Miracle-dz/UniFAR-FTUs huggingface dataset:
The More the Merrier: Efficient Multi-Source Graph Traversal

Graph analytics on social networks, Web data, and communication networks has been widely used in a plethora of applications. Many graph analytics algorithms are based on breadth-first search (BFS) graph traversal, which is not only time-consuming for large datasets but also involves much redundant computation when executed multiple times from different start vertices. In this paper, we propose Multi-Source BFS (MS-BFS), an algorithm that is designed to run multiple concurrent BFSs over the same graph on a single CPU core while scaling up as the number of cores increases. MS-BFS leverages the properties of small-world networks, which apply to many real-world graphs, and enables efficient graph traversal that: (i) shares common computation across concurrent BFSs; (ii) greatly reduces the number of random memory accesses; and (iii) does not incur synchronization costs. We demonstrate how a real graph analytics application---all-vertices closeness centrality---can be efficiently solved with MS-BFS. Furthermore, we present an extensive experimental evaluation with both synthetic and real datasets, including Twitter and Wikipedia, showing that MS-BFS provides almost linear scalability with respect to the number of cores and excellent scalability for increasing graph sizes, outperforming state-of-the-art BFS algorithms by more than one order of magnitude when running a large number of BFSs.
A failure-distance based method to bound the reliability of nonrepairable fault-tolerant systems without the knowledge of minimal cuts

CTMC (continuous-time Markov chains) are a commonly used formalism for modeling fault-tolerant systems. One of the major drawbacks of CTMC is the well-known state-space explosion problem. This paper develops and analyzes a method (SC-BM) to compute bounds for the reliability of nonrepairable fault-tolerant systems in which only a portion of the state space of the CTMC is generated. SC-BM uses the failure distance concept as the method described previously by the authors (1997) but, unlike that method, which is based on the computation of exact failure distances, SC-BM uses lower bounds for failure distances, which are computed on the system fault-tree, avoiding the computation and holding of all minimal cuts as required in the earlier work. This is important because computation of all minimal cuts is NP-hard and the number of minimal cuts can be very large. In some cases SC-BM gives exactly the same bounds as the previous method; in other cases it gives less tight bounds. SC-BM computes tight bounds for the reliability of quite complex systems with an affordable number of generated states for short to quite large mission times. The analysis of several examples seems to show that the bounds obtained by SC-BM appreciably outperform those obtained by simpler methods, and, when they are not equal, are only slightly worse than the bounds obtained by the previous method. In addition, the overhead in CPU time due to computing lower bounds for failure distances seems to be reasonable.
The Role of Affective Information in Social-Cognitive Development: Children's Differentiation of Moral and Conventional Events.

The role of affect in one aspect of social-cognitive development was examined. Specifically, it was hypothesized that children are able to discriminate moral and conventional rules and events at young ages in part because affective informa tion is a salient feature of such events. Based on a standard interview technique, the results of Study 1 provided initial support for this hypothesis, as first and third graders consistently rated hypothetical conventional infractions as affec tively neutral, but tended to regard moral transgressions as affectively negative. Children also were more likely to justify their decisions to intervene in moral sit uations by referring to affect-related considerations. Study 2 provided additional support for the hypothesized importance of affective information by experimen tally manipulating affect prior to a controlled recall task involving moral and con ventional stories. Results showed that an induced negative affective state aided recall of moral but not conventional transgressions. Discussion focused on the potential role of affect in children's understanding of social events.
Dual Expression of the Salmonella Effector SrfJ in Mammalian Cells and Plants

