Miracle-dz/UniFAR-FTUs huggingface dataset:
Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes

The mammalian homotypic fusion and vacuole protein sorting (HOPS) complex is comprised of six subunits: VPS11, VPS16, VPS18, VPS39, VPS41 and the Sec1/Munc18 (SM) family member VPS33A. Human HOPS has been predicted to be a tethering complex required for fusion of intracellular compartments with lysosomes, but it remains unclear whether all HOPS subunits are required. We showed that the whole HOPS complex is required for fusion of endosomes with lysosomes by monitoring the delivery of endocytosed fluorescent dextran to lysosomes in cells depleted of individual HOPS proteins. We used the crystal structure of the VPS16/VPS33A complex to design VPS16 and VPS33A mutants that no longer bind each other and showed that, unlike the wild‐type proteins, these mutants no longer rescue lysosome fusion with endosomes or autophagosomes in cells depleted of the endogenous proteins. There was no effect of depleting either VIPAR or VPS33B, paralogs of VPS16 and VPS33A, on fusion of lysosomes with either endosomes or autophagosomes and immunoprecipitation showed that they form a complex distinct from HOPS. Our data demonstrate the necessity of recruiting the SM protein VPS33A to HOPS via its interaction with VPS16 and that HOPS proteins, but not VIPAR or VPS33B, are essential for fusion of endosomes or autophagosomes with lysosomes.
Cellulosic Ethanol Production by Recombinant Cellulolytic Bacteria Harbouring pdc and adh II Genes of Zymomonas mobilis

The ethanol fermenting genes such as pyruvate decarboxylase (pdc) and alcohol dehydrogenase II (adh II) were cloned from Zymomonas mobilis and transformed into three different cellulolytic bacteria, namely Enterobacter cloacae JV, Proteus mirabilis JV and Erwinia chrysanthemi and their cellulosic ethanol production capability was studied. Recombinant E. cloacae JV was found to produce 4.5% and 3.5% (v/v) ethanol, respectively, when CMC and 4% NaOH pretreated bagasse were used as substrates, whereas recombinant P. mirabilis and E. chrysanthemi with the same substrates could only produce 4%, 3.5%, 1%, and 1.5 % of ethanol, respectively. The recombinant E. cloacae strain produced twofold higher percentage of ethanol than the wild type. The recombinant E. cloacae strain could be improved further by increasing its ethanol tolerance capability through media optimization and also by combining multigene cellulase expression for enhancing ethanol production from various types of lignocellulosic biomass so that it can be used for industrial level ethanol production.
Cowpox with Severe Generalized Eruption, Finland

Cowpox with a severe, generalized eruption was diagnosed in an atopic 4-year-old girl by electron microscopy, virus isolation, polymerase chain reaction, and immunoglobulin (Ig) M and low-avidity IgG antibodies. The hemagglutinin gene of the isolate clustered with a Russian cowpox virus strain, and more distantly, with other cowpox and vaccinia virus strains. The patient’s dog had orthopoxvirus-specific antibodies, indicating a possible transmission route.
Nucleotide Sequence of Tomato Black Ring Virus RNA-1

Summary The sequence of the 7356 nucleotide [excluding the 3′ poly(A)] RNA-1 of tomato black ring virus (TBRV) was determined from overlapping cDNA clones. A putative initiation codon at nucleotide 261 was considered to be the start of an open reading frame which terminates at a UAG codon at position 7053. The predicted translation product is a protein of 2264 amino acids with an M r of 253680 (254K). Comparison of the amino acid sequence of this 254K protein with other viral proteins revealed three regions, each having about 60% homology with a region of the three cowpea mosaic virus (CPMV) proteins (58K, 24K, 87K) which are thought to be involved in replication of the CPMV RNAs. The same regions show similarities, although less extended, with proteins 2C, 3C and 3D of picornaviruses. From these results we suggest that the genome organization of TBRV is similar to that of comoviruses and picornaviruses.
Strain-Specific Protective Effect of the Immunity Induced by Live Malarial Sporozoites under Chloroquine Cover

