Miracle-dz/UniFAR-FTUs huggingface dataset:
Retrospective: Scalpel: Customizing DNN Pruning to the Underlying Hardware Parallelism

Back in 2017, Deep Neural Networks (DNN) models were fundamentally changing the development of artificial intelligence applications. Across various application domains, including computer vision and natural language processing, advanced DNN models were proposed to drive higher prediction accuracy and increased functionality. However, these new models were wider and deeper, resulting in higher computation and memory utilization. This trend increased the hardware demand and resulted in larger training and inference costs. Considering the high redundancy inside these larger DNN models, many researchers proposed pruning to remove unnecessary parameters [1], thereby reducing both the corresponding computation and memory footprints. One critical but common issue of most pruning techniques was neglecting the gap between FLOP reduction and performance improvement on real hardware. Conventional pruning algorithms inserted irregular sparsity into DNN models, thereby converting dense linear algebra computation into the sparse computation. Sparse computation is inherently less efficient because it is very difficult to exploit data-parallel hardware to accelerate the computation. At the same time, due to such irregular sparsity, we need to use special sparse formats (e.g., compressed sparse row format) to store the weight tensors. The DNN computation then needs extra computation (and memory accesses) to decode those sparse formats. Due to these issues, although pruning was dramatically reducing the FLOPs, in many cases by 90% or more, the incurred sparsity can actually hurt the overall performance on both CPUs and GPUs. Further, encoding the sparse format of pruned DNN models incurs additional storage space, which makes it difficult to use pruning to reduce the memory cost. Figure 1 shows the relative execution time, model sizes, and MAC operations of DNN models pruned by Deep Compression [1] with respect to the original DNN models. The first three bars show the relative execution time on the microcontroller, CPU, and GPU. As shown in the figure, the relative execution time is much higher than the relative model sizes and MAC operations. Weight pruning hurts the performance of LeNet-5 (on GPU), ConvNet, NIN, and AlexNet, which causes an execution time increase for these networks.
Identification of Host Insulin Binding Sites on Schistosoma japonicum Insulin Receptors

Schistosoma japonicum insulin receptors (SjIRs) have been identified as encouraging vaccine candidates. Interrupting or blocking the binding between host insulin and the schistosome insulin receptors (IRs) may result in reduced glucose uptake leading to starvation and stunting of worms with a reduction in egg output. To further understand how schistosomes are able to exploit host insulin for development and growth, and whether these parasites and their mammalian hosts compete for the same insulin source, we identified insulin binding sites on the SjIRs. Based on sequence analysis and the predicted antigenic structure of the primary sequences of the SjIRs, we designed nine and eleven peptide analogues from SjIR-1 and SjIR-2, respectively. Using the Octet RED system, we identified analogues derived from SjIR-1 (10) and SjIR-2 (20, 21 and 22) with insulin-binding sequences specific for S. japonicum. Nevertheless, the human insulin receptor (HIR) may compete with the SjIRs in binding human insulin in other positions which are important for HIR binding to insulin. However, no binding occurred between insulin and parasite analogues derived from SjIR-1 (2, 7 and 8) and SjIR-2 (14, 16 and 18) at the same locations as HIR sequences which have been shown to have strong insulin binding affinities. Importantly, we found two analogues (1 and 3), derived from SjIR-1, and two analogues (13 and 15) derived from SjIR-2, were responsible for the major insulin binding affinity in S. japonicum. These peptide analogues were shown to have more than 10 times (in KD value) stronger binding capacity for human insulin compared with peptides derived from the HIR in the same sequence positions. Paradoxically, analogues 1, 3, 13 and 15 do not appear to contain major antigenic determinants which resulted in poor antibody responses to native S. japonicum protein. This argues against their future development as peptide-vaccine candidates.
Methionine-Restricted C57BL/6J Mice Are Resistant to Diet-Induced Obesity and Insulin Resistance but Have Low Bone Density

