Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding Differentially Covarying Needles in a Temporally Evolving Haystack: A Scan Statistics Perspective

Recent results in coupled or temporal graphical models offer schemes for estimating the relationship structure between features when the data come from related (but distinct) longitudinal sources. A novel application of these ideas is for analyzing group-level differences, i.e., in identifying if trends of estimated objects (e.g., covariance or precision matrices) are different across disparate conditions (e.g., gender or disease). Often, poor effect sizes make detecting the differential signal over the full set of features difficult: for example, dependencies between only a subset of features may manifest differently across groups. In this work, we first give a parametric model for estimating trends in the space of SPD matrices as a function of one or more covariates. We then generalize scan statistics to graph structures, to search over distinct subsets of features (graph partitions) whose temporal dependency structure may show statistically significant group-wise differences. We theoretically analyze the Family Wise Error Rate (FWER) and bounds on Type 1 and Type 2 error. On a cohort of individuals with risk factors for Alzheimer's disease (but otherwise cognitively healthy), we find scientifically interesting group differences where the default analysis, i.e., models estimated on the full graph, do not survive reasonable significance thresholds.
Linguistic structure across time: ERP responses to coordinated and uncoordinated noun phrases

ABSTRACT Relatively little is known about how linguistic structure is neurally encoded. The current study examines a relatively subtle manipulation of syntactic and semantic structure: the difference between reading a list of two noun phrases (“sunlit ponds ### green umbrellas”) and their syntactic coordination (“sunlit ponds and green umbrellas”). In two ERP experiments, the presence of the coordinator resulted in an increased anterior negativity across the entire second noun phrase, even though coordination had no direct relevance for the memory recognition task. These findings demonstrate that structural connectedness exerts strong, ongoing differences in neural activity even when structured and unstructured materials are very tightly matched in sequence and content. These differences may reflect ongoing maintenance of structure in memory, or computation of the more complex semantic or discourse representation associated with syntactic coordination.
Is there a therapeutic benefit of complete lymph node dissection in melanoma patients with low tumor burden in the sentinel node?

In the case of a positive sentinel lymph node (SLN), melanoma patients are recommended to proceed to complete lymph node dissection (CLND). However, CLND for SLN-positive patients – especially with minimal tumor burden in SLN – is becoming more controversial. We analyzed the clinical course of 305 SLN-positive patients with a mean follow-up of 51.1 months by Kaplan–Meier analyses. Overall, 58/305 (17%) patients did not undergo CLND. These were compared with a matched selection of 58 comparable patients who underwent CLND. Moreover, 106/305 patients with minimal tumor burden in SLN (<0.1 mm diameter of the largest tumor deposit) were analyzed separately. Of these 106 patients, 34 did not undergo CLND, whereas 72/106 patients were treated by CLND. In the matched groups, the CLND group and the non-CLND group did not differ significantly with respect to clinical characteristics, characteristics of the primary melanoma, and histopathological parameters of SLN. There were no differences in recurrence-free survival (P=0.765) and overall survival (P=0.844). The total number of regional lymph node metastases and time to regional lymph node metastases were not significantly higher for non-CLND patients. The subgroup of patients with minimal tumor burden in SLN also did not benefit significantly from CLND. In our analyses from a single German center, we could not find any evidence for a therapeutic survival benefit for CLND after positive SLN. However, future prospective randomized trials should confirm these data.
Risk Factors for Delayed Extubation after Ventricular Septal Defect Closure: a Prospective Observational Study