SrfJ is an effector of the Salmonella pathogenicity island 2-encoded type III secretion system. Salmonella enterica serovar Typhimurium expresses srfJ under two disparate sets of conditions: media with low Mg2+ and low pH, imitating intravacuolar conditions, and media with myo-inositol (MI), a carbohydrate that can be used by Salmonella as sole carbon source. We investigated the molecular basis for this dual regulation. Here, we provide evidence for the existence of two distinct promoters that control the expression of srfJ. A proximal promoter, PsrfJ, responds to intravacuolar signals and is positively regulated by SsrB and PhoP and negatively regulated by RcsB. A second distant promoter, PiolE, is negatively regulated by the MI island repressor IolR. We also explored the in vivo activity of these promoters in different hosts. Interestingly, our results indicate that the proximal promoter is specifically active inside mammalian cells whereas the distant one is expressed upon Salmonella colonization of plants. Importantly, we also found that inappropriate expression of srfJ leads to reduced proliferation inside macrophages whereas lack of srfJ expression increases survival and decreases activation of defense responses in plants. These observations suggest that SrfJ is a relevant factor in the interplay between Salmonella and hosts of different kingdoms.
CoMo: A Compact Composite Moment-Based Descriptor for Image Retrieval

Low level features play a vital role in image retrieval. Image moments can effectively represent global information of image content while being invariant under translation, rotation, and scaling. This paper briefly presents a moment based composite and compact low-level descriptor for image retrieval. In order to test the proposed feature, the authors employ the Bag-of-Visual-Words representation to perform experiments on two well-known benchmarking image databases. The robust and highly competitive retrieval performances, reported in all tested diverse collections, verify the promising potential that the proposed descriptor introduces.
HYBRID GENETIC ALGORITHMS FOR MINIMIZING THE MAXIMUM COMPLETION TIME FOR THE WAFER PROBING SCHEDULING PROBLEM

ABSTRACT The wafer probing scheduling problem (WPSP) is a variation of the parallel-machine problem, which carries with the objective to minimize the total workload to enhance the utilization rate of machine capacity. However, to minimize the maximum completion time for the wafer probing scheduling problem (WPSP) is very important for equally utilizing the capacity of parallel-machine, while satisfying the requirements of product types, product family, sequence dependent setup time, product-type dependent processing time, due dates of jobs, and capacities of machines. To solve such a complicated problem efficiently and effectively, we adopt the hybrid genetic algorithm approach, which generates initial population with the insertion and savings algorithms for WPSP and provide a new crossover operator to generate better solutions. Considering the disturbance of due dates of jobs in scheduling, we design a new crossover which makes each machine keep the critical sub-schedule in the generation of offspring. The performance of the proposed hybrid genetic algorithm is evaluated by two real-world problems and the solution quality of the proposed approach is analyzed under five levels of mutation rates and four levels of number of generations. Computational results reveal that the hybrid genetic algorithm can efficiently solve the considered problem and the reduction of makespan is related to the mutation rates and the number of generations.
Modeling of salt and gypsum dissolution: applications, evaluation of geomechanical hazards

Abstract This article addresses the problem of modeling the dissolution of cavities in gypsum and halite (salt), followed by the assessment of potential collapse or subsidence of the geological formation, which may induce damaging consequences for population and infrastructures. Hazard prediction relies mostly on numerical modeling. This article discusses several issues associated to the development of dissolution numerical models involving the coupling between transport, dissolution and geomechanical modeling: type of model, parameters and numerical strategies. Hazard prediction relies mostly on numerical modeling. This article discusses several issues associated to the development of dissolution numerical models involving the coupling between transport, dissolution and geomechanical modeling: type of model, parameters and numerical strategies. The methodology is illustrated on several boundary value problems typical of actual situations in mining or civil engineering.
Cross-Border Prices, Costs and Mark-ups

We use data on retail prices and wholesale costs for detailed products at the barcode level from 325 stores of a large grocery chain to measure the effect of the US-Canadian border on market segmentation. Theoretically, we use a model of pricing and location on the circle to document possible patterns of cross-border prices. Empirically, we find clear evidence of international market segmentation. Cross-border price gaps are significantly higher than within country price gaps. Using the precise geographic location of each store, we find that UPC level prices and wholesale costs are discontinuous at the border. Our findings indicate that most differences in cross border prices arise from differences in an apparently tradable component of costs and not from systematic mark-up differences. ∗We thank Michal Fabinger, Robert Johnson, Lorenz Küng, Nick Li, Gloria Sheu and Kelly Shue for excellent research assistance. We gratefully acknowledge financial support from the National Science Foundation.
Functional Cliques in the Amygdala and Related Brain Networks Driven by Fear Assessment Acquired During Movie Viewing