Dietary methionine restriction (MR) extends lifespan, an effect associated with reduction of body weight gain, and improvement of insulin sensitivity in mice and rats as a result of metabolic adaptations in liver, adipose tissue and skeletal muscle. To test whether MR confers resistance to adiposity and insulin resistance, C57BL/6J mice were fed a high fat diet (HFD) containing either 0.86% methionine (control fed; CF) or 0.12% methionine (methionine-restricted; MR). MR mice on HFD had lower body weight gain despite increased food intake and absorption efficiency compared to their CF counterparts. MR mice on HFD were more glucose tolerant and insulin sensitive with reduced accumulation of hepatic triglycerides. In plasma, MR mice on HFD had higher levels of adiponectin and FGF21 while leptin and IGF-1 levels were reduced. Hepatic gene expression showed the downregulation of Scd1 while Pparg, Atgl, Cd36, Jak2 and Fgf21 were upregulated in MR mice on HFD. Restriction of growth rate in MR mice on HFD was also associated with lower bone mass and increased plasma levels of the collagen degradation marker C-terminal telopeptide of type 1 collagen (CTX-1). It is concluded that MR mice on HFD are metabolically healthy compared to CF mice on HFD but have decreased bone mass. These effects could be associated with the observed increase in FGF21 levels.
A Comparative Study of Proprietary Geodata and Volunteered Geographic Information for Germany

In connection with the Web 2.0 movement of the Internet (O’Reilly, 2005) and the progressive development of tools and applications for the collection and provision of spatial information (Turner, 2006), the quality and quantity of so-called Volunteered Geographic Information (VGI) (Goodchild, 2007) underwent a fast-paced worldwide development. Some even speak of a “Wikification of GIS” (Sui, 2008). This spatial data, mostly collected by volunteers, is freely available for the Internet user and can (under certain licensing conditions) be applied to numerous GIS projects and applications. Through advanced data donations, but also by a variety of other non-proprietary data sources, some of these free data providers are able to offer a vast variety of different information. This development in recent years stands in strong contrast to the very expensive commercial spatial data provided by a few companies. Much of this proprietary data is widely used today, for example, in car navigation devices or cell phones. The strong demand for freely available spatial data, though, has boosted the number of VGI available on the Internet. They can be found in very simple forms such as in Wikipedia entries that provide some spatial information like lat-long coordinates (geotag), or in so-called mashups in Google Earth or Google Maps, which combine different information sources. One of the most complex and promising projects in recent years, however, is OpenStreetMap (OSM).
Prospects for Higgs physics at energies up to 100 TeV

We summarize the prospects for Higgs boson physics at future proton–proton colliders with centre of mass (c.m.) energies up to 100 TeV. We first provide the production cross sections for the Higgs boson of the Standard Model from 13 TeV to 100 TeV, in the main production mechanisms and in subleading but important ones such as double Higgs production, triple production and associated production with two gauge bosons or with a single top quark. We then discuss the production of Higgs particles in beyond the Standard Model scenarios, starting with the one in the continuum of a pair of scalar, fermionic and vector dark matter particles in Higgs-portal models in various channels with virtual Higgs exchange. The cross sections for the production of the heavier CP-even and CP-odd neutral Higgs states and the charged Higgs states in two-Higgs doublet models, with a specific study of the case of the Minimal Supersymmetric Standard Model, are then given. The sensitivity of a 100 TeV proton machine to probe the new Higgs states is discussed and compared to that of the LHC with a c.m. energy of 14 TeV and at high luminosity.
Learning View-Specific Deep Networks for Person Re-Identification

In recent years, a growing body of research has focused on the problem of person re-identification (re-id). The re-id techniques attempt to match the images of pedestrians from disjoint non-overlapping camera views. A major challenge of the re-id is the serious intra-class variations caused by changing viewpoints. To overcome this challenge, we propose a deep neural network-based framework which utilizes the view information in the feature extraction stage. The proposed framework learns a view-specific network for each camera view with a cross-view Euclidean constraint (CV-EC) and a cross-view center loss. We utilize the CV-EC to decrease the margin of the features between diverse views and extend the center loss metric to a view-specific version to better adapt the re-id problem. Moreover, we propose an iterative algorithm to optimize the parameters of the view-specific networks from coarse to fine. The experiments demonstrate that our approach significantly improves the performance of the existing deep networks and outperforms the state-of-the-art methods on the VIPeR, CUHK01, CUHK03, SYSU-mReId, and Market-1501 benchmarks.
Influence of Brace Slenderness on the Fracture Life of Rectangular Tubular Steel Bracing Members Subjected to Seismic Inelastic Loading