Objective The objective of our study was to determine the feasibility of early extubation and to identify the risk factors for delayed extubation in pediatric patients operated for ventricular septal defect closure. Methods A prospective, observational study was carried out at our Institute. This study involved consecutive 135 patients undergoing ventricular septal defect closure. Patients were extubated if feasible within six hours after surgery. Based on duration of extubation, patients were divided two groups: Group 1= extubation time ≤ 6 hours, Group 2= extubation time >6 hours. Results A total of 99 patients were in Group 1 and 36 patients in Group 2. Duration of ventilation was 4.4±0.9 hours in Group 1 and 25.9±24.9 hours in Group 2 (P<0.001). Univariate analysis showed that young age, low weight, low partial pressure of oxygen, trisomy 21, multiple ventricular septal defect, high vasoactive inotropic score, transient heart block and low cardiac output syndrome were associated with delayed extubation. However, regression analysis revealed that only trisomy 21 (OR: 0.248; 95%CI: 0.176-0.701; P=0.001), low cardiac output syndrome (OR: 0.291; 95%CI: 0.267-0.979; P=0.001), multiple ventricular septal defect (OR: 0.243; 95%CI: 0.147-0.606; P=0.002) and vasoactive inotropic score (OR: 0.174 95%CI: 0.002-0.062; P=0.039) are strongest predictors for delayed extubation. Conclusion Trisomy 21, low cardiac output syndrome, multiple ventricular septal defect and high vasoactive inotropic score are significant risk factors for delay in extubation. Age, weight, pulmonary artery hypertension, size of ventricular septal defect, aortic cross-clamp and cardiopulmonary bypass time did not affect early extubation.
Derivation of the Isotropic Diffusion Source Approximation (IDSA) for Supernova Neutrino Transport by Asymptotic Expansions

We present Chapman--Enskog and Hilbert expansions applied to the $\BigO(v/c)$ Boltzmann equation for the radiative transfer of neutrinos in core-collapse supernovae. Based on the Legendre expansion of the scattering kernel for the collision integral truncated after the second term, we derive the diffusion limit for the Boltzmann equation by truncation of Chapman--Enskog or Hilbert expansions with reaction and collision scaling. We also give asymptotically sharp results obtained by the use of an additional time scaling. The diffusion limit determines the diffusion source in the \emph{Isotropic Diffusion Source Approximation (IDSA)} of Boltzmann's equation for which the free streaming limit and the reaction limit serve as limiters. Here, we derive the reaction limit as well as the free streaming limit by truncation of Chapman--Enskog or Hilbert expansions using reaction and collision scaling as well as time scaling, respectively. Finally, we motivate why limiters are a good choice for the definition of the source term in the IDSA.
Efficient Protocols for Private Record Linkage

Record linkage allows data from different sources to be integrated to facilitate data mining tasks. However, in many cases, records have to be linked by personally identifiable information. To prevent privacy breaches, ideally records should be linked in a private way such that no information other than the matching result is leaked in the process. In this paper, we present an exact Private Record Linkage (PRL) protocol and an approximate PRL protocol. The exact PRL protocol is based on Oblivious Bloom Intersection, which is an efficient private set intersection protocol. The approximate PRL protocol extends the exact PRL protocol by incorporating Locality Sensitive Hash functions. Both protocols are secure in the semihonest model. We also report the evaluation results based on our C implementation of the protocols. The results show that our protocols are efficient and effective.
Genetic Diversity of Neisseria gonorrhoeae Housekeeping Genes

ABSTRACT Molecular typing of Neisseria gonorrhoeae strains is an important tool for epidemiological studies of gonococcal infection and transmission. The recently developed multilocus sequence typing (MLST) method is based on the genetic variation among housekeeping genes. As a preliminary investigation for the development of such a method, we characterized the genetic diversity at 18 gonococcal housekeeping gene loci. Approximately 17,500 nucleotides, spanning 18 loci, were sequenced from 24 isolates. Including strain FA 1090, which has been fully sequenced, and three unique glnA sequences from GenBank, the number of alleles identified for the 18 loci ranged from 2 to 18, with a mean of 8.3 alleles per locus. The majority of polymorphic sites were distributed randomly along the genes, consistent with evolution of DNA sequences by point mutation. In addition, several examples of clustered mutations and insertions or deletions were detected, which most likely occurred by recombinational events. While purifying selection is the dominant force driving the evolution of these housekeeping genes, positive selection also appeared to operate on the abcZ and gpdh loci. The 25 completely characterized strains each had a unique allelic profile with as few as three loci (pilA, abcZ, and pip or pgi2). Molecular typing based on the allelic profile of housekeeping genes resolved the isolates better than either porB nucleotide sequencing or typing of the opa gene. The allelic profiles for the pilA, abcZ, and serC loci of paired strains from 16 sexual contacts were identical. A potential MLST for N. gonorrhoeae, based on ∼500- to 600-bp gene fragments of seven housekeeping gene loci, would include the pilA, abcZ, serC, glnA, gdh, gnd, and pip loci.
The nature of the torus in the heavily obscured AGN Markarian 3: an X-ray study

