Miracle-dz/UniFAR-FTUs huggingface dataset:
Causal Best Intervention Identification via Importance Sampling

Motivated by applications in computational advertising and systems biology, we consider the problem of identifying the best out of several possible soft interventions at a source node V in an acyclic causal directed graph, to maximize the expected value of a target node Y (located downstream of V ). There is a fixed total budget for sampling under various interventions. Also, there are cost constraints on different types of interventions. We pose this as a best arm identification problem with K arms, where each arm is a soft intervention at V . The key difference from the classical setting is that there is information leakage among the arms. In our setting, each soft intervention is a distinct known conditional probability distribution between V and its parents pa(V ). We propose an efficient successive rejects style algorithm that uses importance sampling to adaptively sample using different interventions and leverage information leakage to choose the best. We provide the first gap dependent (gaps between the various expected target values) simple regret and best arm mis-identification error bounds for this problem. This generalizes the prior bounds available for the simpler case of no information leakage. In the case of no leakage, the number of samples required for identification is (upto polylog factors) Õ(maxi i ∆i ) where ∆i is the gap between the optimal and the i-th best arm. We generalize the previous result for the causal setting and show that Õ(maxi σ2 i ∆i ) is sufficient where σ2 i is the effective variance of an importance sampling estimator that eliminates the i-th best arm out of a set of arms with gaps roughly at most twice as big as ∆i. We also show that σ2 i << i in many cases. Our result also recovers (up to constants) prior gap independent bounds for this setting. We demonstrate that our algorithm empirically outperforms the state of the art, through synthetic experiments. 1 ar X iv :1 70 1. 02 78 9v 1 [ st at . M L ] 1 0 Ja n 20 17
Spatially variable fault friction derived from dynamic modeling of aseismic afterslip due to the 2004 Parkfield earthquake

We investigate fault friction from dynamic modeling of fault slip prior to and following the Mw 6.0 earthquake which ruptured the Parkfield segment of the San Andreas Fault in 2004. The dynamic modeling assumes a purely rate‐strengthening friction law, with a logarithmic dependency on sliding rate: μ=μ*+a−blnvv* . The initial state of stress is explicitly taken into account, and afterslip is triggered by the stress change induced by the earthquake source model given a priori. We consider different initial stress states and two coseismic models, and invert for the other model parameters using a nonlinear inversion scheme. The model parameters include the reference friction μ*, the friction rate dependency characterized by the quantity a‐b, assumed to be either uniform or depth dependent. The model parameters are determined from fitting the transient postseismic geodetic signal measured at continuous GPS stations. Our study provides a view of frictional properties at the kilometers scale over the 0–15 km depth illuminated by the coseismic stress change induced by the Parkfield earthquake. The reference friction is estimated to be between 0.1 and 0.5. With independent a priori constraints on the amplitude of differential stress, the range of possible values narrows down to 0.1–0.17. The friction rate coefficient a‐b is estimated to be ∼ 10− 3 − 10− 2 with a hint that it increases upward from about 1–3 × 10–3 at 3–7 km depth to about 4–7 × 10–3 at 0–1 km depth. It is remarkable that our results are consistent with frictional properties measured on rock samples recovered from the fault zone thanks to the San Andreas Fault Observatory at Depth experiment.
Quality of Kindergarten Education in Singapore: Parents' Views and Expectations.

This paper is a preliminary investigation of parents' views and expectations of the quality of kindergarten education in Singapore . Specifically, it looks at the relationships between type of kindergarten chosen and socio-economic status of parents. Other variables explored include the quality of trainers, parental expectations and satisfaction and academic record of the kindergarten setting. It also looks at the impact of childrearing values and beliefs among the Malay, Chinese and Tamil ethnic parental groups on both parental expectations and choice of kindergartens. Based on a sample of 437 parent clients from 10 kindergarten centers, the study found that parents generally from all ethnic groups, place a high value on kindergarten education. Good facilities, qualified staff and an academic-oriented program were taken as indicative of a high quality kindergarten center. The type of kindergarten was found to have some mediation effect on the level of quality parents expect of kindergarten education. There was no significant relationship linking parental views, distance and cost of kindergartens. Parental expectations were also higher from the higher socio-economic status group who rate cognitive, social skills and discipline training as important features. The implications of the findings with reference to advising parents and trainers and recommendations for further research are discussed.
Reflections on Friction in Quantum Mechanics

