Miracle-dz/UniFAR-FTUs huggingface dataset:
TIR fluorescence reader for selective detection of cell membranes

A novel setup for fluorescence measurements of surfaces of biological samples, in particular cell membranes, is described. The method is based on multiple total internal reflections (TIR) of a laser beam at the surface of a multi-well plate, such that 96 individual samples are excited simultaneously. Main prerequisites are an appropriate thickness and high transmission of the glass bottom, a non-cytotoxic adhesive, and appropriate glass rods for TIR illumination. Fluorescence from the cell surface is detected simultaneously using an integrating CCD camera and appropriate optical filters. For validation of the system, cells incubated with the fluorescence marker NBD as well as transfected cells expressing a fluorescent membrane protein are used. In addition, intracellular translocation of a fluorescent protein kinase c fusion protein upon stimulation is examined. The method appears well suitable for high throughput screening (HTS), since neither washing of the samples nor any readjustment of the equipment after changing of individual plates are necessary.
Multi-domain disfluency and repair detection

This paper investigates automatic detection of different types of self-repairs in spontaneous speech under different social contexts, from casual conversations to government hearings. The work shows that a simple CRF-based model is effective for cross-domain training, which is important for contexts where annotated data is not available. The approach explicitly represents common types of disfluencies observed in multi-domain data both in the model state space and the features extracted. In addition, the model incorporates an expanded state space for recognizing the repair structure, unlike prior work that annotates only the reparandum.
The molecular basis of mechanisms underlying polarization vision

The underlying mechanisms of polarization sensitivity (PS) have long remained elusive. For rhabdomeric photoreceptors, questions remain over the high levels of PS measured experimentally. In ciliary photoreceptors, and specifically cones, little direct evidence supports any type of mechanism. In order to promote a greater interest in these fundamental aspects of polarization vision, we examined a varied collection of studies linking membrane biochemistry, protein–protein interactions, molecular ordering and membrane phase behaviour. While initially these studies may seem unrelated to polarization vision, a common narrative emerges. A surprising amount of evidence exists demonstrating the importance of protein–protein interactions in both rhabdomeric and ciliary photoreceptors, indicating the possible long-range ordering of the opsin protein for increased PS. Moreover, we extend this direction by considering how such protein paracrystalline organization arises in all cell types from controlled membrane phase behaviour and propose a universal pathway for PS to occur in both rhabdomeric and cone photoreceptors.
Synchronization Constraints for Interconnect Synthesis

Interconnect synthesis tools ease the burden on the designer by automatically generating and optimizing communication hardware. In this paper we propose a novel capability for FPGA interconnect synthesis tools that further simplifies the designer's effort: automatic cycle-level synchronization of data delivery. This capability enables the creation of interconnect with significantly reduced hardware cost, provided that communicating modules have fixed latency and do not apply upstream backpressure. To do so, the designer specifies constraints on the lengths, in clock cycles, of multi-hop logical communication paths. The tool then uses an integer programming-based method to insert balancing registers into optimal locations, satisfying the designer's constraints while minimizing register usage. On an example convolutional neural network application, the new approach uses 43% less area than a FIFO-based synchronization scheme.
Female pelvic floor: endovaginal MR imaging of normal anatomy.

PURPOSE To demonstrate the anatomy of the female pelvic floor with endovaginal magnetic resonance (MR) imaging. MATERIALS AND METHODS Ten healthy nulliparous volunteers (age, 22-26 years) underwent MR imaging with an endovaginal coil. Findings on endovaginal MR images in the volunteers were correlated with findings on endovaginal MR images and cross-sectional anatomic slices obtained in three cadavers. RESULTS The endovaginal coil was well tolerated by all volunteers. Pelvic floor structures such as the pelvic diaphragm and the urogenital diaphragm were well depicted. Previously undescribed urethral supporting structures--the periurethral and paraurethral ligaments--were visualized. The zonal anatomy of the urethra was clearly visible. The endovaginal MR imaging findings in the volunteers correlated with the endovaginal MR findings and gross anatomy in the cadavers. CONCLUSION Endovaginal MR imaging clearly demonstrates the anatomy of the female pelvic floor and urethra.
ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants

Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1–6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants. Database URL: www.compubio. in/chlorossrdb/
NGF regulates the PC12 cell cycle machinery through specific inhibition of the Cdk kinases and induction of cyclin D1