The efficacy of a whole-sporozoite malaria vaccine would partly be determined by the strain-specificity of the protective responses against malarial sporozoites and liver-stage parasites. Evidence from previous reports were inconsistent, where some studies have shown that the protective immunity induced by irradiated or live sporozoites in rodents or humans were cross-protective and in others strain-specific. In the present work, we have studied the strain-specificity of live sporozoite-induced immunity using two genetically and immunologically different strains of Plasmodium cynomolgi, Pc746 and PcCeylon, in toque monkeys. Two groups of monkeys were immunized against live sporozoites of either the Pc746 (n = 5), or the PcCeylon (n = 4) strain, by the bites of 2–4 sporozoite-infected Anopheles tessellates mosquitoes per monkey under concurrent treatments with chloroquine and primaquine to abrogate detectable blood infections. Subsequently, a group of non-immunized monkeys (n = 4), and the two groups of immunized monkeys were challenged with a mixture of sporozoites of the two strains by the bites of 2–5 infective mosquitoes from each strain per monkey. In order to determine the strain-specificity of the protective immunity, the proportions of parasites of the two strains in the challenge infections were quantified using an allele quantification assay, Pyrosequencing™, based on a single nucleotide polymorphism (SNP) in the parasites’ circumsporozoite protein gene. The Pyrosequencing™ data showed that a significant reduction of parasites of the immunizing strain in each group of strain-specifically immunized monkeys had occurred, indicating a stronger killing effect on parasites of the immunizing strain. Thus, the protective immunity developed following a single, live sporozoite/chloroquine immunization, acted specifically against the immunizing strain and was, therefore, strain-specific. As our experiment does not allow us to determine the parasite stage at which the strain-specific protective immunity is directed, it is possible that the target of this immunity could be either the pre-erythrocytic stage, or the blood-stage, or both.
Design of dual band, wideband planar antenna using meta material

A planar dual band antenna with wideband characteristics using metamaterial (MTM) is proposed in this paper. Stepped impedance resonator (SIR) inspired metamaterial is loaded in the patch of the antenna. SIR metamaterial is different from conventional composite right left handed (CRLH) metamaterial as it doesn't realize its metamaterial behavior from structures like interdigital capacitor, meanderline and vias connections and the resulting structure is palnar. First resonance of the proposed antenna is centered at 2.765 GHz and second resonance is generated at 6.4 GHz. Wideband width of 1.3 GHz produced at 6.4 GHz. The proposed structure shows positive gain and good radiation characteristics. The proposed antenna has been simulated using commercially available HFSS software. Prototype of the proposed structure is validated experimentally.
Using MEDLINE as a knowledge source for disambiguating abbreviations in full-text biomedical journal articles

Biomedical abbreviations and acronyms are widely used in biomedical literature. Since many abbreviations represent important content in biomedical literature, information retrieval and extraction benefits from identifying the meanings of biomedical abbreviations. Since many abbreviations are ambiguous, it would be important to map abbreviations to their full forms, which ultimately represent the meanings of the abbreviations. In this study, we present a novel unsupervised method that applies MEDLINE records as a knowledge source for disambiguating abbreviations in full-text biomedical journal articles. We first automatically generated from MEDLINE records a knowledge source or dictionary of abbreviation-full pairs. We then trained on MEDLINE records and predicted the full forms of abbreviations in full-text journal articles by applying supervised machine-learning algorithms in an unsupervised fashion. We report up to 92% prediction precision and up to 91% coverage.
Observation of the density minimum in deeply supercooled confined water

Small angle neutron scattering (SANS) is used to measure the density of heavy water contained in 1D cylindrical pores of mesoporous silica material MCM-41-S-15, with pores of diameter of 15 ± 1 Å. In these pores the homogenous nucleation process of bulk water at 235 K does not occur, and the liquid can be supercooled down to at least 160 K. The analysis of SANS data allows us to determine the absolute value of the density of D2O as a function of temperature. We observe a density minimum at 210 ± 5 K with a value of 1.041 ± 0.003 g/cm3. We show that the results are consistent with the predictions of molecular dynamics simulations of supercooled bulk water. Here we present an experimental report of the existence of the density minimum in supercooled water, which has not been described previously.
Rumor Spreading Model Considering the Importance and Fuzziness of Information