One of the greatest challenges involved in studying the brain mechanisms of fear is capturing the individual's unique instantaneous experience. Brain imaging studies to date commonly sacrifice valuable information regarding the individual real-time conscious experience, especially when focusing on elucidating the amygdala's activity. Here, we assumed that by using a minimally intrusive cue along with applying a robust clustering approach to probe the amygdala, it would be possible to rate fear in real time and to derive the related network of activation. During functional magnetic resonance imaging scanning, healthy volunteers viewed two excerpts from horror movies and were periodically auditory cued to rate their instantaneous experience of "I'm scared. " Using graph theory and community mathematical concepts, data-driven clustering of the fear-related functional cliques in the amygdala was performed guided by the individually marked periods of heightened fear. Individually tailored functions derived from these amygdala activation cliques were subsequently applied as general linear model predictors to a whole-brain analysis to reveal the correlated networks. Our results suggest that by using a localized robust clustering approach, it is possible to probe activation in the right dorsal amygdala that is directly related to individual real-time emotional experience. Moreover, this fear-evoked amygdala revealed two opposing networks of co-activation and co-deactivation, which correspond to vigilance and rest-related circuits, respectively.
Changes in Vaginal Bacterial Concentrations with Intravaginal Metronidazole Therapy for Bacterial Vaginosis as Assessed by Quantitative PCR

Several fastidious bacteria have been associated with bacterial vaginosis (BV) using broad-range bacterial PCR methods such as consensus sequence 16S rRNA gene PCR, but their role in BV remains poorly defined. We describe changes in vaginal bacterial concentrations following metronidazole therapy for BV. Vaginal swabs were collected from women with BV diagnosed using Amsel clinical criteria, and vaginal fluid was assessed by Gram stain to generate Nugent scores. Follow-up swabs were collected 1 month after a 5-day course of vaginal 0.75% metronidazole gel and analyzed for 24 subjects with cured BV and 24 subjects with persistent BV. Changes in bacterial concentrations were measured using eight bacterium-specific 16S rRNA gene quantitative PCR assays. DNA from several fastidious BV-associated bacteria (BVAB) were present at high concentrations in the vagina prior to treatment. Successful antibiotic therapy resulted in 3- to 4-log reductions in median bacterial loads of BVAB1 (P = 0.02), BVAB2 (P = 0.0004), BVAB3 (P = 0.03), a Megasphaera-like bacterium (P < 0.0001), Atopobium species (P < 0.0001), Leptotrichia/Sneathia species (P = 0.0002), and Gardnerella vaginalis (P < 0.0001). Median posttreatment bacterial levels did not change significantly in subjects with persistent BV except for a decline in levels of BVAB3. The presence or absence of BV is reflected by vaginal concentrations of BV-associated bacteria such as BVAB1, BVAB2, Leptotrichia/Sneathia species, Atopobium species, Gardnerella vaginalis, and a Megasphaera-like bacterium, suggesting that these bacteria play an important role in BV pathogenesis and may be suitable markers of disease and treatment response.
The relationship between multiple traumatisation, emotion regulation and violent behaviour

To date, a significant proportion of research has predominantly focused upon childhood abuse and neglect (CAB) without considering the impact of exposure to wider forms of trauma. This thesis therefore examines the impact of exposure to recurrent CAN and multiple traumatisation (i.e. exposure to recurrent CAN and at least one wider form of trauma) upon emotion regulation (ER) and the perpetration of violence. Chapter Two presents a systematic review that explored the literature on factors associated with the impact of recurrent CAN in comparison to multiple forms of victimisation among an adolescent and young adult population. Chapter Three explores the construct of coping and critiques the Brief COPE (Carver, 1997) assessment. Chapter Four presents an empirical paper exploring the impact of recurrent CAN and multiple traumatisation on ER and coping, in addition to the role of ER in relation to aggressive behaviour among university students (n=237) and the general population (n=95). Statistically significant findings demonstrated that both recurrent CAN and multiple traumatisation were predictive of difficulties both in ER and violent behaviour. A number of further variables including optimism, violent attitudes and level of education were also found to contribute to difficulties in ER and violent behaviour.
Lost to follow up: contributing factors and challenges in South African patients on antiretroviral therapy.