We have examined the effects of NGF on components of the PC12 cell cycle machinery. We show that NGF represses over 6–8 d the levels of specific cdk kinase proteins and the G2-M phase specific cyclin B1 and the S phase marker PCNA as well as the level of phosphorylation of the retinoblastoma (Rb) protein. All of these changes may provide a basis for a NGF block to cell cycling. Unexpectedly, the G1 phase-specific cyclin D1 was dramatically increased by inducers of differentiation (NGF and FGF), but not by inducers of proliferation (EGF and insulin). Although the levels of cyclin D1/cdk2 and cyclin D1/cdk4 complexes increased following NGF treatment, as did cyclin D1/Rb complexes, the associated kinase activities declined, indicating that NGF also induces an inhibitor of cdk kinase activity. In agreement, NGF induced the cdk inhibitory protein, p21, which was found in cyclin D1/cdk kinase complexes after NGF treatment. We show that vector over expression of cyclin D1 in PC12 is sufficient on its own to arrest the cells in G1 phase and inhibit expression of PCNA. These results indicate that NGF induction of cyclin D1 and inactivation of cdk kinases, the latter possibly by increase of p21, play a central role in the NGF block of PC12 cell cycling.
Aerobic Exercise As a Potential Way to Improve Self-Control after Ego-Depletion in Healthy Female College Students

Purpose: To test whether aerobic exercise can help build self-control stamina in healthy female young adults. Stamina in this context is defined as the capability to endure ego depletion, which can be measured with a self-control task following another activity also requiring self-control. Methods: Forty-five healthy undergraduate women were randomized to either an experimental group or control group. Participants in the experimental group were required to run in their campus running field for 30 min for a period of 5 weeks. Individuals in the control group were required to do diary entries regarding self-control in their daily lives, also for a period of 5 weeks. Before and after the 5-week intervention, participants completed a pain threshold test, a color word Stroop task and the following Cold Pressor Task (CPT) (with and without a distraction component). Results: There was significant decrease of pain tolerance in session 2 relative to session 1 in the control group, but no such decline was found in the experimental group (though the improvement of pain tolerance was not significant), possibly suggesting successful self-control against this kind of decline. Conclusions: Five weeks of aerobic exercise increased self-control after ego depletion in terms of pain tolerance. These findings suggest that aerobic exercise may serve as a potential effective intervention for enhancing self-control in a college female population.
Batf3-dependent CD103+ dendritic cells are major producers of IL-12 that drive local Th1 immunity against Leishmania major infection in mice

The role of different DC subsets in priming and maintenance of immunity against Leishmania major (L. major) infection is debated. The transcription factor basic leucine zipper transcription factor, ATF‐like 3 (Batf3) is essential for the development of mouse CD103+ DCs and some functions of CD8α+ DCs. We found that CD103+ DCs were significantly reduced in the dermis of Batf3‐deficient C57BL/6 mice. Batf3−/− mice developed exacerbated and unresolved cutaneous pathology following a low dose of intradermal L. major infection in the ear pinnae. Parasite load was increased 1000‐fold locally and expanded systemically. Batf3 deficiency did not affect L. major antigen presentation to T cells, which was directly exerted by CD8α− conventional DCs (cDCs) in the skin draining LN. However, CD4+ T‐cell differentiation in the LN and skin was skewed to nonprotective Treg‐ and Th2‐cell subtypes. CD103+ DCs are major IL‐12 producers during L. major infection. Local Th1 immunity was severely hindered, correlating with impaired IL‐12 production and reduction in CD103+ DC numbers. Adoptive transfer of WT but not IL‐12p40−/− Batf3‐dependent DCs significantly improved anti‐L. major response in infected Batf3−/− mice. Our results suggest that IL‐12 production by Batf3‐dependent CD103+ DCs is crucial for maintenance of local Th1 immunity against L. major infection.
Investigation of fracture properties of California asphalt mixtures using semicircular bending and beam fatigue tests

Fatigue cracking is a primary distress in asphalt concrete (AC) due to repetitive stresses and strains caused by both traffic loading and environmental factors. The fatigue resistance of AC is investigated by a number of fatigue tests. The main objective of this study is to investigate the use of the semi-circular bending (SCB) test as a quality assurance/quality control (QA/QC) measure for field construction. The comparison of fracture properties of seven AC mixtures from the SCB and beam fatigue test (BFT) is conducted. The J c and K 1c values for the seven mixtures were determined. The BFT was performed on the same mixtures and the initial stiffness, N f and plateau value (PV) were determined. The coefficient of variation (CV) ranged from 0% to 38% for J c and from 0% to 35% for K 1c. The CV ranged from 10% to 93% for the initial stiffness, 2% to 83% for N f and 8% to 167% for PV. The SCB J c and BFT N f and PV indicated lower fracture properties for PG64-10RAP (LIME), AN-HMA and WMA-ADVERA mixtures than other mixtures. The BFT N f and PV achieved similar ranking for all mixtures. There is good correlation between N f and PV with J c, and not a good correlation between the initial stiffness with J c, N f and PV. This has indicated that the initial stiffness is not a good representative for fracture properties of AC while J c, N f and PV are better indicators. The results of this study indicate that the SCB test has a great potential as a QA/QC test of fracture properties of asphalt mixtures.
1311 Option Pricing Using EGARCH Models