In this paper, to study rum or spreading model for the web forum of which the topological structure has a strong heterogeneity, we propose a novel susceptible-exposed-infected-removed (SEIR) model by introducing the importance and fuzziness of the content of the rum or. We derive mean-field equations characterizing the dynamics of the SEIR model on heterogeneous network. Then a steady-state analysis is conducted to investigate the critical threshold and the final size of the rum or spreading. The simulation results demonstrate that small fuzziness can effectively reduce the maximum rumor influence. In addition, the critical threshold is independent of the stifling rate. We also get a conclusion that whether a rum or can spread is related to the fuzziness of rum or itself.
How we see poverty

How we think about poverty is colored by how we measure it. For economists, that often means seeing poverty through quantities measured in large, representative surveys. The surveys give a comprehensive view, but favor breadth over depth. Typical economic surveys are limited in their ability to tease out informal activity, and, while they capture yearly sums, they offer little about how the year was actually lived by families. Year-long financial diaries provide a complementary way of seeing poverty, with a focus on week by week choices and challenges. The result is a re-framing of poverty and its relationship to money, calling for greater attention to financial access and a broader notion of how finance matters.
Low Power Design Techniques for CMOS Circuits & Systems

Power consumption is a primary concern of designing integrated circuits in deeply scaled CMOS technologies. Present-day technologies possess computing capabilities that make things possible, such as real-time operations. High-speed computation has thus become the expected norm from the average user, instead of being the province of the few with access to a powerful mainframe. Power must be added to the portable unit, even when power is available in non-portable applications, the issue of low-power design is becoming critical. Thus, it is evident that methodologies for the design of high-throughput, low-power digital systems are needed. Techniques for low-power operation are shown in this paper, which use the lowest possible supply voltage coupled with architectural, logic style, circuit, and technology optimizations. Index terms – low power design, dynamic power, static power, switching activities, Leakage power, power optimization.
A NOTE ON THE BEHAVIOUR OF THE BLACK-SCHOLES IMPLIED VOLATILITY CLOSE TO EXPIRY

We consider the behaviour of the Black-Scholes implied volatility in the small time to expiry limit under the condition of no arbitrage. We present formulae describing the exact asymptotics of the implied volatility in this situation. Some basic properties of the time-scaled implied volatility are also derived. It is established that there exist arbitrage free markets in which implied volatility may fail to converge to any value, finite or infinite. We present a complete description of the small time to expiry asymptotics of the Black-Scholes implied volatility under the condition of no arbitrage and a very weak technical condition. The presented formulae are in terms of the option and stock prices, strike price and time to expiry. In the process of obtaining these results, we derive small time to expiry asymptotics of the Black-Scholes price of a European call option as well as a number of interesting properties of the time-scaled implied volatility. Our results show that close to expiry the at-the-money (ATM) implied volatility behaves very di! erently to the implied volatility of options that are not ATM. The final section of the note demonstrates that implied volatility may fail to converge, to a finite or infinite limit, as time to expiry goes to zero even in the simple case of the Black-Scholes model with time-dependent volatility. Suppose that the stock price follows a Geometric Brownian Motion, viz. dSt = rSt dt + ! St dWt
Investigating Excessive Delays in Mobile Broadband Networks

Systematic monitoring of performance characteristics of mobile broadband networks can help users, operators, and regulators understand this increasingly critical infrastructure. We report the results of a measurement study of round trip delays in two mobile networks in Norway using over 200 geographically distributed subscriptions for a period of one month. In general, we find high variation in delay within the same radio access type and RRC state. Across both networks we study, we observe connections with round trip delays of several seconds, often multiple times per hour, that are more frequent when nodes are moving. Correlating these extreme delay events with available metadata, we find they are related to handovers, radio state transitions, and retransmissions at the link and physical layers.
3D face reconstruction and multimodal person identification from video captured using smartphone camera

