Miracle-dz/UniFAR-FTUs huggingface dataset:
Needles and straw in haystacks: Empirical Bayes estimates of possibly sparse sequences

An empirical Bayes approach to the estimation of possibly sparse sequences observed in Gaussian white noise is set out and investigated. The prior considered is a mixture of an atom of probability at zero and a heavy-tailed density y, with the mixing weight chosen by marginal maximum likelihood, in the hope of adapting between sparse and dense sequences. If estimation is then carried out using the posterior median, this is a random thresholding procedure. Other thresholding rules employing the same threshold can also be used. Probability bounds on the threshold chosen by the marginal maximum likelihood approach lead to overall risk bounds over classes of signal sequences of length n, allowing for sparsity of various kinds and degrees. The signal classes considered are nearly black sequences where only a proportion η is allowed to be nonzero, and sequences with normalized p norm bounded by η, for η > 0 and 0 1. Simulations show excellent performance. For appropriately chosen functions y, the method is computationally tractable and software is available. The extension to a modified thresholding method relevant to the estimation of very sparse sequences is also considered.
Unintentional Processing of Motivational Valence

Recent motivational affective priming studies (Moors & De Houwer, 2001; Moors, De Houwer, & Eelen, 2004) showed that primes that indicate success on a goal-inducing task facilitate positive target responses whereas primes that indicate failure on that task facilitate negative target responses. In the current studies, we examined whether these priming effects depend on consciously intentional processing of the motivational valence of the primes. In Experiment 1, the outcome of success or failure was presented not only immediately before the target (i.e., the prime) but also a second time after the target response. This should encourage participants to ignore the prime. In Experiment 2, participants were asked to respond to the targets within 600 ms after target onset. As a result, participants had little opportunity to process the motivational prime valence in a consciously intentional way. Nevertheless, strong affective priming effects were found in both studies. These results provide additional support for the claim that motivational valence can be processed without the conscious intention to do so.
Performance analysis of the memory management unit under scale-out workloads

Much attention has been given to the efficient execution of the scale-out applications that dominate in datacenter computing. However, the effects of the hardware support in the Memory Management Unit (MMU) in combination with the distinct characteristics of the scale-out applications have been largely ignored until recently. In this paper, we comprehensively quantify the MMU overhead on a real machine leveraging the use of performance counters on a collection of emerging scale-out applications. We show that the MMU overhead accounts for up to 16% of the total execution time due to the high TLB miss rates and the interference between page walks and application data in the cache hierarchy. We find that decreasing the MMU overhead - with large pages - may improve the application performance by up to 13.9%. However, the limited MMU support for large pages in combination with the workloads' low memory locality may even harm the performance when large pages are enabled. By comparing the expected and measured application speedup, we observe a performance gap of up to 3.8%, indicating that any improvements in the MMU may result in more efficient utilization of the available execution resources. Finally, we find that the MMU overhead remains high for most scale-out applications even in the presence of large pages, leaving ample space for optimizations. In response, we present upper bounds for perfect MMU optimizations that motivate rethinking its design in the context of the scale-out applications.
The Cold Transit of Southern Ocean Upwelling

The upwelling of deep waters in the Southern Ocean is a critical component of the climate system. The time and zonal mean dynamics of this circulation describe the upwelling of Circumpolar Deep Water and the downwelling of Antarctic Intermediate Water. The thermodynamic drivers of the circulation and their seasonal cycle play a potentially key regulatory role. Here an observationally constrained ocean model and an observation‐based seasonal climatology are analyzed from a thermodynamic perspective, to assess the diabatic processes controlling overturning in the Southern Ocean. This reveals a seasonal two‐stage cold transit in the formation of intermediate water from upwelled deep water. First, relatively warm and saline deep water is transformed into colder and fresher near‐surface winter water via wintertime mixing. Second, winter water warms to form intermediate water through summertime surface heat fluxes. The mixing‐driven pathway from deep water to winter water follows mixing lines in thermohaline coordinates indicative of nonlinear processes.
Memory-enhancing intra-basolateral amygdala infusions of clenbuterol increase Arc and CaMKIIα protein expression in the rostral anterior cingulate cortex