Distinctly quantum friction effects of three types are surveyed: internalfriction, measurement-induced friction, and quantum-fluctuation-induced friction. We demonstrate that external driving will lead to quantum internal friction, and critique the measurement-based interpretation of friction. We conclude that in general systems will experience internal and external quantum friction over and beyond the classical frictional contributions.
An RTP Payload Format for Generic Forward Error Correction

This document specifies a payload format for generic forward error correction of media encapsulated in RTP. It is engineered for FEC algorithms based on the exclusive-or (parity) operation. The payload format allows end systems to transmit using arbitrary block lengths and parity schemes. It also allows for the recovery of both the payload and critical RTP header fields. Since FEC is sent as a separate stream, it is backwards compatible with non-FEC capable hosts, so that receivers which do not wish to implement FEC can just ignore the extensions.
Relationship between the Severity of Diversion Colitis and the Composition of Colonic Bacteria: A Prospective Study

Background/Aims Diversion colitis is the inflammation of the excluded segment of the colon in patients undergoing ostomy. It has been suggested that a change in colonic flora may lead to colitis; however, direct evidence for this disease progression is lacking. The aim of this study was to evaluate the relationship between the severity of diversion colitis and the composition of colonic bacteria. Methods We used culture methods and polymerase chain reaction to analyze the colonic microflora of patients who underwent rectal cancer resection with or without diversion ileostomy. In the diversion group, we also evaluated the severity of colonoscopic and pathologic colitis before reversal. Results This study enrolled 48 patients: 26 in the diversion group and 22 in the control group. Significant differences were observed between the two groups in the levels of Staphylococcus (p=0.038), Enterococcus (p<0.001), Klebsiella (p<0.001), Pseudomonas (p=0.015), Lactobacillus (p=0.038), presence of anaerobes (p=0.019), and Bifidobacterium (p<0.001). A significant correlation between the severity of colitis and bacterial composition was only observed for Bifidobacterium (p=0.005, correlation coefficient=-0.531). Conclusions The colonic microflora differed significantly between the diversion and control groups. Bifidobacterium was negatively correlated with the severity of diversion colitis.
Intermittency in the plankton: a multifractal analysis of zooplankton biomass variability

We present the first evidence that variability in zooplankton biomass can be characterized as a multifractal. An hourly tune series of vertically integrated acoustic biomass measurements, taken from a fixed mooring on the Atlantic coastline, provided the data for our analysis. Two measures of variability were analyzed: the first difference squared and the squared difference from the mean. When integrated over time, these quantities provide estimates of biomass variability. The distribution in time of these measures of variability is highly intermittent. We show that such intermittency is well described by the scaling properties of multifractals. In zooplankton ecology, potential applications of this analysis include comparing plankton variability distributions to those of passive scalars and environmental variables, quantifying spatial or temporal heterogeneity in intermittent quantities, and determining scales over which similar processes are operating.
Pathological confirmation of 4 cases with isolated cortical vein thrombosis previously misdiagnosed as brain tumor

Isolated cortical vein thrombosis (ICoVT) is a rare form of cerebral venous thrombosis and is easily misdiagnosed as brain tumor due to its atypical clinical presentations and radiological findings similar to brain tumors. The present study focused on 4 patients with ICoVT, 2 men and 2 women. In the 2 male patients, the onset of disease was insidious, with progressive numbness and weakness in limbs as the major symptoms. By contrast, 2 female patients suffered from acute onset of symptoms, presenting with headache and seizures. Brain computed tomography and magnetic resonance imaging showed large hemorrhagic lesions surrounded by massive edemas in the 4 patients. Brain biopsies were performed in the 4 patients due to concern for brain tumors. However, the pathological results supported the diagnosis of ICoVT, and the subsequent anticoagulant treatment administered was effective for all 4 patients. In conclusion, ICoVT can be easily misdiagnosed as brain tumor because of the atypical clinical and imaging features. The results suggested that the possibility of ICoVT always be considered in patients with neuroimaging showing cortical hemorrhagic lesions with massive edemas.
Symmetry, Saddle Points, and Global Geometry of Nonconvex Matrix Factorization