Axial compressive strains that develop in rectangular steel tube braces subjected to cyclic inelastic loading can lead to local buckling and brace fracture. In this study, the influence of the brace effective slenderness on this strain demand is examined as an attempt to assess the effect of brace slenderness on brace fracture. Past test data indicating an impact of brace slenderness on brace fracture is first reviewed. Brace axial deformations at onset of buckling and at first yielding in compression are evaluated using elastic buckling theory. Finite element analysis of bracing members exhibiting different effective slenderness ratios is carried out to evaluate the strain demand after inelastic buckling has occurred and plastic hinging has formed. The strain demand prior to brace buckling and plastic hinging is small and has negligible effect on brace fracture. Compressive strains that develop after brace buckling has occurred and plastic hinging has formed generally decrease as the brace effective slenderness ratio is increased.
Root-zone temperature and nitrogen affect the yield and secondary metabolite concentration of fall- and spring-grown, high-density leaf lettuce.

BACKGROUND Understanding the effects of temperature and nitrogen levels on key variables, particularly under field conditions during cool seasons of temperate climates, is important. Here, we document the impact of root-zone heating and nitrogen (N) fertility on the accumulation and composition of fall- and spring-grown lettuce biomass. A novel, scalable field system was employed. RESULTS Direct-seeded plots containing a uniform, semi-solid, and nearly stable rooting medium were established outdoors in 2009 and 2010; each contained one of eight combinations of root-zone heating (-/+) and N fertility (0, 72, 144, and 576 mg day(-1)). Root-zone heating increased but withholding N decreased biomass accumulation in both years. Low N supplies were also associated with greater anthocyanin and total antioxidant power but lower N and phosphorus levels. Tissue chlorophyll a and vitamin C levels tracked root-zone temperature and N fertility more closely in 2009 and 2010, respectively. CONCLUSIONS Experimentally imposed root-zone temperature and N levels influenced the amount and properties of fall- and spring-grown lettuce tissue. Ambient conditions, however, dictated which of these factors exerted the greatest effect on the variables measured. Collectively, the results point to the potential for gains in system sustainability and productivity, including with respect to supplying human nutritional units.
Probabilistic risk assessment of the environmental impacts of pesticides in the Crocodile (west) Marico catchment, North-West Province

External agricultural inputs, such as pesticides, may pose risks to aquatic ecosystems and affect aquatic populations, communities and ecosystems. To predict these risks, a tiered approach was followed, incorporating both the PRIMET and PERPEST models. The first-tier PRIMET model is designed to yield a relatively worst-case risk assessment requiring a minimum of input data, after which the effects of the risks can be refined using a higher tier PERPEST model. The risk assessment initially depends on data supplied from local landowners, pesticide characteristic, application scheme and physical scenario of the environment under question. Preliminary results are presented, together with ecotoxicological data on several frequently-used pesticides in a section of the Crocodile (west) Marico Water Management Area (WMA) in South Africa. This area is historically known to have a high pesticide usage, with deltamethrin, aldicarb, parathion, cypermethrin and dichlorvos being the main pesticides used. Deltamethrin was indicated as having the highest probability of risks to aquatic organisms occurring in the study area. Cypermethrin, parathion, dichlorvos, carbaryl, bromoxynil, linuron, methomyl and aldicarb were all indicated as having possible risks (ETR 1-100) to the aquatic environment. Pesticides posing no risk included fenamiphos, abamectin, pendimethalin, captan, endosulfan, alachlor, bentazone and cyromazine (ETR < 1). The pesticides posing a possible risk to the aquatic ecosystem were evaluated further to determine their effects on 8 grouped endpoints using the PERPEST effect model. Deltamethrin and cypermethrin were again noted as posing the greatest risk and clear effects were eminent for aquatic insects and macro-crustaceans, followed by micro-crustaceans and rotifers. High percentages of clear effects on insects were also observed for carbaryl, parathion and dichlorvos. Linuron was indicated as having minimal clear effects on community metabolism, macrophytes and phytoplankton classes, while lesser clear effects of bromoxynil occurred on periphyton communities. Application of both the lower-tier PRIMET and higher-tier PERPEST models showed similar trends in that they both ranked the top 5 pesticides in the same order of risk. This approach offers a significant improvement over the presently-used simulation models or use of safety factors. It is therefore especially useful in developing countries such as South Africa, where pesticide environmental risk information is scarce. Although these models were effectively used in this study, it still has to be validated further under South African conditions.
Norovirus and Sapovirus Epidemiology and Strain Characteristics among Navajo and Apache Infants