In this paper we report the results of an X-ray monitoring campaign on the heavily obscured Seyfert galaxy Markarian 3 carried out between the fall of 2014 and the spring of 2015 with NuSTAR, Suzaku and XMM-Newton. The hard X-ray spectrum of Markarian 3 is variable on all the time scales probed by our campaign, down to a few days. The observed continuum variability is due to an intrinsically variable primary continuum seen in transmission through a large, but still Compton-thin column density (N_H~0.8-1.1$\times$10$^{24}$ cm$^{-2}$). If arranged in a spherical-toroidal geometry, the Compton scattering matter has an opening angle ~66 degrees and is seen at a grazing angle through its upper rim (inclination angle ~70 degrees). We report a possible occultation event during the 2014 campaign. If the torus is constituted by a system of clouds sharing the same column density, this event allows us to constrain their number (17$\pm$5) and individual column density, [~(4.9$\pm$1.5)$\times$10$^{22}$ cm$^{-2}$]. The comparison of IR and X-ray spectroscopic results with state-of-the art "torus" models suggests that at least two thirds of the X-ray obscuring gas volume might be located within the dust sublimation radius. We report also the discovery of an ionized absorber, characterised by variable resonant absorption lines due to He- and H-like iron. This discovery lends support to the idea that moderate column density absorbers could be due to clouds evaporated at the outer surface of the torus, possibly accelerated by the radiation pressure due to the central AGN emission leaking through the patchy absorber.
Auditory, Visual and Audiovisual Speech Processing Streams in Superior Temporal Sulcus

The human superior temporal sulcus (STS) is responsive to visual and auditory information, including sounds and facial cues during speech recognition. We investigated the functional organization of STS with respect to modality-specific and multimodal speech representations. Twenty younger adult participants were instructed to perform an oddball detection task and were presented with auditory, visual, and audiovisual speech stimuli, as well as auditory and visual nonspeech control stimuli in a block fMRI design. Consistent with a hypothesized anterior-posterior processing gradient in STS, auditory, visual and audiovisual stimuli produced the largest BOLD effects in anterior, posterior and middle STS (mSTS), respectively, based on whole-brain, linear mixed effects and principal component analyses. Notably, the mSTS exhibited preferential responses to multisensory stimulation, as well as speech compared to nonspeech. Within the mid-posterior and mSTS regions, response preferences changed gradually from visual, to multisensory, to auditory moving posterior to anterior. Post hoc analysis of visual regions in the posterior STS revealed that a single subregion bordering the mSTS was insensitive to differences in low-level motion kinematics yet distinguished between visual speech and nonspeech based on multi-voxel activation patterns. These results suggest that auditory and visual speech representations are elaborated gradually within anterior and posterior processing streams, respectively, and may be integrated within the mSTS, which is sensitive to more abstract speech information within and across presentation modalities. The spatial organization of STS is consistent with processing streams that are hypothesized to synthesize perceptual speech representations from sensory signals that provide convergent information from visual and auditory modalities.
Contrast Effects in the Response to Art

Slides of traditional and abstract paintings were rated for either preference or complexity by 120 Ss following their earlier exposure to a contrasting series of slides of another type of art. Traditional art was liked more when it followed abstract art than when it was viewed after its own type of art. Abstract art, on the other hand, was liked less when it followed traditional art than when it followed the same type of art. Complexity judgments for both types of art, compared to their ratings without an earlier contrasting series, increased after seeing another type of art, although traditional art increased more than abstract art did. These findings were related to several theoretical approaches to cognition, general psychology, aesthetics, and the practical problems of art education. The research also illustrates that the humanistic content of experimental psychology can be broadened by including aesthetics and that experimental aesthetics can be liberalized by using slides showing real art.
NetShield: massive semantics-based vulnerability signature matching for high-speed networks