We propose a general theory for studying the geometry of nonconvex objective functions with underlying symmetric structures. In specific, we characterize the locations of stationary points and the null space of the associated Hessian matrices via the lens of invariant groups. As a major motivating example, we apply the proposed general theory to characterize the global geometry of the low-rank matrix factorization problem. In particular, we illustrate how the rotational symmetry group gives rise to infinitely many non-isolated strict saddle points and equivalent global minima of the objective function. By explicitly identifying all stationary points, we divide the entire parameter space into three regions: ($\cR_1$) the region containing the neighborhoods of all strict saddle points, where the objective has negative curvatures; ($\cR_2$) the region containing neighborhoods of all global minima, where the objective enjoys strong convexity along certain directions; and ($\cR_3$) the complement of the above regions, where the gradient has sufficiently large magnitudes. We further extend our result to the matrix sensing problem. This allows us to establish strong global convergence guarantees for popular iterative algorithms with arbitrary initial solutions.
The transient BMAP/G/l queue

We derive the two-dimensional transforms of the transient workload and queue-length distributions in the single-server queue with general service times and a batch Markovian arrival process (BMAP). This arrival process includes the familiar phase-type renewal process and the Markov modulated Poisson process as special cases, as well as superpositions of these processes, and allows correlated interarrival times and batch sizes. Numerical results are obtained via two-dimensional transform inversion algorithms based on the Fourier-series method. From the numerical examples we see that predictions of system performance based on transient and stationary performance measures can be quite different
Evaluation of Milk Trace Elements, Lactate Dehydrogenase, Alkaline Phosphatase and Aspartate Aminotransferase Activity of Subclinical Mastitis as and Indicator of Subclinical Mastitis in Riverine Buffalo (Bubalus bubalis)

Mastitis is a highly morbid disease that requires detection at the subclinical stage. Tropical countries like India mainly depend on milch buffaloes for milk. The present study was conducted to investigate whether the trace minerals viz. copper (Cu), iron (Fe), zinc (Zn), cobalt (Co) and manganese (Mn) and enzyme activity of lactate dehydrogenase (LDH), alkaline phosphatase (ALP) and aspartate aminotransferase (AST) in riverine buffalo milk can be used as an indicator of subclinical mastitis (SCM) with the aim of developing suitable diagnostic kit for SCM. Trace elements and enzyme activity in milk were estimated with Atomic absorption Spectrophotometer, GBC 932 plus and biochemical methods, respectively. Somatic cell count (SCC) was done microscopically. The cultural examination revealed Gram positive bacteria as the most prevalent etiological agent. A statistically significant (p<0.01) increase in SCC, Fe, Zn, Co and LDH occurred in SCM milk containing gram positive bacterial agents only. ALP was found to be elevated in milk infected by both gram positive and negative bacteria. The percent sensitivity, specificity and accuracy, predictive values and likelihood ratios were calculated taking bacterial culture examination and SCC≥2×105 cells/ml of milk as the benchmark. Only ALP and Zn, the former being superior, were found to be suitable for diagnosis of SCM irrespective of etiological agents. LDH, Co and Fe can be introduced in the screening programs where Gram positive bacteria are omnipresent. It is recommended that both ALP and Zn be measured together in milk to diagnose buffalo SCM, irrespective of etiology.
Consensus in the presence of partial synchrony