BACKGROUND Patients who do not return for follow-up at clinics providing comprehensive HIV/AIDS care require special attention. This is particularly true where resources are limited and clinic loads are high. Themba Lethu Clinic at Helen Joseph Hospital in Johannesburg is a facility supported by PEPFAR funding through Right to Care (Grant CA-574-A-00-02-00018); more than 800 HIV/AIDS patients are seen there each week. Data on a sample of patients who failed to return for follow-up were analysed to identify the causes and to plan strategies to overcome the problem. METHODS A group of 182 patients who missed follow-up appointments at the clinic were identified. Their files were examined to identify possible contributing factors. The patients were then contacted telephonically and asked their reasons for non-attendance. RESULTS Results show that the leading cause of failure to follow up was financial (34% of patients). Patients cited transport costs and having to pay to open a file at each visit as the biggest monetary obstacles to obtaining treatment. Fifty-five per cent of patients lost to follow-up showed an improvement in CD4 count on treatment. Death accounted for 27% of the patients lost to follow-up and the mean ( +/- standard deviation (SD)) duration of treatment in this group was only 8 ( +/- 6) weeks. Of the patients in this group who had been seen at 4 months, 60% had failed to respond to treatment. The mean duration of ARV treatment before being lost to follow-up was 21 ( +/- 28) weeks. The mean CD4+ count was 92 ( +/- 74.5) cells/ microl and the mean number of visits was 3.33 ( +/- 2.17). Seventy-four per cent of the patients were on regimen 1A, and only 1 cited side-effects of medication as a reason for not returning. CONCLUSIONS This study highlighted financial difficulty as the major obstacle to obtaining treatment. There is evidence in support of providing ARV treatment free of charge to HIVpositive patients who qualify, as occurs in other provinces in South Africa. It is also suggested that providing ARV therapy at more local clinics in the community would make treatment more accessible. Provision of several months' supply of medicines per visit would help to reduce transport costs and minimise patient expenditure. These interventions may reduce the incidence of patients lost to follow-up in this community.
Functional and structural deficits at accumbens synapses in a mouse model of Fragile X

Fragile X is the most common cause of inherited intellectual disability and a leading cause of autism. The disease is caused by mutation of a single X-linked gene called fmr1 that codes for the Fragile X mental retardation protein (FMRP), a 71 kDa protein, which acts mainly as a translation inhibitor. Fragile X patients suffer from cognitive and emotional deficits that coincide with abnormalities in dendritic spines. Changes in spine morphology are often associated with altered excitatory transmission and long-term plasticity, the most prominent deficit in fmr1-/y mice. The nucleus accumbens, a central part of the mesocortico-limbic reward pathway, is now considered as a core structure in the control of social behaviors. Although the socio-affective impairments observed in Fragile X suggest dysfunctions in the accumbens, the impact of the lack of FMRP on accumbal synapses has scarcely been studied. Here we report for the first time a new spike timing-dependent plasticity paradigm that reliably triggers NMDAR-dependent long-term potentiation (LTP) of excitatory afferent inputs of medium spiny neurons (MSN) in the nucleus accumbens core region. Notably, we discovered that this LTP was completely absent in fmr1-/y mice. In the fmr1-/y accumbens intrinsic membrane properties of MSNs and basal excitatory neurotransmission remained intact in the fmr1-/y accumbens but the deficit in LTP was accompanied by an increase in evoked AMPA/NMDA ratio and a concomitant reduction of spontaneous NMDAR-mediated currents. In agreement with these physiological findings, we found significantly more filopodial spines in fmr1-/y mice by using an ultrastructural electron microscopic analysis of accumbens core medium spiny neuron spines. Surprisingly, spine elongation was specifically due to the longer longitudinal axis and larger area of spine necks, whereas spine head morphology and postsynaptic density size on spine heads remained unaffected in the fmr1-/y accumbens. These findings together reveal new structural and functional synaptic deficits in Fragile X.
The choroid plexus harbors a circadian oscillator modulated by estrogens

