Miracle-dz/UniFAR-FTUs huggingface dataset:
Reducing the optimum value : FPT inapproximability , for Set

Fixed parameter ρ(k) inapproximability in minimization problems, is given some instance I of a problem with optimum opt, find some k ≥ opt and prove that it is not possible to compute a solution of value ρ(k) · k, usually, under the Exponential Time Conjecture eth. If opt is known inapproximability in terms of opt implies inapproximability in terms of k. An (r, t)-fpt-hardness is showing that the problem admits no r(opt) approximation that runs in time t(opt)nO(1) (for maximization problems any solution has to be super constant). In this paper we are only interested in t(opt) that is super exponential in opt. Fellows [6] conjectured that Set cover and Clique are (r, t)-fpt-hard for any pair of non-decreasing functions r, t and input parameter k. We give the first inapproximability for these problems that runs in time super exponential in opt. Our paper is also the first to introduce systematic techniques to reduce the value of the optimum. We prove that under the exponential time hypothesis (eth) [10] and the projection game conjecture [15], Set cover is (r, t)-fpt-hard for r(opt) = (logopt)1+γ and t(opt) = exp(Θ(opt(logopt f ))) for a constants f, γ > 0. Note that t(opt) is significantly super-exponential in opt. Under eth alone we can get c ln opt inapproximability for some constant c with the same running time in opt as above. Under a qualitatively stronger version of the pgc, we can improve this hardness to r(opt) = optδ and t(opt) = exp(exp(optδ)) for some constant δ > 0. For Clique we prove that for any running time t(opt) (even huge) there is a super constant increasing function x(opt) so that Clique is (r, t)-fpt-hard for r(opt) = x(opt). We also prove x(opt) inapproximability in time 2o(n) time with n the Clique instance size. Feige et al. [5], show that instances of Clique with opt ≤ log n can be solved exactly in time significantly smaller than nlogn, np admits sub-exponential simulation. We improve [5], in two ways. We prove x(opt) inapproximability for Clique which may be much stronger than ruling out an exact solution, for such small values of opt. However, our main improvement is that this inapproximability holds even for time 2o(n), an almost exponentially larger running time than the running time of Feige et al [5]. The Minimum Maximal Independent Set (mmis) problem, is to find the maximal independent set containing minimum number of vertices, in a given graph. Assuming eth, we prove that for any r, t the problem admits no (r, t)-fpt approximation. In this case we say that we proved the the Fellows Conjecture for the problem.
Parental understanding of wheeze and its impact on asthma prevalence estimates

The epidemiology of wheeze in children, when assessed by questionnaires, is dependent on parents' understanding of the term “wheeze”. In a questionnaire survey of a random population sample of 4,236 children aged 6–10 yrs, parents' definition of wheeze was assessed. Predictors of a correct definition were determined and the potential impact of incorrect answers on prevalence estimates from the survey was assessed. Current wheeze was reported by 13.2% of children. Overall, 83.5% of parents correctly identified “whistling or squeaking” as the definition of wheeze; the proportion was higher for parents reporting wheezy children (90.4%). Frequent attacks of reported wheeze (adjusted odds ratio (OR) 3.0), maternal history of asthma (OR 1.5) and maternal education (OR 1.5) were significantly associated with a correct answer, while the converse was found for South Asian ethnicity (OR 0.6), first language not English (OR 0.6) and living in a deprived neighbourhood (OR 0.6). In summary, the present study showed that misunderstanding could lead to an important bias in assessing the prevalence of wheeze, resulting in an underestimation in children from South Asian and deprived family backgrounds. Prevalence estimates for the most severe categories of wheeze might be less affected by this bias and questionnaire surveys on wheeze should incorporate measures of parents' understanding of the term wheeze.
Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes

Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4∼3.9 × 106 copies per gram dry weight) and of intertidal mudflat (5.5∼5.8 × 106 copies per gram dry weight) was observed, but higher abundance (6.9 × 106 to 1.02 × 108 copies per gram dry weight) was found in subsurface samples of both sediment types. Aerobic MOB were more abundant in surface layers (6.7∼11.1 × 105 copies per gram dry weight) than the subsurface layers (1.2∼5.9 × 105 copies per gram dry weight) based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal mudflat, but less pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51 × 108 copies per gram dry weight) and pmoA gene (1.56 × 107 copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of mcrA gene-harboring communities in nSCS and stratification of mcrA and pmoA gene diversity and abundance in the Mai Po Nature Reserve.
A bipartite sequence element associated with matrix/scaffold attachment regions.