In this paper, we propose a novel approach for reconstructing 3D face in real-life scenarios. Our main objective is to address the most challenging issue that involves reconstructing depth information from a video that is recorded from frontal camera of the smartphone. Such videos recorded using smart-phones impose lot of challenges, such as motion blur, non-frontal perspectives and low resolution. This limits the applicability of state-of-the-art algorithms, which are mostly based on landmark detection. This situation is addressed with the Scale-Invariant Feature Transformation (SIFT) followed by feature matching to generate consistent tracks. These tracks are further processed to generate a 3D point cloud using Point/Cluster based Multi-view stereo (PMVS/ CMVS). The usage of PMVS/CMVS will however fail to generate a dense 3D cloud points on the weak surfaces of face, such as cheeks, nose and forehead. This issue is addressed by multi-view reconstruction of these weakly supported surfaces using Visual-Hull. The effectiveness of our method is evaluated on a newly collected dataset, which simulates a realistic identification scenario using a smartphone.
Lane estimation for autonomous vehicles using vision and LIDAR

Autonomous ground vehicles, or self-driving cars, require a high level of situational awareness in order to operate safely and efficiently in real-world conditions. A system able to quickly and reliably estimate the location of the roadway and its lanes based upon local sensor data would be a valuable asset both to fully autonomous vehicles as well as driver assistance technologies. To be most useful, the system must accommodate a variety of roadways, a range of weather and lighting conditions, and highly dynamic scenes with other vehicles and moving objects. Lane estimation can be modeled as a curve estimation problem, where sensor data provides partial and noisy observations of curves. The number of curves to estimate may be initially unknown and many of the observations may be outliers and false detections (e.g., due to tree shadows or lens flare). The challenge is to detect lanes when and where they exist, and to update the lane estimates as new observations are received. This thesis describes algorithms for feature detection and curve estimation, as well as a novel curve representation that permits fast and efficient estimation while rejecting outliers. Locally observed road paint and curb features are fused together in a lane estimation framework that detects and estimates all nearby travel lanes. The system handles roads with complex geometries and makes no assumptions about the position and orientation of the vehicle with respect to the roadway. Early versions of these algorithms successfully guided a fully autonomous Land Rover LR3 through the 2007 DARPA Urban Challenge, a 90 km urban race course, at speeds up to 40 km/h amidst moving traffic. We evaluate these and subsequent versions with a ground truth dataset containing manually labeled lane geometries for every moment of vehicle travel in two large and diverse datasets that include more than 300,000 images and 44 km of roadway. The results illustrate the capabilities of our algorithms for robust lane estimation in the face of challenging conditions and unknown roadways. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Diversity in Object Proposals

Current top performing object recognition systems build on object proposals as a preprocessing step. Object proposal algorithms are designed to generate candidate regions for generic objects, yet current approaches are limited in capturing the vast variety of object characteristics. In this paper we analyze the error modes of the state-of-the-art Selective Search object proposal algorithm and suggest extensions to broaden its feature diversity in order to mitigate its error modes. We devise an edge grouping algorithm for handling objects without clear boundaries. To further enhance diversity, we incorporate the Edge Boxes proposal algorithm, which is based on fundamentally different principles than Selective Search. The combination of segmentations and edges provides rich image information and feature diversity which is essential for obtaining high quality object proposals for generic objects. For a preset amount of object proposals we achieve considerably better results by using our combination of different strategies than using any single strategy alone.
Attenuation of ischemia/reperfusion injury in rats by a caspase inhibitor.

