Miracle-dz/UniFAR-FTUs huggingface dataset:
Workflows with Passbacks and Incremental Verification of Their Correctness

SUMMARY In this paper, we discuss a fundamental theory of incremental veriﬁcation for workﬂows. Incremental veriﬁcation is a method to help multiple designers share and collaborate on huge workﬂows while maintaining their consistency. To this end, we introduce passbacks in work-ﬂows and their consistency property in the control ﬂow perspective. pass-backs indicate redoing of works. Workﬂows with passbacks are useful to naturally represent human works. To deﬁne the consistency property above, we deﬁne normality of workﬂows with passbacks and total correctness of normal workﬂows based on transition system-based semantics of normal workﬂows. We further extend workﬂows to sorted workﬂows and deﬁne their vertical division and composition. We also extend total correctness to normal sorted workﬂows, for the sake of incremental veriﬁcation of a large-scale workﬂow with passbacks via vertical division and composition.
Acoustic characterization of Mysis relicta

It is possible to increase the sampling resolution and the available information on zooplankton populations by applying acoustic sampling techniques. Knowledge of an organism's acoustic target strength (TS) is critical for translating acoustic data into meaningful biological information, such as numerical abundance. We have taken several approaches to evaluate the acoustic TS of Mysis relicta, a key benthic‐pelagic invertebrate in the Laurentian Great Lakes. This included in situ TS measurements with a dual‐beam 420‐kHz system and comparison among net‐based, optical plankton counter (OPC)‐based, and acoustic‐based estimates of numerical abundance of mysids. In addition, based on the in situ TS data, we modified a model previously applied primarily to marine zooplankton taxa. The resulting predicted TS was compared to other TS estimates. The estimated mean TSs from the in situ TS measurements and the OPC‐acoustic comparison were within a narrow range (–76 to –74.8 dB). Analysis of the net‐acoustic data comparison resulted in an estimated average TS of –73.1 dB. We suggest that the net‐acoustic discrepancy relative to other methods is due to net avoidance and low filtering efficiency. The model predicted similar mean TSs for the size distribution present when R (reflectivity coefficient) was changed to 0.0675. We hypothesized that the modification of the model parameter values was necessary because of the differences in the medium surrounding marine vs. freshwater zooplankton.
Channelopathy pathogenesis in autism spectrum disorders

Autism spectrum disorder (ASD) is a syndrome that affects normal brain development and is characterized by impaired social interaction as well as verbal and non-verbal communication and by repetitive, stereotypic behavior. ASD is a complex disorder arising from a combination of multiple genetic and environmental factors that are independent from racial, ethnic and socioeconomical status. The high heritability of ASD suggests a strong genetic basis for the disorder. Furthermore, a mounting body of evidence implies a role of various ion channel gene defects (channelopathies) in the pathogenesis of autism. Indeed, recent genome-wide association, and whole exome- and whole-genome resequencing studies linked polymorphisms and rare variants in calcium, sodium and potassium channels and their subunits with susceptibility to ASD, much as they do with bipolar disorder, schizophrenia and other neuropsychiatric disorders. Moreover, animal models with these genetic variations recapitulate endophenotypes considered to be correlates of autistic behavior seen in patients. An ion flux across the membrane regulates a variety of cell functions, from generation of action potentials to gene expression and cell morphology, thus it is not surprising that channelopathies have profound effects on brain functions. In the present work, we summarize existing evidence for the role of ion channel gene defects in the pathogenesis of autism with a focus on calcium signaling and its downstream effects.
A population‐based study of human papillomavirus genotype prevalence in the United States: Baseline measures prior to mass human papillomavirus vaccination