Activation of β-adrenoceptors in the basolateral complex of the amygdala (BLA) modulates memory through interactions with multiple memory systems. The cellular mechanisms for this interaction remain unresolved. Memory-modulating BLA manipulations influence expression of the protein product of the immediate early gene activity-regulated cytoskeletal-associated protein (Arc) in the dorsal hippocampus, and hippocampal expression of Arc protein is critically involved in memory consolidation and long-term potentiation. The present studies examined whether this influence of the BLA is specific to the hippocampus and to Arc protein. Like the hippocampus, the rostral portion of the anterior cingulate cortex (rACC) is involved in the consolidation of inhibitory avoidance (IA) memory, and IA training increases Arc protein in the rACC. Because the BLA interacts with the rACC in the consolidation of IA memory, the rACC is a potential candidate for further studies of BLA modulation of synaptic plasticity. The alpha isoform of the Calcium/Calmodulin-dependent protein kinase II (CaMKIIα) and the immediate early gene c-Fos are involved in long-term potentiation and memory. Both Arc and CaMKIIα proteins can be translated in isolated synapses, where the mRNA is localized, but c-Fos protein remains in the soma. To examine the influence of memory-modulating manipulations of the BLA on expression of these memory and plasticity-associated proteins in the rACC, male Sprague–Dawley rats were trained on an IA task and given intra-BLA infusions of either clenbuterol or lidocaine immediately after training. Findings suggest that noradrenergic stimulation of the BLA may modulate memory consolidation through effects on both synaptic proteins Arc and CaMKIIα, but not the somatic protein c-Fos. Furthermore, protein changes observed in the rACC following BLA manipulations suggest that the influence of the BLA on synaptic proteins is not limited to those in the dorsal hippocampus.
Functional Cus1p Is Found with Hsh155p in a Multiprotein Splicing Factor Associated with U2 snRNA

ABSTRACT To explore the dynamics of snRNP structure and function, we have studied Cus1p, identified as a suppressor of U2 snRNA mutations in budding yeast. Cus1p is homologous to human SAP145, a protein present in the 17S form of the human U2 snRNP. Here, we define the Cus1p amino acids required for function in yeast. The segment of Cus1p required for binding to Hsh49p, a homolog of human SAP49, is contained within an essential region of Cus1p. Antibodies against Cus1p coimmunoprecipitate U2 snRNA, as well as Hsh155p, a protein homologous to human SAP155. Biochemical fractionation of splicing extracts and reconstitution of heat-inactivated splicing extracts from strains carrying a temperature-sensitive allele ofCUS1 indicate that Cus1p and Hsh155p reside in a functional, high-salt-stable complex that is salt-dissociable from U2 snRNA. We propose that Cus1p, Hsh49p, and Hsh155p exist in a stable protein complex which can exchange with a core U2 snRNP and which is necessary for U2 snRNP function in prespliceosome assembly. The Cus1p complex shares functional as well as structural similarities with human SF3b.
Sequential randomized algorithms: A probabilistic cutting plane technique based on maximum volume ellipsoid center

A sequential randomized algorithm is developed for robust optimization which is to minimize a linear objective function subject to a parameter dependent convex constraint for all uncertain parameter values. The algorithm is realized as a probabilistic cutting plane technique based on maximum volume ellipsoid center, where candidates of the optimal value and of the optimal solution are sequentially updated by a series of cutting planes generated by random samples of the uncertain parameters. This algorithm stops in a finite number of iterations which is of polynomial order of the problem size, and provides a feasible solution of a chance constraint optimization which corresponds to a probabilistic relaxation of the robust optimization with a prescribed probability. Then, it is shown that the algorithm can find a suboptimal value whose lower bound is the optimal value of the chance constrained optimization with the prescribed probability and whose upper bound is determined by the optimal value of the robust optimization.
X-linked Charcot-Marie-Tooth disease with connexin 32 mutations