BACKGROUND Z-Val-Ala-Asp(OMe)-CH2F (ZVAD-fmk), a tripeptide inhibitor of the caspase interleukin-1beta-converting enzyme family of cysteine proteases, may reduce myocardial reperfusion injury in vivo by attenuating cardiomyocyte apoptosis within the ischemic area at risk. METHODS AND RESULTS Sprague-Dawley rats were subjected to a 30-minute coronary occlusion followed by a 24-hour reperfusion. An inert vehicle (dimethylsulfoxide; group 1, n=8) or ZVAD-fmk, at a total dose of 3.3 mg/kg (group 2, n=8), was administered intravenously every 6 hours starting at 30 minutes before coronary occlusion until 24 hours of reperfusion. At this 24-hour point, hemodynamics were assessed by means of cardiac catheterization; then, the rats were killed, and the left ventricle was excised and sliced. The myocardial infarct size/ischemic area at risk and the count of presumed apoptotic cardiomyocytes (terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling [TUNEL]-positive cells) within the ischemic area at risk were assessed through triphenyltetrazolium chloride staining and TUNEL methods, respectively. Peak positive left ventricular dP/dt was higher (P=.02) and left ventricular end-diastolic pressure was lower (P=.04) in group 2 than in group 1. The infarct size/ischemic area at risk of group 2 (52.4+/-4.0%) was smaller (P=.02) than that of group 1 (66.6+/-3.7%), and TUNEL-positive cells were fewer (P=.0002) (group 2, 3.1+/-0.9%; group 1, 11.1+/-1.0%). Agarose gel electrophoresis revealed DNA laddering in the border zone myocardium of group 1, but DNA ladder formation was attenuated in group 2. CONCLUSIONS ZVAD-fmk was effective in reducing myocardial reperfusion injury, which could at least be partially attributed to the attenuation of cardiomyocyte apoptosis.
ETH Zurich at TREC Clinical Decision Support 2016

This paper describes ETH Zurich’s submission to the TREC 2016 Clinical Decision Support (CDS) track. In three successive stages, we apply query expansion based on literal as well as semantic term matches, rank documents in a negation-aware manner and, ﬁnally, re-rank them based on clinical intent types as well as semantic and conceptual afﬁnity to the medical case in question. Empirical results show that the proposed method can distill patient representations from raw clinical notes that result in a retrieval performance superior to that of manually constructed case descriptions.
Reduced Brainstem Inhibition during Anticipated Pelvic Visceral Pain Correlates with Enhanced Brain Response to the Visceral Stimulus in Women with Irritable Bowel Syndrome

Cognitive factors such as fear of pain and symptom-related anxiety play an important role in chronic pain states. The current study sought to characterize abnormalities in preparatory brain response before aversive pelvic visceral distention in irritable bowel syndrome (IBS) patients and their possible relationship to the consequences of distention. The brain functional magnetic resonance imaging (fMRI) blood oxygen level-dependent (BOLD) response to anticipated and delivered mild and moderate rectal distention was recorded from 14 female IBS patients and 12 healthy controls. During cued anticipation of distention, activity decreased in the insula, supragenual anterior cingulate cortex (sACC), amygdala, and dorsal brainstem (DBS) of controls. IBS patients showed less anticipatory inactivation. Group differences were significant in the right posterior insula and bilateral DBS. Self-rated measures of negative affect during scanning were higher in patients than controls (p < 0.001), and the anticipatory BOLD decreases in DBS were inversely correlated with these ratings. During subsequent distention, both groups showed activity increases in insula, dorsal ACC, and DBS and decreases in the infragenual ACC. The increases were more extensive in patients, producing significant group differences in dorsal ACC and DBS. The amplitude of the anticipatory decrease in the pontine portion of DBS was associated with greater activation during distention in right orbitofrontal cortex and bilateral sACC. Both regions have been associated previously with corticolimbic inhibition and cognitive coping. Deficits in preparatory inhibition of DBS, including the locus ceruleus complex and parabrachial nuclei, may interfere with descending corticolimbic inhibition and contribute to enhanced brain responsiveness and perceptual sensitivity to visceral stimuli in IBS.
SocialProbe: Understanding Social Interaction Through Passive WiFi Monitoring

In this paper, we present an approach to extract social behavior and interaction patterns of mobile users by passively monitoring WiFi probe requests and null data frames that are sent by smartphones for network control/management purposes. By analyzing the temporal and spatial correlations of the Receive Signal Strength Indicators (RSSI) of packets from these low rate transmissions, we are able to discover proximity relationships, occupancy patterns, and social interactions among users. We evaluate the SocialProbe system using commodity off-the-shelf smartphones and WiFi Access Points in two locations, a research lab and a public dining area. The result shows that the proposed approach is able to obtain reliable social relationships and interactions in a non-intrusive way.