Currently, two prophylactic human papillomavirus (HPV) vaccines targeting HPV 16 and 18 have been shown to be highly efficacious for preventing precursor lesions although the effectiveness of these vaccines in real‐world clinical settings must still be determined. Toward this end, an ongoing statewide surveillance program was established in New Mexico to assess all aspects of cervical cancer preventive care. Given that the reduction in cervical cancer incidence is expected to take several decades to manifest, a systematic population‐based measurement of HPV type‐specific prevalence employing an age‐ and cytology‐stratified sample of 47,617 women attending for cervical screening was conducted prior to widespread HPV vaccination. A well‐validated polymerase chain reaction (PCR) method for 37 HPV genotypes was used to test liquid‐based cytology specimens. The prevalence for any of the 37 HPV types was 27.3% overall with a maximum of 52% at age of 20 years followed by a rapid decline at older ages. The HPV 16 prevalences in women aged ≤20 years, 21–29 years or ≥30 years were 9.6, 6.5 and 1.8%, respectively. The combined prevalences of HPV 16 and 18 in these age groups were 12.0, 8.3 and 2.4%, respectively. HPV 16 and/or HPV 18 were detected in 54.5% of high‐grade squamous intraepithelial (cytologic) lesions (HSIL) and in 25.0% of those with low‐grade SIL (LSIL). These baseline data enable estimates of maximum HPV vaccine impact across time and provide critical reference measurements important to assessing clinical benefits and potential harms of HPV vaccination including increases in nonvaccine HPV types (i.e., type replacement).
Stt7-dependent Phosphorylation during State Transitions in the Green Alga Chlamydomonas reinhardtii*

Photosynthetic organisms are able to adapt to changes in light conditions by balancing the light excitation energy between the light-harvesting systems of photosystem (PS) II and photosystem I to optimize the photosynthetic yield. A key component in this process, called state transitions, is the chloroplast protein kinase Stt7/STN7, which senses the redox state of the plastoquinone pool. Upon preferential excitation of photosystem II, this kinase is activated through the cytochrome b6f complex and required for the phosphorylation of the light-harvesting system of photosystem II, a portion of which migrates to photosystem I (state 2). Preferential excitation of photosystem I leads to the inactivation of the kinase and to dephosphorylation of light-harvesting complex (LHC) II and its return to photosystem II (state 1). Here we compared the thylakoid phosphoproteome of the wild-type strain and the stt7 mutant of Chlamydomonas under state 1 and state 2 conditions. This analysis revealed that under state 2 conditions several Stt7-dependent phosphorylations of specific Thr residues occur in Lhcbm1/Lhcbm10, Lhcbm4/Lhcbm6/Lhcbm8/Lhcbm9, Lhcbm3, Lhcbm5, and CP29 located at the interface between PSII and its light-harvesting system. Among the two phosphorylation sites detected specifically in CP29 under state 2, one is Stt7-dependent. This phosphorylation may play a crucial role in the dissociation of CP29 from PSII and/or in its association to PSI where it serves as a docking site for LHCII in state 2. Moreover, Stt7 was required for the phosphorylation of the thylakoid protein kinase Stl1 under state 2 conditions, suggesting the existence of a thylakoid protein kinase cascade. Stt7 itself is phosphorylated at Ser533 in state 2, but analysis of mutants with a S533A/D change indicated that this phosphorylation is not required for state transitions. Moreover, we also identified phosphorylation sites that are redox (state 2)-dependent but independent of Stt7 and additional phosphorylation sites that are redox-independent.
Expression of GABAB receptor in the avian auditory brainstem: Ontogeny, afferent deprivation, and ultrastructure

Nucleus magnocellularis (NM), nucleus angularis (NA), and nucleus laminaris (NL), second‐ and third‐order auditory neurons in the avian brainstem, receive GABAergic input primarily from the superior olivary nucleus (SON). Previous studies have demonstrated that both GABAA and GABAB receptors (GABABRs) influence physiological properties of NM neurons. We characterized the distribution of GABABR expression in these nuclei during development and after deafferentation of the excitatory auditory nerve (nVIII) inputs. We used a polyclonal antibody raised against rat GABABRs in the auditory brainstem during developmental periods that are thought to precede and include synaptogenesis of GABAergic inputs. As early as embryonic day (E)14, dense labeling is observed in NA, NM, NL, and SON. At earlier ages immunoreactivity is present in somas as diffuse staining with few puncta. By E21, when the structure and function of the auditory nuclei are known to be mature, GABAB immunoreactivity is characterized by dense punctate labeling in NM, NL, and a subset of NA neurons, but label is sparse in the SON. Removal of the cochlea and nVIII neurons in posthatch chicks resulted in only a small decrease in immunoreactivity after survival times of 14 or 28 days, suggesting that a major proportion of GABABRs may be expressed postsynaptically or on GABAergic terminals. We confirmed this interpretation with immunogold TEM, where expression at postsynaptic membrane sites is clearly observed. The characterization of GABABR distribution enriches our understanding of the full complement of inhibitory influences on central auditory processing in this well‐studied neuronal circuit. J. Comp. Neurol. 489:11–22, 2005. © 2005 Wiley‐Liss, Inc.
improvement of lattice QCD with two flavors of Wilson quarks