We have identified a MAR/SAR recognition signature (MRS) which is common to a large group of matrix and scaffold attachment regions. The MRS is composed of two degenerate sequences (AATAAYAA and AWWRTAANNWWGNNNC) within close proximity. Analysis of >300 kb of genomic sequence from a variety of eukaryotic organisms shows that the MRS faithfully predicts 80% of MARs and SARs. In each case where we find a MRS, the corresponding DNA region binds specifically to the nuclear scaffold. Although all MRSs are associated with a SAR, not all known SARs and MARs contain a MRS, suggesting that at least two classes exist, one containing a MRS, the other not. Evidence is presented that the two sequence elements of the bipartite MRS occupy a position on the nucleosome near the dyad axis, together creating a putative protein binding site. The identification of a MAR- and SAR-associated DNA element is an important step forward towards understanding the molecular mechanisms of these elements. It will allow: (i) analysis of the genomic location of SARs, e.g. in relationship to genes, based on sequence information alone, rather than on the basis of an elaborate biochemical assay; (ii) identification and analysis of proteins that specifically bind to the MRS.
Roles of the Espin Actin-Bundling Proteins in the Morphogenesis and Stabilization of Hair Cell Stereocilia Revealed in CBA/CaJ Congenic Jerker Mice

Hearing and vestibular function depend on mechanosensory staircase collections of hair cell stereocilia, which are produced from microvillus-like precursors as their parallel actin bundle scaffolds increase in diameter and elongate or shorten. Hair cell stereocilia contain multiple classes of actin-bundling protein, but little is known about what each class contributes. To investigate the roles of the espin class of actin-bundling protein, we used a genetic approach that benefited from a judicious selection of mouse background strain and an examination of the effects of heterozygosity. A congenic jerker mouse line was prepared by repeated backcrossing into the inbred CBA/CaJ strain, which is known for excellent hearing and minimal age-related hearing loss. We compared stereocilia in wild-type CBA/CaJ mice, jerker homozygotes that lack espin proteins owing to a frameshift mutation in the espin gene, and jerker heterozygotes that contain reduced espin levels. The lack of espins radically impaired stereociliary morphogenesis, resulting in stereocilia that were abnormally thin and short, with reduced differential elongation to form a staircase. Mean stereociliary diameter did not increase beyond ∼0.10–0.14 µm, making stereocilia ∼30%–60% thinner than wild type and suggesting that they contained ∼50%–85% fewer actin filaments. These characteristics indicate a requirement for espins in the appositional growth and differential elongation of the stereociliary parallel actin bundle and fit the known biological activities of espins in vitro and in transfected cells. The stereocilia of jerker heterozygotes showed a transient proximal-distal tapering suggestive of haploinsufficiency and a slowing of morphogenesis that revealed previously unrecognized assembly steps and intermediates. The lack of espins also led to a region-dependent degeneration of stereocilia involving shortening and collapse. We conclude that the espin actin-bundling proteins are required for the assembly and stabilization of the stereociliary parallel actin bundle.
Identification of Divergent Protein Domains by Combining HMM-HMM Comparisons and Co-Occurrence Detection

Identification of protein domains is a key step for understanding protein function. Hidden Markov Models (HMMs) have proved to be a powerful tool for this task. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in sequenced organisms. This is done via sequence/HMM comparisons. However, this approach may lack sensitivity when searching for domains in divergent species. Recently, methods for HMM/HMM comparisons have been proposed and proved to be more sensitive than sequence/HMM approaches in certain cases. However, these approaches are usually not used for protein domain discovery at a genome scale, and the benefit that could be expected from their utilization for this problem has not been investigated. Using proteins of P. falciparum and L. major as examples, we investigate the extent to which HMM/HMM comparisons can identify new domain occurrences not already identified by sequence/HMM approaches. We show that although HMM/HMM comparisons are much more sensitive than sequence/HMM comparisons, they are not sufficiently accurate to be used as a standalone complement of sequence/HMM approaches at the genome scale. Hence, we propose to use domain co-occurrence — the general domain tendency to preferentially appear along with some favorite domains in the proteins — to improve the accuracy of the approach. We show that the combination of HMM/HMM comparisons and co-occurrence domain detection boosts protein annotations. At an estimated False Discovery Rate of 5%, it revealed 901 and 1098 new domains in Plasmodium and Leishmania proteins, respectively. Manual inspection of part of these predictions shows that it contains several domain families that were missing in the two organisms. All new domain occurrences have been integrated in the EuPathDomains database, along with the GO annotations that can be deduced.
A Wireless Network in MosquitoNet