ABSTRACT The suprachiasmatic nucleus (SCN) of the hypothalamus is considered the master circadian oscillator in mammals. However, extra-SCN structures in the brain also display daily rhythms. Recently, we have demonstrated that the choroid plexus (CP) expresses core clock genes that are subjected to circadian regulation in a sex-dependent manner. By using CP explants cultured from female knock-in mice carrying the Period-luciferase transgene, we show that CP exhibits endogenous circadian rhythms of PERIOD2::LUCIFERASE expression. Furthermore, we demonstrate that estrogen declines following ovariectomy modulates the daily rhythm expression of Bmal1, Per1 and Per2 in female rat CP, corroborating data obtained in experiments where rat CP epithelial cell (CPEC) cultures were incubated with 17β-estradiol (E2). The molecular mechanism underlying these effects was also investigated, and we provide evidence that the estrogen receptor (ER) mediates the response of clock genes to E2. In conclusion, our study proves that the CP harbors a circadian oscillator that is modulated by estrogens and demonstrates that E2 regulation occurs through an estrogen-receptor-dependent mechanism.
QoS-aware end-to-end connectivity provision in a heterogenous military environment

Tactical ad-hoc networks are evolving today towards complex heterogeneous networks with various subnetworks in terms of architecture, protocols and security. Provision of QoS-aware end-to-end connectivity for such networks is a great challenge. If we also take into account communication issues like unpredictable connectivity, preferential forwarding for special traffic classes, intermittency due to node or communication link failure, the problem becomes more complex. Within crucial issues, the most important solutions are those for rapid autoconfiguration, zero-management and self-healing networks as well as cooperation between routing and signaling protocols in order to assure QoS-aware end-to-end connectivity. In the scope of this paper, we propose novel QoS-aware mechanisms supporting a real-time services provision in a highly mobile environment.
Directional Coronary Collateral Growth with Chronic Circumflex Occlusion in the Dog

The object of this study was to determine whether coronary collateral resistances were dependent on the direction of perfusion and to investigate whether a pattern of collateral growth with gradual circumflex occlusion could be discerned. In 12 dogs an Ameroid occluder was placed on the circumflex for 1 month, and in six dogs for 3 months; 12 dogs served as controls. The circumflex, left anterior descending, and right coronary arteries were separately but simultaneously perfused in an isolated heart preparation in which the vasculature was maximally dilated with dipyridamole. Collateral flows were determined by measuring retrograde flows for two vessels simultaneously. The results showed that collateral flows from the right to the left coronaries in control dogs were 3.5-fold larger than when these collateral beds were perfused in the opposite direction. This difference in the 1-and 3-month Ameroid groups was approximately 20-fold. Relative to the control group, the collateral resistances from right to left coronary vessels were an average of 10-fold less in the 1- and 3-month groups, but there was no significant difference in resistance in the collaterals perfused from the left to the right. The results strongly suggest that collateral proliferation occurs in response to hypoxia rather than to a pressure gradient, and that collateral development is toward the hypoxic area.
Symmetry-invariant optimization in deep networks

Recent works have highlighted scale invariance or symmetry that is present in the weight space of a typical deep network and the adverse effect that it has on the Euclidean gradient based stochastic gradient descent optimization. In this work, we show that these and other commonly used deep networks, such as those which use a max-pooling and sub-sampling layer, possess more complex forms of symmetry arising from scaling based reparameterization of the network weights. We then propose two symmetry-invariant gradient based weight updates for stochastic gradient descent based learning. Our empirical evidence based on the MNIST dataset shows that these updates improve the test performance without sacrificing the computational efficiency of the weight updates. We also show the results of training with one of the proposed weight updates on an image segmentation problem.