We consider O(a) improvement for two flavor lattice QCD. The improvement term in the action is computed non-perturbatively for a large range of the bare coupling. The position of the critical line and higher order lattice artifacts remaining after improvement are estimated. We also discuss the behavior of the HMC algorithm in our simulations.
Comparison of crestal bone loss and implant stability among the implants placed with conventional procedure and using osteotome technique: a clinical study.

To overcome the limitations of implant placement in knife-edge ridges, Summer introduced the osteotome technique in 1994. It has been claimed that using bone condensing to prepare the implant site in soft maxillary bone avoids the risk of heat generation, and implants can be placed precisely with increased primary stability. The purpose of this clinical study was to evaluate the crestal bone loss exhibited by the bone around early nonfunctionally loaded implants placed with conventional implant placement technique and with Summer's osteotome technique and to evaluate whether the bone-compression technique provides better primary stability than the conventional technique. A total of 10 Uniti implants were placed in the maxillary anterior region of 5 patients. One implant site was prepared using the conventional technique with drills (control group A), and second site was prepared using the osteotome technique (experimental group B) and an MIS bone compression kit. Resonance frequency measurements (RFMs) were made on each implant at the time of fixture placement and on the 180th day after implant fixture placement. The peri-implant alveolar bone loss was evaluated radiographically. Differences between the alveolar crest and the implant shoulder in radiographs were obtained immediately after implant insertion and on the 180th day after implant placement. The RFMs demonstrated a significantly higher stability of implants in control group A than in experimental group B on the day of surgery (P = .026). However, no statistically significant difference in stability was found between both groups on 180th day after implant placement (P = .076). A significant difference was found in the crestal bone levels after 180 days of surgery between two groups (P = 0) with less crestal bone loss with group A. Within the limitations of this study we concluded that the osteotome technique is good for the purpose for which it was introduced, that is, for knife-edge ridges, and it should not be considered a substitute for conventional procedures for implant placement.
No Change in Anterior Chamber Dimensions After Femtosecond LASIK for Hyperopia

Objective: To compare the changes in anterior chamber volume (ACV), anterior chamber depth (ACD) and anterior chamber angle (ACA) before and 6 months after femtosecond laser in situ keratomileusis (LASIK) for hyperopia using the Pentacam HR device. Methods: A total of 24 eyes of 24 consecutive hyperopic patients undergoing femtosecond LASIK were examined preoperatively and 6 months postoperatively. Anterior chamber volume; ACDs in the central, superior, inferior, nasal, and temporal quadrants; and ACA were measured using the Pentacam HR device. Comparisons of preoperative versus postoperative values were performed using paired Student t test. Linear regression analysis was performed to evaluate correlations between ACV change, central ACD change, age, and attempted maximum ablation depth. Results: Preoperative and postoperative mean ACVs were 153.6 and 158.2 &mgr;L, respectively. Preoperative and postoperative mean ACDs were 2.81, 2.28, 2.53, 2.16, and 2.61 mm, and 2.84, 2.31, 2.54, 2.16, and 2.65 mm, respectively. Preoperative and postoperative mean ACAs were 33.3° and 32.0°, respectively. There were not statistically significant differences in ACV, ACDs, and ACA from preoperatively to 6 months after femtosecond LASIK (all P>0.05). The change of central ACD was correlated significantly with age at 6 months postoperatively (R2=0.18, P=0.039). Conclusions: Anterior chamber profiles, including ACV, ACA, and central and peripheral ACDs did not significantly change after femtosecond LASIK for hyperopia.
Orexin/hypocretin system modulates amygdala-dependent threat learning through the locus coeruleus