Norovirus and sapovirus are important causes of acute gastroenteritis (AGE) among American Indian infants. We investigated the prevalence and molecular epidemiology of norovirus and sapovirus in American Indian infants who have historically experienced a high burden of AGE compared to other US populations. Stool samples were collected from 241 children with AGE (cases) and from 343 infants without AGE (controls) ≤9 months of age from 2002–2004. Cases experienced forceful vomiting and/or 3 or more watery or looser-than-normal stools in 24 hours. Stools were tested by real-time RT-PCR for norovirus GI, GII and GIV and sapovirus GI, GII, GIV and GV. Positive samples were genotyped after sequencing conventional RT-PCR products. Norovirus was identified in 76 (31.5%) of the cases and 70 (20.4%) of the controls (p<0.001). GII.3 and GII.4 Farmington Hills were the most frequently identified genotypes in 14.5% and 30.3% of cases and 17.1% and 27.1% of controls, respectively. Sapovirus GI and GII genotypes were identified in 8 (3.3%) of cases and 8 (2.3%) of controls and a single GIV virus was detected in a control. The same norovirus and sapovirus genotypes were circulating in the general U.S. population in the same time period. The high detection rate of norovirus in healthy controls suggests significant asymptomatic transmission in young infants in these communities.
Predicting Lameness in Sheep Activity Using Tri-Axial Acceleration Signals

Simple Summary Monitoring livestock farmed under extensive conditions is challenging and this is particularly difficult when observing animal behaviour at an individual level. Lameness is a disease symptom that has traditionally relied on visual inspection to detect those animals with an abnormal walking pattern. More recently, accelerometer sensors have been used in other livestock industries to detect lame animals. These devices are able to record changes in activity intensity, allowing us to differentiate between a grazing, walking, and resting animal. Using these on-animal sensors, grazing, standing, walking, and lame walking were accurately detected from an ear attached sensor. With further development, this classification algorithm could be linked with an automatic livestock monitoring system to provide real time information on individual health status, something that is practically not possible under current extensive livestock production systems. Abstract Lameness is a clinical symptom associated with a number of sheep diseases around the world, having adverse effects on weight gain, fertility, and lamb birth weight, and increasing the risk of secondary diseases. Current methods to identify lame animals rely on labour intensive visual inspection. The aim of this current study was to determine the ability of a collar, leg, and ear attached tri-axial accelerometer to discriminate between sound and lame gait movement in sheep. Data were separated into 10 s mutually exclusive behaviour epochs and subjected to Quadratic Discriminant Analysis (QDA). Initial analysis showed the high misclassification of lame grazing events with sound grazing and standing from all deployment modes. The final classification model, which included lame walking and all sound activity classes, yielded a prediction accuracy for lame locomotion of 82%, 35%, and 87% for the ear, collar, and leg deployments, respectively. Misclassification of sound walking with lame walking within the leg accelerometer dataset highlights the superiority of an ear mode of attachment for the classification of lame gait characteristics based on time series accelerometer data.
Disease Modification for Parkinson's Disease: Axonal Regeneration and Trophic Factors

Disease modification and structural neuroprotection have been the holy grail for Parkinson's disease (PD) experimental therapeutics. Theoretically, there are a number of ways to implement such therapeutics, but to date all have failed. This review examines the potential of axonal regeneration and trophic factor delivery for the nigrostriatal system as 2 such approaches that historically have initiated much excitement. However, we conclude this discussion with the following question: has science passed these approaches by? © 2018 International Parkinson and Movement Disorder Society
Total-body skeletal muscle mass: estimation by a new dual-energy X-ray absorptiometry method.