Accuracy and speed are the two most important metrics for Network Intrusion Detection/Prevention Systems (NIDS/NIPSes). Due to emerging polymorphic attacks and the fact that in many cases regular expressions (regexes) cannot capture the vulnerability conditions accurately, the accuracy of existing regex-based NIDS/NIPS systems has become a serious problem. In contrast, the recently-proposed vulnerability signatures (a.k.a data patches) can exactly describe the vulnerability conditions and achieve better accuracy. However, how to efficiently apply vulnerability signatures to high speed NIDS/NIPS with a large ruleset remains an untouched but challenging issue. This paper presents the first systematic design of vulnerability signature based parsing and matching engine, NetShield, which achieves multi-gigabit throughput while offering much better accuracy. Particularly, we made the following contributions: (i) we proposed a candidate selection algorithm which efficiently matches thousands of vulnerability signatures simultaneously requiring a small amount of memory; (ii) we proposed an automatic lightweight parsing state machine achieving fast protocol parsing. Experimental results show that the core engine of NetShield achieves at least 1.9+Gbps signature matching throughput on a 3.8GHz single-core PC, and can scale-up to at least 11+Gbps under a 8-core machine for 794 HTTP vulnerability signatures.
Peripheral Digit Ischemic Syndrome Can Be a Manifestation of Postoperative Thrombotic Thrombocytopenic Purpura

Abstract: In addition to common dysfunction of the brain and kidney, thrombotic thrombocytopenic purpura (TTP) may present with atypical clinical features due to the involvement of other organs such as the lung, pancreas, heart, eye, and skin. We have also observed the unusual presentation of peripheral digit ischemic syndrome (PDIS) in some patients with postoperative TTP. To clarify this relationship between TTP and PDIS, the hematologic data from the medical records of patients with known diagnoses of thrombotic microangiopathy (TM) were examined in a single institution. A total of 94 patients were diagnosed with TM. Among these patients, PDIS developed in six patients and in all these patients PDIS occurred with postoperative TTP. Four patients also had acute respiratory distress syndrome (ARDS). Because of delayed diagnosis of TTP, only two patients survived and four died. One patient responded to plasma exchange and survived, and another patient recovered from postoperative TTP without plasma exchange. However, both patients required the amputation of multiple digits. In conclusion, PDIS is another atypical manifestation of TTP and has occurred exclusively in patients with postoperative TTP in this series. Once PDIS developed, the prognosis was poor and amputation of digits was needed in surviving patients. Early recognition of this atypical manifestation of TTP is essential for a favorable outcome.
Estimation of Economic Discounting Rate for Practical Project Appraisal: The Case of Turkey

This study focuses on estimating an economic discounting rate (EDR) to be used in project appraisals by the State Planning Organisation (SPO) of Turkey. The EDR is a policy tool used for selecting the best projects to meet the economic targets of development plans and to enable planners to choose the most profitable and feasible projects. Since the resources available to the economy are scarce, planners are expected to use cost-benefit analysis (CBA) especially, Net Present Value (NPV) criteria. The NPV is considered to be more reliable than the internal rate of return. Therefore, selection of an appropriate social discount rate is a key issue in the application of CBA for project appraisal. In this article, an attempt is made to estimate the EDR of Turkey via a "growth models" approach, providing fresh evidence for enhancing the project appraisal system in Turkey. The results reveal that the EDR of Turkey is 12.94% in the estimation period of 1985-2009.
Blood-Brain Barrier: Penetration of Morphine, Codeine, Heroin, and Methadone after Carotid Injection