Objective: To relate X-linked Charcot-Marie-Tooth disease (CMTX) phenotypes to gender and type of neuropathy by the study of a large series of CMTX patients with proven Cx32 point mutations. Background: CMTX is an X-linked form of Charcot-Marie-Tooth disease, caused by mutations in the connexin 32 gene. Males are usually more severely affected and have slower nerve conduction velocities than females. Methods: Forty-eight patients from 10 families with Cx32 mutations were examined clinically and electrophysiologically. Mutations were characterized in index cases by automatic sequencing and detected in at-risk individuals by polymerase chain reaction (PCR)-restriction or single strand conformation polymorphism (SSCP) analysis. Two patients from different families had light and electron microscopy examination of a sural nerve biopsy. Results: Males (n = 21) were more severely affected than females (n = 27), although six of the females were severely disabled. In the majority of males, the median motor nerve conduction velocity (MNCV) was between 30 and 40 m/s, whereas in females it ranged from 30 to normal values. Two children with mutation, a 6-year-old boy and a 7-year-old girl, were normal clinically and electrophysiologically. In most patients, the amplitude of motor nerve compound muscle action potentials (CMAP) was reduced in all nerves tested. MNCV was reduced as a function of the degree of axonal loss. A significant correlation was found between the decrease in CMAP amplitude and MNCV in the median, ulnar, and peroneal nerves. Sural nerve biopsies in one patient with a missense and one with a nonsense mutation both showed axonal neuropathy. Conclusion: Electrophysiologic and histologic findings support primary axonal neuropathy in CMTX with Cx32 mutations. Clinical and electrophysiologic data in males with different missense mutations in the of Cx32 gene differed significantly. Furthermore, males with a nonsense mutation (Arg22Stop) had earlier onset and a more severe phenotype than males with missense mutations.
Associations of systemic diseases, smoking and contact lens wear with severity of dry eye

Citation information: Lee S‐Y, Petznick A & Tong L. Associations of systemic diseases, smoking and contact lens wear with severity of dry eye. Ophthalmic Physiol Opt 2012, 32, 518–526. doi: 10.1111/j.1475‐1313.2012. 00931.x
Multicycle Dynamics of the Aksay Bend Along the Altyn Tagh Fault in Northwest China: 2. The Realistically Complex Fault Geometry

We study rupture behavior of the Aksay bend along the Altyn Tagh fault in northwest China over multiple earthquake cycles. A finite element method is used to numerically simulate spontaneous rupture during a coseismic process, and a viscoelastic model is used to analytically compute the fault stresses during an interseismic process. We find that the Aksay bend is an effective barrier to halt dynamically propagating ruptures from either side of the bend within a range of model parameters, with statistically only about 10% of ruptures jumping across the bend and propagating through almost the entire local fault system. Secondary complexities in fault geometry within the bend, in particular those portions that align relatively well with the regional strike of the fault system, play a critical role in these occasionally jumping ruptures. Well‐developed fault patches with shear stress close to shear strength allow dynamically propagating ruptures to penetrate into the bend and are more susceptible to the dynamic triggering that enables rupture to jump across the bend onto the other strand. We identify additionally nine large rupture scenarios with different occurrences, and most of them rupture one strand outside the bend with triggered slip on some portions of the same or the other strand within the bend. Slip rate distributions from the models show significantly reduced fault slip within the bend and a permanently locked portion on the south strand near the peak of the Altun Mountains. These findings have important implications for seismic hazard assessments of complex fault systems worldwide.
PAPR reduction using the combination of precoding and Mu-Law companding techniques for OFDM systems

The high peak-to-average power ratio (PARR) of OFDM signals is a primary disadvantage that single-carrier modulation does not have. Because of using muti-carrier modulation technique, OFDM systems also exhibit a large out-of-band (OOB) emission that can potentially interfere with neighboring transmissions. The precoding scheme using with more null subcarriers achieves significant better PAPR reduction than that using with less subcarriers. But the use of more null subcarriers promotes out-of-band power emission and reduces the transmission rate. The compander, applying Mu (μ)-Law compression and expansion at the transmitter and receiver, is simple and nonlinear method for reducing PAPR. Although the use of nonlinear companding signal has effective reduction in PAPR, it also promotes OOB emission. This paper presents a combination scheme, which using a combination of precoding by utilizing least null subcarriers in frequency domain and nonlinear companding technique by applying proper Mu-Law characteristic in time domain, for reducing PAPR. Simulation results show that the proposed scheme achieves a beneficial trade-off between the reduction of PAPR and OOB power emission in OFDM systems.
An empirical study of human Web assistants: implications for user support in Web information systems