An emerging technology for wireless connectivity provides one of the best combinations of bandwidth, coverage area, and cost for a wireless data network. It also teaches important lessons about software-hardware interface design. To support this vision of ubiquitous connectivity, we are studying issues of wireless and mobile computing at the network, system, and application levels. Our two main goals are to provide seemingly continuous connectivity for mobile hosts, and to support system- and application-level adaptation to dynamically changing network characteristics. We are investigating changes and extensions to standard networking application program interfaces (APIs) that will allow well-written applications to deal gracefully with widely varying network characteristics. When switching between available services, network characteristics can change significantly, even while an application is running.
Locking Made Easy

A priori, locking seems easy: To protect shared data from concurrent accesses, it is sufficient to lock before accessing the data and unlock after. Nevertheless, making locking efficient requires fine-tuning (a) the granularity of locks and (b) the locking strategy for each lock and possibly each workload. As a result, locking can become very complicated to design and debug. We present GLS, a middleware that makes lock-based programming simple and effective. GLS offers the classic lock-unlock interface of locks. However, in contrast to classic lock libraries, GLS does not require any effort from the programmer for allocating and initializing locks, nor for selecting the appropriate locking strategy. With GLS, all these intricacies of locking are hidden from the programmer. GLS is based on GLK, a generic lock algorithm that dynamically adapts to the contention level on the lock object. GLK is able to deliver the best performance among simple spinlocks, scalable queue-based locks, and blocking locks. Furthermore, GLS offers several debugging options for easily detecting various lock-related issues, such as deadlocks. We evaluate GLS and GLK on two modern hardware platforms, using several software systems (i.e., HamsterDB, Kyoto Cabinet, Memcached, MySQL, SQLite) and show how GLK improves their performance by 23% on average, compared to their default locking strategies. We illustrate the simplicity of using GLS and its debugging facilities by rewriting the synchronization code for Memcached and detecting two potential correctness issues.
NoC Interface for a Protocol Processor

In this paper we present our design and implementation of Network-on-Chip (NoC) support into our TACO protocol processor architecture. Our signaling scheme is Virtual Component Interface standard (VCI) compliant. Due to the dataand I/O-intensive nature of protocol processing, memory access from I/O logic plays a key role in NoC interface design. We have addressed this problem by using dual-port memory for protocol data units (PDUs) and a separate single port memory for other user data. We evaluated our NoC interface with VHDL synthesis of a case study in IPv6 processing. Based on our simulations and synthesis, the logic part is able to operate at 200 MHz in 0.18 μm CMOS technology. Adding a NoC interface into our architecture did not considerably increase area and power costs.
Year-Long Monitoring of Physico-Chemical and Biological Variables Provide a Comparative Baseline of Coral Reef Functioning in the Central Red Sea

Coral reefs in the central Red Sea are sparsely studied and in situ data on physico-chemical and key biotic variables that provide an important comparative baseline are missing. To address this gap, we simultaneously monitored three reefs along a cross-shelf gradient for an entire year over four seasons, collecting data on currents, temperature, salinity, dissolved oxygen (DO), chlorophyll-a, turbidity, inorganic nutrients, sedimentation, bacterial communities of reef water, and bacterial and algal composition of epilithic biofilms. Summer temperature (29–33°C) and salinity (39 PSU) exceeded average global maxima for coral reefs, whereas DO concentration was low (2–4 mg L-1). While temperature and salinity differences were most pronounced between seasons, DO, chlorophyll-a, turbidity, and sedimentation varied most between reefs. Similarly, biotic communities were highly dynamic between reefs and seasons. Differences in bacterial biofilms were driven by four abundant families: Rhodobacteraceae, Flavobacteriaceae, Flammeovirgaceae, and Pseudanabaenaceae. In algal biofilms, green crusts, brown crusts, and crustose coralline algae were most abundant and accounted for most of the variability of the communities. Higher bacterial diversity of biofilms coincided with increased algal cover during spring and summer. By employing multivariate matching, we identified temperature, salinity, DO, and chlorophyll-a as the main contributing physico-chemical drivers of biotic community structures. These parameters are forecast to change most with the progression of ocean warming and increased nutrient input, which suggests an effect on the recruitment of Red Sea benthic communities as a result of climate change and anthropogenic influence. In conclusion, our study provides insight into coral reef functioning in the Red Sea and a comparative baseline to support coral reef studies in the region.
Non-asymptotic theory of random matrices: extreme singular values

The classical random matrix theory is mostly focused on asymptotic spectral properties of random matrices as their dimensions grow to infinity. At the same time many recent applications from convex geometry to functional analysis to information theory operate with random matrices in fixed dimensions. This survey addresses the non-asymptotic theory of extreme singular values of random matrices with independent entries. We focus on recently developed geometric methods for estimating the hard edge of random matrices (the smallest singular value).
Encouraging Bystanders to Promote Positive Parenting and Prevent Child Maltreatment in Retail Settings: Results of an Exploratory Qualitative Study