Labeled morphine, codeine, heroin, or methadone was injected as a bolus into the common carotid artery of the rat, and the rat was decapitated 15 seconds later. The brain uptake of the drug was calculated by measurement of the brain content of the drug as a percentage of a labeled, highly diffusible reference substance simultaneously injected. The uptake of morphine was below measurability; the uptake of codeine was 24 percent; heroin, 68 percent; and methadone, 42 percent. Brain uptakes of morphine and codeine were also studied after intravenous injection and correlated well with uptakes after carotid injection; the uptake of codeine being nearly complete by 30 seconds. These studies indicate that brain uptake of certain of these drugs is very rapid and that uptake of heroin injected intravenously is probably limited by the regional flow of blood in the brain. The possible relation of this rapid penetration of the blood-brain barrier by heroin to its strongly addictive properties is discussed.
Age and Abundance Discrimination in Old Stellar Populations Using Mid-Ultraviolet Colors

The rest-frame mid-ultraviolet spectral region (2000-3200 Å) is important in analyzing the stellar populations of the "red envelope" systems observed at high redshifts. Here we explore the usefulness of the mid-UV for determining ages and abundances of old populations. We work with a theoretical set of low-resolution spectra and broadband colors because tests show that these are at present more realistic than high-resolution models. A mid-UV to optical/IR wavelength baseline provides good separation of population components because the main-sequence turnoff dominates the integrated light between 2500 and 4000 Å. Mid-UV spectral features are not sensitive to the dwarf/giant mixture in the population, unlike those in the optical region. We find a 6 mag difference in the mid-UV continuum level (normalized at V) over the metallicity range -1.5 < log(Z/Z☉) < +0.5 and a comparable difference (per unit log t) for ages in the range 4-16 Gyr. Logarithmic derivatives of mid-UV colors with respect to age or metal abundance are 3-10 times larger than for the UBV region. Most of the spectral information on old populations therefore resides below 4000 Å. Measurement of a single mid-UV color is capable of placing a strong lower bound on the mean metallicity of an old population. We investigate the capability of UBV and mid-UV broadband colors to separately determine age and abundance, taking into account precision in the color measurements. We find that the mid-UV improves resolution in log t, log Z space by about a factor of 3 for a given observational precision. Contamination by hot, post-He flash evolutionary phases can seriously affect the mid-UV spectra of old populations. A simple estimate shows that contamination can reach over 80% in some cases. However, this is straightforward to remove as long as far-UV measurements are available. We find that extinction should have relatively small effects on parameters derived for old populations from the mid-UV. Finally, we show that a 4 Gyr, solar abundance model based on empirical spectra for nearby stars provides an excellent fit to the mid-UV spectrum of the Local Group elliptical galaxy M32. This indicates that the poorer results obtained from theoretical spectra do arise from limitations of the synthesis models for individual stars.
Effect of spinal surgery on lung function in Duchenne muscular dystrophy.

BACKGROUND--The effect on subsequent respiratory function of spinal stabilisation for scoliosis in Duchenne muscular dystrophy is unclear. In order to clarify this clinical problem, changes in the forced vital capacity of a group of children with Duchenne muscular dystrophy who had undergone spinal surgery were measured and compared with a group of children with Duchenne muscular dystrophy who had not had surgery. METHODS--In this retrospective study 17 boys with Duchenne muscular dystrophy who underwent spinal stabilisation at a mean age of 14.9 years (surgical group) were compared with 21 boys with Duchenne muscular dystrophy who had not had surgery (non-surgical group). The mean (SD) Cobb angle of the surgical group at 14.9 years was 57 (16.4) degrees, and of the non-surgical group at 15 years was 45 (29.9) degrees. Forced vital capacity expressed as percentage predicted (% FVC) was measured in total over a seven year period in the surgical group and over 6.5 years in the non-surgical group, and regression equations were calculated. Survival curves for both groups were also constructed. RESULTS--No difference was found between spinal stabilisation (surgical group) and the non-surgical group in the rate of deterioration of % FVC which was 3-5% per year. There was no difference in survival in either group. CONCLUSIONS--Spinal stabilisation in Duchenne muscular dystrophy does not alter the decline in pulmonary function, nor does it improve survival.