Various e m p i r i d studies have shown that the time-varying volatility of asset returns can be described by GARCH (generalized autoregressive conditional heteroskedasticity) models. The corresponding GARCH option pricing model of Duan (1995) is capable of depicting the "smile-effect" which often can be found in option prices. In some derivative markets, however, the slope of the smile is not symmetrical. In this paper an option pricing model in the context of the EGARCH (Exponential GARCH) process will be developed. Extensive numerical analyses suggest that the EGARCH option pricing model is able to explain the different slopes of the smile curve. R C U d Plusieurs etudes empiriques suggbrent d'apprthender la volatilit6 temporelle de variables financibres h l'aide de modbles GARCH (generalized autoregressive conditional heteroskedasticity). Duan (1995) rtussit h l'aide d'un modble GARCH h d&rire les "smile-effect'' souvent observts lors d e la fixation des prix d'option. N h m o i n s sur certains marchts dtrivatifs, la pente de l'effet "smile" n'est pas symttrique. L'objet de cet article est de modtliser les prix d'option h partir d'un modble EGARCH (Exponential GARCH). Les analyses numtriques pdsentees h partir de ce modble montrent que ces dtveloppements sont h m&me d'expliquer difftrentes pentes pour l'effet "smile".
EFFECT OF PROCESS PARAMETERS AND TOOL SHAPE ON THE MACHINABILITY OF A PARTICULATE FILLED-POLYMER COMPOSITE MATERIAL FOR RAPID TOOLING

This paper presents the results of an experimental study on the effects of machining parameters (cutting speed, feed, depth of cut) and tool shape on chip formation, surface topography, resultant cutting force and surface roughness produced in flat and ball end milling of the Ren Shape-Express 2000™ aluminum particulate filled-polymer composite material. This material is shown to exhibit a brittle-to-ductile transition in chip formation with decreasing cutting speed. The transition is explained by the strain-rate sensitivity of the polymer matrix and is found to correlate well with a corresponding change in the surface roughness. The absence of clear feed marks on the milled surface explains why molds made from the composite material require less hand polishing than machined metal molds. The influence of cutting conditions and tool shape (flat end vs. ball-nose) on the cutting force, surface roughness, and workpiece breakout are discussed and relevant comparisons with conventional metal and polymer machining are made.
SENSEVAL-2 The Swedish Framework

In this paper we describe the organisation and results of the SENSEVAL-2 exercise for Swedish. We present some of the experiences we gained by participating as developers and organisers in the exercise. We particularly focus on the choice of the lexical and corpus material, the annotation process, the scoring scheme, the motivations for choosing the lexical-sample branch of the exercise, the participating systems and the official results.
Elevated Levels of Hemoglobin A1c Are Associated With Cerebral White Matter Disease in Patients With Stroke

Background and Purpose— This study was conducted to investigate the association of cerebral white matter disease (WMD) on MRI with vascular risk factors and laboratory findings in consecutive first acute ischemic stroke patients. Methods— Acute ischemic stroke patients underwent MRI ⩽24 hours after stroke onset and follow-up on day 2. WMD was scored on fluid attenuated inversion recovery MRI according to the Wahlund score. Vascular risk factors and laboratory parameters were assessed during hospital stay. Univariate and multiple logistic regression analyses were performed. Results— We included 512 patients with first acute ischemic stroke (mean age, 68.5 [SD, 13.2] years; 192 women (37.5%); median National Institutes of Health Stroke Scale on admission, 3 [interquartile range, 1–6]; and median Wahlund score, 4 [interquartile range, 2–9]). WMD was present in 460 (89.8%) patients. In univariate analysis, age, arterial hypertension, reduced estimated glomerular filtration rate, hemoglobin A1c (HbA1c) levels, diabetes mellitus, and female sex were associated with the presence of WMD (P<0.05). In multiple regression analysis, age, arterial hypertension, and elevated levels of HbA1c (P<0.05) remained independently associated with the extent of WMD. Conclusions— Among known risk factors, higher levels of HbA1c were associated with cerebral WMD in stroke patients. This may suggest that chronic disturbance of glycemia measured by HbA1c plays a role in the pathophysiology of WMD. Clinical Trial Registration— URL: http://www.clinicaltrials. gov. Unique identifier: NCT00715533.
Green scheduling for radiant systems in buildings