The concept of partial synchrony in a distributed system is introduced. Partial synchrony lies between the cases of a synchronous system and an asynchronous system. In a synchronous system, there is a known fixed upper bound Δ on the time required for a message to be sent from one processor to another and a known fixed upper bound &PHgr; on the relative speeds of different processors. In an asynchronous system no fixed upper bounds Δ and &PHgr; exist. In one version of partial synchrony, fixed bounds Δ and &PHgr; exist, but they are not known a priori. The problem is to design protocols that work correctly in the partially synchronous system regardless of the actual values of the bounds Δ and &PHgr;. In another version of partial synchrony, the bounds are known, but are only guaranteed to hold starting at some unknown time T, and protocols must be designed to work correctly regardless of when time T occurs. Fault-tolerant consensus protocols are given for various cases of partial synchrony and various fault models. Lower bounds that show in most cases that our protocols are optimal with respect to the number of faults tolerated are also given. Our consensus protocols for partially synchronous processors use new protocols for fault-tolerant “distributed clocks” that allow partially synchronous processors to reach some approximately common notion of time.
Dynamical relaxation and the orbits of low-mass extrasolar planets

We consider the evolution of a system containing a population of massive planets formed rapidly through a fragmentation process occurring on a scale on the order of 100 au and a lower mass planet that assembles in a disc on a much longer time-scale. During the formation phase, the inner planet is kept on a circular orbit owing to tidal interaction with the disc, while the outer planets undergo dynamical relaxation. Interaction with the massive planets left in the system after the inner planet forms may increase the eccentricity of the inner orbit to high values, producing systems similar to those observed.
Humoral Mucosal and Systemic Immunity Results in Long-Term HIV-1 Neutralizing Prime-Boost Immunization Regimen in Mice Intranasal HIV-1-gp160-DNA/gp41 Peptide

An intranasal DNA vaccine prime followed by a gp41 peptide booster immunization was compared with gp41 peptide and control immunizations. Serum HIV-1-speciﬁc IgG and IgA as well as IgA in feces and vaginal and lung secretions were detected after immunizations. Long-term humoral immunity was studied for up to 12 mo after the booster immunization by testing the presence of HIV-1 gp41- and CCR5-speciﬁc Abs and IgG/IgA-secreting B lymphocytes in spleen and regional lymph nodes in immunized mice. A long-term IgA-speciﬁc response in the intestines, vagina, and lungs was obtained in addition to a systemic immune response. Mice immunized only with gp41 peptides and L3 adjuvant developed a long-term gp41-speciﬁc serum IgG response systemically, although over a shorter period (1–9 mo), and long-term mucosal gp41-speciﬁc IgA immunity. HIV-1-neutralizing serum Abs were induced that were still present 12 mo after booster immunization. HIV-1 SF2-neutralizing fecal and lung IgA was detectable only in the DNA-primed mouse groups. Intranasal DNA prime followed by one peptide/L3 adjuvant booster immunization, but not a peptide prime followed by a DNA booster, was able to induce B cell memory and HIV-1-neutralizing Abs for at least half of a mouse’s life span. The Journal of Immunology, 2004, 173: 7078–7089.
A Large, Cross-Sectional Observational Study of Serum BDNF, Cognitive Function, and Mild Cognitive Impairment in the Elderly

Objective: The clinical relationship between brain-derived neurotrophic factor (BDNF) and cognitive function or mild cognitive impairment (MCI) is not well-understood. The purpose of this study was to identify the relationship between serum BDNF and cognitive function and MCI, and determine whether serum BDNF level might be a useful biomarker for assessing risk for MCI in older people. Materials and Methods: A total of 4463 individuals aged 65 years or older (mean age 72 years) participating in the study. We measured performance in a battery of neuropsychological and cognitive function tests; serum BDNF concentration. Results: Eight hundred twenty-seven participants (18.8%) had MCI. After adjustment for sex, age, education level, diabetes, and current smoking, serum BDNF was associated with poorer performance in the story memory, and digit symbol substitution task scores. Serum BDNF was marginally associated with the presence of MCI (odds ratio, 95% confidence interval: 1.41, 1.00–1.99) when BDNF was 1.5 SD lower than the mean value standardized for sex and age, education level, diabetes, and current smoking. Conclusion: Low serum BDNF was associated with lower cognitive test scores and MCI. Future prospective studies should establish the discriminative value of serum BDNF for the risk of MCI.
Extraarticular Manifestations of Rheumatoid Arthritis in a Multiethnic Cohort of Predominantly Hispanic and Asian Patients