User support is an important element in reaching the goal of universal usability for Web information systems. Recent developments indicate that human involvement in user support is a step towards this goal. However, most such efforts are currently being pursued on a purely intuitive basis. This, empirical findings about the role of human assistants are important. In this paper we present the findings from a field study of a general user support model for Web information systems. We show that integrating human assistance into Web systems is a way to provide efficient user support. Further, this integration makes a Web site more fun to use and increases the user's trust in the site. The support also improves the site atmosphere. Our findings are summarised as recommendations and design guidelines for decision-makers and developers Web systems.
The prognosis of cyclical vomiting syndrome

AIMS The medium term prognosis of cyclical vomiting syndrome (CVS) was studied to determine the proportion of affected individuals who had gone on to develop headaches fulfilling the International Headache Society criteria for migraine. METHODS Twenty six (76%) of 34 CVS sufferers identified from the authors' clinical records were traced, and all agreed to participate. Each child was matched to a control, and telephone interviews were conducted using a standardised questionnaire. RESULTS Thirteen (50%) of the subjects had continuing CVS and/or migraine headaches while the remainder were currently asymptomatic. The prevalence of past or present migraine headaches in subjects (46%) was significantly higher than in the control population (12%). CONCLUSION Results support the concept that CVS is closely related to migraine.
Health Status of Older US Workers and Nonworkers, National Health Interview Survey, 1997–2011

Introduction Many US workers are increasingly delaying retirement from work, which may be leading to an increase in chronic disease at the workplace. We examined the association of older adults’ health status with their employment/occupation and other characteristics. Methods National Health Interview Survey data from 1997 through 2011 were pooled for adults aged 65 or older (n = 83,338; mean age, 74.6 y). Multivariable logistic regression modeling was used to estimate the association of socioeconomic factors and health behaviors with 4 health status measures: 1) self-rated health (fair/poor vs good/very good/excellent); 2) multimorbidity (≤1 vs ≥2 chronic conditions); 3) multiple functional limitations (≤1 vs ≥2); and 4) Health and Activities Limitation Index (HALex) (below vs above 20th percentile). Analyses were stratified by sex and age (young–old vs old–old) where interactions with occupation were significant. Results Employed older adults had better health outcomes than unemployed older adults. Physically demanding occupations had the lowest risk of poor health outcomes, suggesting a stronger healthy worker effect: service workers were at lowest risk of multiple functional limitations (odds ratio [OR], 0.82; 95% confidence interval [CI], 0.71–0.95); and blue-collar workers were at lowest risk of multimorbidity (OR, 0.84; 95% CI, 0.74–0.97) and multiple functional limitation (OR, 0.84; 95% CI, 0.72–0.98). Hispanics were more likely than non-Hispanic whites to report fair/poor health (OR, 1.62; 95% CI, 1.52–1.73) and lowest HALex quintile (OR, 1.21; 95% CI, 1.13–1.30); however, they were less likely to report multimorbidity (OR, 0.78; 95% CI, 0.73–0.83) or multiple functional limitations (OR, 0.82; 95% CI, 0.77–0.88). Conclusion A strong association exists between employment and health status in older adults beyond what can be explained by socioeconomic factors (eg, education, income) or health behaviors (eg, smoking). Disability accommodations in the workplace could encourage employment among older adults with limitations.
Water erosion impact on soil and carbon redistributions within uplands of the Mekong