In this paper we look at the problem of peak power reduction for buildings with electric radiant floor heating systems. Uncoordinated operation of a multi-zone radiant floor heating system can result in temporally correlated electricity demand surges or peaks in the building's electricity consumption. As peak power prices are 200-400 times that of the nominal rate, this uncoordinated activity can result in high electricity costs and expensive system operation. We have previously presented green scheduling as an approach for reducing the aggregate peak power consumption in buildings while ensuring that indoor thermal comfort is always maintained. This paper extends the theoretical results for general affine dynamical systems and applies them to electric radiant floor heating systems. The potential of the proposed method in reducing the peak power demand is demonstrated for a small-scale system through simulation in EnergyPlus and for a large-scale system through simulation in Matlab.
Stochastic Multichannel Sensing for Cognitive Radio Systems: Optimal Channel Selection for Sensing with Interference Constraints

This paper considers the problem of sensing and transmission strategy of multiple parallel channels owned by the primary user, referred as stochastic multichannel sensing. The traffic parameters follow the Markovian traffic assumption and are not identically distributed among the channels. In order to obtain the optimal probabilities of channel selection for sensing, we formulate a maximization problem for the secondary user throughput with interference constraints to the primary user. The solution to the problem is obtained via linear programming. Numerical results show that the proposed stochastic sensing achieves higher normalized effective throughput and lower av- erage collision probability than the conventional deterministic sensing in a non-identical traffic environment. Additionally, the proposed method greatly reduces computational overheads and memory space. Index Terms—Cognitive radio, dynamic spectrum access, spec- trum sensing, throughput maximization, linear programming. I. INTRODUCTION
The ER Chaperone LHS 1 Is Involved in Asexual Development and Rice Infection by the Blast Fungus Magnaporthe oryzae

Mihwa Yi,a,1 Myoung-Hwan Chi,a Chang Hyun Khang,b Sook-Young Park,a Seogchan Kang,c Barbara Valent,b and Yong-Hwan Leea,2 a Department of Agricultural Biotechnology, Center for Fungal Genetic Resources and Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea b Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506 c Department of Plant Pathology, Pennsylvania State University, University Park, Pennsylvania 16802
Long-term follow-up of asymptomatic healthy subjects with frequent and complex ventricular ectopy.

From 1973 to 1983 we followed 73 asymptomatic healthy subjects who were discovered to have frequent and complex ventricular ectopy. Ventricular ectopy in these subjects was measured by 24-hour ambulatory electrocardiography, which showed a mean frequency of 566 ventricular ectopic beats per hour (range, 78 to 1994), with multiform ventricular ectopic beats in 63 per cent, ventricular couplets in 60 per cent, and ventricular tachycardia in 26 per cent. Asymptomatic healthy status was confirmed by extensive noninvasive cardiologic examination, although cardiac catheterization of a subsample of subjects disclosed serious coronary artery disease in 19 per cent. Follow-up for 3.0 to 9.5 years (mean, 6.5) was accomplished in 70 subjects (96 per cent) and documented one sudden death and one death from cancer. Calculation of a standardized mortality ratio (Monson's U.S. data, 8th revision) for 448 person-years of follow-up indicated that 7.4 deaths were expected, whereas 2 occurred (standardized mortality ratio, 27; P less than 0.05). A comparison of survival of the study cohort with that of persons without coronary artery disease or with mild disease, patients with moderate disease, and men with unrecognized myocardial infarction showed a favorable prognosis for the study cohort over 10 years. We conclude that the long-term prognosis in asymptomatic healthy subjects with frequent and complex ventricular ectopy is similar to that of the healthy U.S. population and suggests no increased risk of death.
Deep supercooling, vitrification and limited survival to –100°C in the Alaskan beetle Cucujus clavipes puniceus (Coleoptera: Cucujidae) larvae

SUMMARY Larvae of the freeze-avoiding beetle Cucujus clavipes puniceus (Coleoptera: Cucujidae) in Alaska have mean supercooling points in winter of –35 to –42°C, with the lowest supercooling point recorded for an individual of –58°C. We previously noted that some larvae did not freeze when cooled to –80°C, and we speculated that these larvae vitrified. Here we present evidence through differential scanning calorimetry that C. c. puniceus larvae transition into a glass-like state at temperatures <–58°C and can avoid freezing to at least –150°C. This novel finding adds vitrification to the list of insect overwintering strategies. While overwintering beneath the bark of fallen trees, C. c. puniceus larvae may experience low ambient temperatures of around –40°C (and lower) when microhabitat is un-insulated because of low snow cover. Decreasing temperatures in winter are correlated with loss of body water from summer high levels near 2.0 to winter lows near 0.4 mg mg–1 dry mass and concomitant increases in glycerol concentrations (4–6 mol l–1) and thermal hysteresis. Finally, we provide direct evidence that Cucujus from Wiseman, Alaska, survive temperatures to –100°C.