Significance The hypothalamic orexin (hypocretin) system controls survival-related processes such as food intake, arousal, and stress. Here we show that orexins also play an important role in learning about stimuli that predict harm. We demonstrate that blocking orexin activity in the noradrenergic locus coeruelus (LC) reduces, whereas increasing its activity enhances, threat learning in a Pavlovian auditory threat conditioning paradigm. Moreover, we demonstrate a direct functional connection between orexin enhancement of LC activity and amygdala-dependent memory processes. Strong, aversive memories can lead to fear and anxiety disorders that have a negative impact on individuals and their quality of life. The orexin system may represent a unique treatment target for these disorders. Survival in a dangerous environment requires learning about stimuli that predict harm. Although recent work has focused on the amygdala as the locus of aversive memory formation, the hypothalamus has long been implicated in emotional regulation, and the hypothalamic neuropeptide orexin (hypocretin) is involved in anxiety states and arousal. Nevertheless, little is known about the role of orexin in aversive memory formation. Using a combination of behavioral pharmacology, slice physiology, and optogenetic techniques, we show that orexin acts upstream of the amygdala via the noradrenergic locus coeruleus to enable threat (fear) learning, specifically during the aversive event. Our results are consistent with clinical studies linking orexin levels to aversive learning and anxiety in humans and dysregulation of the orexin system may contribute to the etiology of fear and anxiety disorders.
Impact of a Pentavalent Combination Vaccine on Immunization Timeliness in a State Medicaid Population

Background: Use of combination vaccines has been associated with improved coverage rates, but their effect on timeliness remains to be explored. This study assessed the effect of diphtheria-tetanus-acellular pertussis/hepatitis B/inactivated polio vaccine (DTaP/HepB/IPV) on the timeliness of vaccine administration. Methods: This retrospective cohort study used administrative claims data from the Georgia Medicaid program. Children with 24 months of continuous enrollment and at least 4 vaccine-related office visits were stratified into 2 cohorts: those with at least 3 DTaP/HepB/IPV doses (DTaP/HepB/IPV cohort) and those with at least 3 doses of DTaP but no doses of DTaP/HepB/IPV (reference cohort). Children who received any dose of HepB/Hib were excluded to isolate the effect of the study vaccine. Timeliness was measured as the percentage of children who received their vaccines on time and the cumulative days undervaccinated. Results: There were 2880 children in the DTaP/HepB/IPV cohort and 2672 in the reference cohort. After controlling for covariates, receipt of DTaP/HepB/IPV was associated with significantly improved timeliness for 3 doses of DTaP (on-time rates: 66.3% vs. 60.8%, P < 0.0001; cumulative days undervaccinated: 29.5 vs. 70.4 days, P < 0.0001). Significantly improved timeliness was also observed in the DTaP/HepB/IPV cohort for IPV, HepB, Hib, 4 DTaPs, and the combination series assessed (P < 0.001 for all comparisons). Conclusions: Use of DTaP/HepB/IPV in this Medicaid population was associated with improved on-time vaccination and fewer undervaccinated days. These findings, along with previous research associating combination vaccines with improved coverage rates, provide quantitative data to support the ACIP, AAP, and AAFP preference for combination vaccines.
Serum COMP-C 3 b complexes in rheumatic diseases and relation to anti-TNF-alpha treatment