erosion removed annually 14.1 t ha � -1 of sediment and 0.69 t ha � -1 of SOC from the study site. This is equivalent to 7.75 and 0.51 Pg yr �1 , respectively, for the uplands of the Mekong basin as a whole. When compared to the bulk soil, the eroded soil material was enriched in SOC and BC by factors of 2.3 and 1.4, respectively. The annual yields of soil material from the micro-catchment were 3 times lower for sediment and 6 times lower for SOC than those from the micro-plots. From the micro-plots to the catchment, the yields decreased by a factor of 25 for sediment and 59 for SOC. Although a considerable amount of soil material is detached from its original site by water erosion, most of this material is redistributed within the landscapes, being deposited in places acting as sinks, such as hillslopes, and valley bottoms where BC is preferentially deposited. The loads from the catchment of 0.56 t ha � -1 yr � -1 for sediment and 0.016 t ha � -1 yr � -1 for SOC were considerable, corresponding to 0.31 Pg of sediment and 0.01 Pg of SOC for the Mekong basin uplands as a whole. These results on the selective water erosion of soil material, SOC and BC on sloping lands of South-East Asia allow the source and sink functions of the sloping lands of tropical landscapes to be better understood.
A computer based model for lung cancer analysis

In this paper, we have presented an innovative methodology to convey connection between physical and mechanical properties of lung tissue in some lung cancer diseases. It is proposed in this method to combine computed tomography (CT) medical images, image processing and Finite Element (FE) technique to grasp the patient lung tissue response under gradual stages of lung cancer. Finite Element models based on lung CT images of different patients are used to analyse the real behaviour of lung tissue and detect the difference between mechanical parameters in both normal and pathologic cases. Results show that normal lungs display distinct superiority in strength, and expansion properties. It is also notable that we have present new mechanical parameters to clearly describe the evolution of different patient’s lung cancers cases. Investigating lung cancer using such techniques is very promising to enhances data monitoring towards the development of automated diagnosis systems.
Association between Mycobacterium avium subspecies paratuberculosis and lymph node size in New Zealand farmed deer (Cervus elaphus)

AIMS: To develop and validate criteria for identification of abnormal lymph nodes (LN) at commercial slaughter, for the purpose of national surveillance for Mycobacterium avium subspecies paratuberculosis (Map) in New Zealand farmed deer. This included estimation of the predictive value of abnormal LN for Map infection; a standard circumference cut-point for measurement of abnormal LN; and identification of risk factors associated with increasing LN circumference. METHODS: In Study 1, official assessors sampled 129 LN with macroscopically visible abnormalities (abnormal LN) from 76 deer herds between May and November 2007. LN samples were cultured for Map, with culture-negative LN further examined for typical histopathological changes. The predictive value of abnormal LN for Map infection was calculated and significance of herd location (North or South Island) assessed. In Study 2, the circumferences of 412 mesenteric LN (MLN) from 79 herds were measured between October 2007 and January 2009, with samples cultured for Map and examined for eight histopathological features. The minimum circumference of an abnormal MLN was defined, based on an arbitrary >95% specificity of a culture-positive Map diagnosis. Associations between the predictor variables Map culture status, carcase weight, animal age and gender, and histopathological features, and increasing MLN circumference were assessed using a linear mixed-effects model. RESULTS: Based solely on culture, the predictive value of abnormal LN for Map infection was 92.2 (95% CI: 86.2–96.2)% with no difference between the North and South Islands (p = 0.09). Inclusion of three culture-negative LN with histopathological changes typical of Map infection increased the predictive value estimate to 94.6 (95% CI: 89.2–97.3)%. The minimum circumference of an abnormal MLN was defined as 55 mm, with a sensitivity of Map detection at this cut-point of approximately 12%. Increasing MLN circumference was positively associated with the presence of moderate follicular hyperplasia (p < 0.01), focal granulomas (p < 0.01) and a synergistic interaction between focal granulomas and Map status (p = 0.03). CONCLUSIONS: Deer MLN with macroscopically visible abnormalities and/or a circumference of >55 mm have >95% likelihood of Map infection. However, sensitivity of Map diagnosis in MLN with circumference of >55 mm was 12%, indicating use of abnormal LN as a sole criterion in national surveillance for Map in slaughtered deer will underestimate animal-level prevalence.