ABSTRACT Community-level bystander approaches with media campaigns have successfully reduced sexual violence, but these programs have not been developed for child maltreatment prevention. This study informs the development of such programs in retail settings. Data were collected using focus groups with parents (n = 29) and surveys with child abuse experts (n = 10). Participants were asked how retail environments and employees could support parents during shopping excursions and what employees should do if they witnessed a concerning interaction. Participants highlighted (a) the need for in-depth training of employees to engage with parents and children to promote positive interactions and intervene in concerning situations; (b) the importance of the built environment (i.e., physical design and layout) to reduce stress and establish positive social norms through store-wide messaging; and (c) the role of parents in establishing expectations and actively including children in shopping. Future research should test approaches to training and engaging retail employees as supportive bystanders.
Topology Control for Time-Evolving and Predictable Delay-Tolerant Networks

In delay tolerant networks (DTNs), the lack of continuous connectivity, network partitioning, and long delays make design of network protocols very challenging. Previous DTN research mainly focuses on routing and information propagation. However, with large number of wireless devices' participation, how to maintain efficient and dynamic topology of the DTN becomes crucial. In this paper, we study the topology control problem in a predictable DTN where the time-evolving network topology is known a priori or can be predicted. We first model such time-evolving network as a directed space-time graph which includes both spacial and temporal information. The aim of topology control is to build a sparse structure from the original space-time graph such that (1) the network is still connected over time and supports DTN routing between any two nodes; (2) the total cost of the structure is minimized. We prove that this problem is NP-hard, and then propose two greedy-based methods which can significant reduce the total cost of topology while maintain the connectivity over time. Finally, we illustrate how the proposed methods can work for undirected DTNs. Simulations have been conducted on both random DTN networks and real-world DTN tracing data. Results demonstrate the efficiency of the proposed topology control methods.
Organizational readiness in corrections

IMPROVING OFFENDER REENTRY has become a primary concern of many correctional agencies due to the growing size and cost of incarcerating individuals. Over the last 3 decades, the criminal justice system has grown to control one in thirty-one adults (Pew Foundation, 2009). This amounts to approximately 7.3 million adults either incarcerated or on some type of community supervision (Bureau of Justice Statistics, 2010). The increase has been reflected in the increasing corrections budget, estimated at 68 billion dollars, outgrowing the spending on any other government service (Pew Foundation, 2009). Furthermore, Langan and Levin (2002) examined 1994 recidivism data from 15 states and found that approximately 68 percent of individuals were re-arrested within three years. The same data revealed that a little over half of those released were re-incarcerated for either a new sentence or a technical violation within the following 3 years. As a means of addressing these rising numbers, many correctional agencies are pursuing the use of evidence-based practices in reentry to increase public safety and the opportunities for individuals to succeed once released. However, implementation of these practices is often met with resistance and challenge. This article examines the impact of a continuous on-site training model to advance the implementation of evidence-based practices in correctional settings.
Fidelity to and satisfaction with prescribed curriculum in an Arab educational context: ESL teachers' perspective

ABSTRACT Educational institutions in the Arab Gulf are requiring rapid changes to enhance English language learning to keep up with globalization and economic growth. This urges the need for investigating policy changes such as effectiveness in curriculum orientations and their impact on the actual process of teaching in order to gauge how educational institutions are performing. This paper reports the findings of a survey study on curriculum enactment in the English Language Foundation Program of a higher education institution in the Arab Gulf region. Data collection methods included a survey and interview with teachers investigating their opinions about the curriculum, how much support it offers teachers to reach the objectives of the course, and whether/to what extent as well as the reasons why they feel they need to modify the curriculum at the implementation level. Results showed that most teachers exercised discretion in using the prescribed curriculum materials due to individual contextual factors. Results also indicated that either when implementing the prescribed or modified materials, most participants highlighted the importance of using reliable quality resource materials that can help teachers as well as students to enhance the learning process. Findings have implications for English as a second language curriculum design in Arab higher educational contexts.
Hit Song Science Once Again a Science?

We are interested in the Music Information Retrieval task that aims at predicting whether a given song will be a commercial success prior to its distribution, based on its audio. This is the topic of what is commonly referred to as ‘Hit Song Science’ (HSS). The underlying assumption behind HSS is that popular songs are similar with respect to a set of features that make them appealing to a majority of people. These features could then be exploited by learning machines in order to predict whether a song will rise to a high position in the chart.