BACKGROUND Skeletal muscle (SM) is an important body-composition component that remains difficult and impractical to quantify by most investigators outside of specialized research centers. A large proportion of total-body SM is found in the extremities, and a large proportion of extremity lean soft tissue is SM. A strong link should thus exist between appendicular lean soft tissue (ALST) mass and total-body SM mass. OBJECTIVE The objective was to develop prediction models linking ALST estimated by dual-energy X-ray absorptiometry (DXA) with total-body SM quantified by multislice magnetic resonance imaging in healthy adults. DESIGN ALST and total-body SM were evaluated with a cross-sectional design in adults [body mass index (in kg/m(2)) < 35] with an SM-prediction model developed and validated in model-development and model-validation groups, respectively. The model-development and model-validation groups included 321 and 93 ethnically diverse adults, respectively. RESULTS ALST alone was highly correlated with total-body SM (model 1: R(2) = 0.96, SEE = 1.63 kg, P < 0.001), although multiple regression analyses showed 2 additional predictor variables: age (model 2: 2-variable combined R(2) = 0.96, SEE = 1.58 kg, P < 0.001) and sex (model 3: 3-variable combined R(2) = 0.96, SEE = 1.58 kg, P < 0.001). All 3 models performed well in the validation group. An SM-prediction model based on the SM-ALST ratio was also developed, although this model had limitations when it was applied across all subjects. CONCLUSION Total-body SM can be accurately predicted from DXA-estimated ALST, thus affording a practical means of quantifying the large and clinically important SM compartment.
Molecular and functional characterization of a new X-linked chronic granulomatous disease variant ( X 91 + ) case with a double missense mutation in the cytosolic gp 91 phox C-terminal tail STASIA

We report here two atypical cases of X-linked CGD patients (first cousins) in which cytochrome b(558) is present at a normal level but is not functional (X91+). The mutations were localized by single-strand conformational polymorphism of reverse transcriptase-polymerase chain reaction amplified fragments and then identified by sequence analysis. They consisted in two base substitutions (C919 to A and C923 to G), changing His303 to Asn and Pro304 to Arg in the cytosolic gp91phox C-terminal tail. Mismatched polymerase chain reaction and genomic DNA sequencing showed that mothers had both wild-type and mutated alleles, confirming that this case was transmitted in an X-linked fashion. A normal amount of FAD was found in neutrophil membranes, both in the X91+ patients and their parents. Epstein-Barr virus-transformed B lymphocytes from the X91+ patients acidified normally upon stimulation with arachidonic acid, indicating that the mutated gp91phox still functioned as a proton channel. A cell-free translocation assay demonstrated that the association of the cytosolic factors p47phox and p67phox with the membrane fraction was [. ] STASIA, Marie José, et al. Molecular and functional characterization of a new X-linked chronic granulomatous disease variant (X91+) case with a double missense mutation in the cytosolic gp91phox C-terminal tail. Biochimica et Biophysica Acta, 2002, vol. 1586, no. 3, p. 316-30 DOI : 10.1016/S0925-4439(01)00110-7
Quality of Monitoring of Stochastic Events by Proportional-Share Mobile Sensor Coverage

There is significant interest in using mobile sensors to protect geographical regions against hazards, in which the sensing resources are distributed according to the varying importance of the sub-regions, such as their numbers of residents exposed to the hazards. The quality of monitoring (QoM) resulting from such proportional-share allocation of the coverage time, in terms of the amount of information captured, is not well understood. In this paper, we analyze the QoM properties of proportional-share mobile sensor coverage, at different fairness time scales, as a function of a wide range of event types, stochastic event staying times, and stochastic event arrival/departure dynamics. Based on the QoM analysis, we optimize a class of periodic mobile coverage schedules that achieve accurate proportional sharing while maximizing the QoM of the total system.