AbstractWe conducted a study to determine the prevalence of extraarticular manifestations (ExRA) in a cohort of predominantly Hispanic and Asian patients with rheumatoid arthritis (RA), to identify factors associated with the development of ExRA, and to compare the prevalence of ExRA between Hispanic and Asian patients.Patients with RA followed in the outpatient rheumatology clinics of a public hospital were included if they were aged ≥18 years and met the 1987 American College of Rheumatology criteria for the diagnosis of RA. We performed a cross-sectional analysis in which patients with ExRA were identified based on predefined criteria. We compared sociodemographic and clinical characteristics in patients with and without ExRA. Multivariate logistic regression was used to examine the association between sociodemographic variables, clinical characteristics, and the presence of ExRA.The prevalence of ExRA was 21.5%, and the most common manifestations were subcutaneous nodules (17.2%) and interstitial lung disease (3.6%). Hispanic patients were significantly more likely to develop ExRA than Asian patients (odds ratio, 2.53; 95% confidence interval, 1.26–5.09). The development of ExRA was also associated with disease duration, male sex, and seropositivity for serum rheumatoid factor.
On the influence of dopamine-relat ed genetic variat ion on dopamine-relat ed disorders

3 4 ABSTRACT Rati onal e Dopamine synthesizing neurons are involved in a wide variety of functions. The most prominent dopamine pathways originate in the midbrain. The development, function and survival of these dopaminergic neurons are under the influence of numerous transcription and neurotrophic factors. Subtle differences in the genes encoding these factors may be of importance for several psychiatric and neurodegenerative disorders. LMX1A, LMX1B and PITX3 are transcription factors that are essential for the development, specification and survival of midbrain dopaminergic neurons. BDNF is a neurotrophic factor involved in neurodevelopmental processes including differentiation and survival of dopaminergic neurons. Another protein of importance for dopaminergic neurotransmission is the dopamine transporter (DAT) that mediates reuptake and inactivation of extracellular dopamine and is hence of fundamental importance in regulating dopamine transmission. The specific aim of this thesis was to investigate the possible influence of polymorphisms in these dopamine-related genes on dopamine-related disorders, i.e. Parkinson's disease (PD), attention-deficit/hyperactivity disorder (ADHD), social anxiety disorder (SAD) and schizophrenia. O O bservati ons Three single nucleotide polymorphisms (SNPs) in LMX1A and one in LMX1B were associated with PD. After splitting for gender, six SNPs were associated with PD in women and four in men (Paper I). Two SNPs in PITX3 were associated with PD in patients with an early age of onset when compared either to controls or to PD patients with late onset (Paper II). One of the PITX3 polymorphisms was also associated with schizophrenia, as were two polymorphisms in LMX1A, and one SNP in LMX1B (Paper III). We assessed longitudinal, quantitative phenotypes of hyperactivity-impulsivity and inattention, and found that the Met allele of the Val66Met polymorphism in the BDNF gene was associated with increased persistent hyperactivity-impulsivity symptoms as well as with increased age-specific inattention symptoms (Paper IV). The amygdala, essential for detection of biologically relevant stimuli and fear generation, is under excitatory influence of dopamine. Positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) were used to investigate if a variable number of tandem repeat (VNTR) polymorphism in the DAT gene (SLC6A3) influences amygdala function during processing of aversive emotional stimuli in SAD patients and healthy controls, respectively. The 9-repeat allele was associated with significantly increased amygdala activity, as assessed with PET, across tests (i.e. public speaking, processing of angry and neutral faces) in SAD patients, but with decreased amygdala activity in controls. Moreover, 9-repeat carriers, regardless of diagnosis, displayed augmented amygdala reactivity, …