Introduction: Cartilage oligomeric matrix protein (COMP) is found at elevated concentrations in sera of patients with joint diseases such as rheumatoid arthritis (RA) and osteoarthritis (OA). We recently showed that COMP activates complement via the alternative pathway and that COMP-C3b complexes are present in sera of RA patients, but not in healthy controls. We now set out to elaborate on the information provided by this marker in a variety of diseases and larger patient cohorts. Methods: COMP-C3b levels in sera were measured by using an enzyme-linked immunosorbent assay (ELISA) capturing COMP and detecting C3b. Serum COMP was measured by using ELISA. Results: COMP-C3b levels were significantly elevated in patients with RA as well as in systemic lupus erythematosus (SLE), compared with healthy controls. SLE patients with arthritis had significantly higher COMP-C3b levels than did those without. COMP-C3b was furthermore elevated in patients with ankylosing spondylitis (AS), psoriatic arthritis (PsA), reactive arthritis, systemic sclerosis, and OA. COMP-C3b did not correlate with COMP in any of the patient groups. COMP-C3b correlated with disease activity in RA, but not in other diseases. COMP-C3b levels in RA patients decreased on treatment with tumor necrosis factor (TNF)-a inhibitors, whereas the levels increased in patients with AS or PsA. The changes of COMP-C3b did not parallel the changes of C-reactive protein (CRP). Conclusions: COMP-C3b levels are elevated in several rheumatologic diseases and correlate with inflammatory measures in RA. COMP-C3b levels in RA decrease during TNF-a inhibition differently from those of CRP, suggesting that formation of COMP-C3b relates to disease features not reflected by general inflammation measures.
miRNA Expression Profiling Enables Risk Stratification in Archived and Fresh Neuroblastoma Tumor Samples

Purpose: More accurate assessment of prognosis is important to further improve the choice of risk-related therapy in neuroblastoma (NB) patients. In this study, we aimed to establish and validate a prognostic miRNA signature for children with NB and tested it in both fresh frozen and archived formalin-fixed paraffin-embedded (FFPE) samples. Experimental Design: Four hundred-thirty human mature miRNAs were profiled in two patient subgroups with maximally divergent clinical courses. Univariate logistic regression analysis was used to select miRNAs correlating with NB patient survival. A 25-miRNA gene signature was built using 51 training samples, tested on 179 test samples, and validated on an independent set of 304 fresh frozen tumor samples and 75 archived FFPE samples. Results: The 25-miRNA signature significantly discriminates the test patients with respect to progression-free and overall survival (P < 0.0001), both in the overall population and in the cohort of high-risk patients. Multivariate analysis indicates that the miRNA signature is an independent predictor of patient survival after controlling for current risk factors. The results were confirmed in an external validation set. In contrast to a previously published mRNA classifier, the 25-miRNA signature was found to be predictive for patient survival in a set of 75 FFPE neuroblastoma samples. Conclusions: In this study, we present the largest NB miRNA expression study so far, including more than 500 NB patients. We established and validated a robust miRNA classifier, able to identify a cohort of high-risk NB patients at greater risk for adverse outcome using both fresh frozen and archived material. Clin Cancer Res; 17(24); 7684–92. ©2011 AACR.
Beating Atari with Natural Language Guided Reinforcement Learning

We introduce the first deep reinforcement learning agent that learns to beat Atari games with the aid of natural language instructions. The agent uses a multimodal embedding between environment observations and natural language to self-monitor progress through a list of English instructions, granting itself reward for completing instructions in addition to increasing the game score. Our agent significantly outperforms Deep Q-Networks (DQNs), Asynchronous Advantage Actor-Critic (A3C) agents, and the best agents posted to OpenAI Gym on what is often considered the hardest Atari 2600 environment: Montezuma's Revenge.
Event-Based Resilient Formation Control of Multiagent Systems

This paper focuses on the time-varying formation tracking issue for nonlinear multiagent systems (MASs). Based on the explicit characterizations of frequency, duration, and magnitude properties for deception attacks, a hybrid framework is proposed for time-varying formation tracking of nonlinear MASs. To realize the desired formation tracking performance under deception attacks, the distributed edge-based event-triggered communication strategies are proposed with Zeno-freeness. The designed strategies are resilient to deception attacks under some appropriate assumptions, to realize a predefined formation and simultaneously track the convex combination of leaders’ states. The designed control strategies render that we do not need to detect when the deception attack happens. Furthermore, the obtained results can be deduced to deal with consensus/synchronization problems, target enclosing problems for MASs with one/multiple leaders, where the communication is attacked by malicious attackers. An example of time-varying formation tracking of unmanned aerial vehicles is provided to show the effectiveness of the obtained results.