% in all patients in group II. At rest, there were no differences between the groups in ejection fraction, left ventricular diameter indices, wall stress, and short axis contraction. However, patients in group II had reduced long axis contraction compared with group I: peak systolic velocity 8.6 (0.6)v 11.9 (2.2) cm/s (p < 0.001); excursion 11 (2) v 14 (2) mm (p < 0.01). A resting velocity of < 9.5 cm/s was the best indicator of poor exercise tolerance (sensitivity 90%, specificity 100%). CONCLUSIONS Markers of reduced long axis contraction may provide simple and reliable indices of subclinical left ventricular dysfunction in asymptomatic patients with severe aortic regurgitation.
Input and interaction in language acquisition: The language of primary caregivers

Introduction It has been clear since the late 1960s and early 1970s that there are systematic differences between speech to children and speech among adults (Snow 1972; Phillips 1973; contributions to Snow and Ferguson 1977). Child-directed speech (CDS) tends to consist of short, well-formed utterances, to contain fewer false starts or hesitations, and to include fewer complex sentences and subordinate clauses (Snow 1972; Phillips 1973). It is characteristically higher in pitch, more exaggerated in intonation, and slower in tempo than speech among adults (Garnica 1977). It is also highly redundant, as reflected in the incidence of part or whole repetitions (Broen 1972; Snow 1972), much more closely tied to the immediate context (Phillips 1973; Snow 1977a), and employs a number of special discourse features which serve to involve the child in interaction and to clarify and upgrade the child's own contributions (Cross 1977; Snow 1977b). Given that these differences appear to constitute adaptations to the child's limited linguistic ability, they have often been seen as a way of shifting the burden of explanation away from the sort of innate language acquisition device proposed by Chomsky (1965). However, while it is certainly true that any adequate theory of language acquisition must specify the way in which children make use of the input they receive, it has become increasingly clear that the relationship between child-directed speech and the child's acquisition of language is much less straightforward than a generally facilitative model of CDS would lead us to assume.
Influence of lymphatic tissue on the development of adjuvant-induced polyarthritis in rats.

The experimental model of rheumatoid arthritis has not yet been established. Currently, two acceptable models of rheumatoid disease are being studied (Pearson, 1964), i.e. adjuvant-induced polyarthritis in rats and homologous disease (Ryzewska and Ryzewski, 1965; Ryzewski and Ryzewska, 1965). Polyarthritis appearing in rats after a subcutaneous injection of spleen cell suspension or homogenate with Freund's adjuvant was first described by Stoerk, Bielifiski, and Budzilovich (1954). These results were confirmed by Pearson (1956), who used for the immunization skeletal muscles with Freund's adjuvant or adjuvant alone. The development of adjuvant-induced polyarthritis in rats and the course of the disease have since been described in greater detail (Waksman, Pearson, and Sharp, 1960; Ward and Jones, 1962b; Pearson, 1963). It was found that a single intradermal injection of Freund's adjuvant (killed tubercle-either saprophytic bacilli or chemical fractions of it, mineral oil, and an emulsifying agent) was sufficient to produce polyarthritis. The paw is the most effective site of injection. A few hours after adjuvant administration a local inflammatory reaction develops at the injection site and persists during the whole latent period of the disease. The onset of the disease usually occurs on the 10th to the 16th day or later, being characterized by polyarthritis which often affects many of the peripheral joints but also some of the joints in the tail and at the base of the spine. The arthritis may be transitory or may become chronic. Histologically, there is an acute and subacute synovitis with proliferation of synovial lining cells, mononuclear infiltration of the articular cartilage and para-articular tissues, invasion of bone and articular cartilage by connective tissue pannus, and periosteal new bone formation. These destructive changes often cause fibrous or bony ankylosis (Pearson and Wood, 1962). Adjuvant polyarthritis is accompanied by inflammatory lesions of other tissues, including acute and chronic dermatitis, inflammation of serous membranes manifested by diarrhoea and urethritis, and inflammatory changes in the eye giving rise to conjunctivitis, keratitis, and iritis. In the lymph nodes draining the adjuvant injection site, in the lungs, and occasionally in the liver, the typical "post-adjuvant miliary granulomata" can easily be shown. They consist of an oil drop in the middle with histiocytes and lymphocytes at the circumference (Pearson, Waksman, and Sharp, 1961). Jones and Ward (1963) also observed purulent infiltrations in the spleen capsule, pleura, bronchi, and heart muscles. The pathogenesis of adjuvant-induced polyarthritis in rats has not so far been established. Three main mechanisms may be involved:
Probing the role of protostellar feedback in clustered star formation , Mapping outflows in the collapsing protocluster NGC 2264-C

Context. The role played by protostellar feedback in clustered star formation is still a matter of debate. In particular, protostellar outflows have been proposed as a source of turbulence in cluster-forming clumps, which may provide support against global collapse for several free-fall times. Aims. Here, we seek to test the above hypothesis in the case of the well-documented NGC 2264-C protocluster, by quantifying the amount of turbulence and support injected in the surrounding medium by protostellar outflows. Methods. Using the HERA heterodyne array on the IRAM 30 m telescope, we carried out an extensive mapping of NGC 2264-C in the three molecular line transitions 12 CO(2–1), 13 CO(2–1), and C 18 O(2–1). Results. We found widespread high-velocity 12 CO emission, testifying to the presence of eleven outflow lobes, closely linked to the compact millimeter continuum sources previously detected in the protocluster. We carried out a detailed analysis of the dynamical parameters of these outflows, including a quantitative evaluation of the overall momentum flux injected in the cluster-forming clump. These dynamical parameters were compared to the gravitational and turbulent properties of the clump. Conclusions. We show that the population of protostellar outflows identified in NGC 2264-C is likely to contribute a significant fraction of the observed turbulence but cannot efficiently support the protocluster against global collapse. Gravity appears to largely dominate the dynamics of the NGC 2264-C clump at the present time; however it is possible that an increase in the star formation rate during the later evolution of the protocluster will trigger enough outflows to finally halt the contraction of the cloud.
Detailed Analysis of Directional Radio Channel Measurements

Physical models describe the radio channel by characterizing the multipath propagation. Also, measurements are frequently employed in the establishment of such models, or for tuning the existing ones. This paper presents a systematic analysis of double-directional radio channel data, obtained by combining two single-input multiple-output measurements (forward and reverse), each, containing the channel frequency responses at the locations of a virtual rectangular antenna array. The measurement setup uses a vector network analyzer, which, together with the adopted data processing, represents an affordable, but very consistent, alternative to more sophisticated equipment, given that, a physical analysis of the identified channel contributions provided sensible results. The study comprised three main steps: 1) the characterization of each single-directional channel by employing a high-resolution algorithm to obtain the parameters of a chosen number of multipath components (MPCs); 2) the classification of the obtained MPCs in a twofold way, first, by grouping MPCs using clustering tools, and, second, by classifying these clusters according to their type of interaction with the propagation scenario; and 3) the extraction of typical values for the number of clusters, the number of MPCs per cluster, rules for power decay, and statistical distributions for inter and intracluster delays and azimuths.