Miracle-dz/UniFAR-FTUs huggingface dataset:
A multiple-baseline stereo

A stereo matching method is presented which uses multiple stereo pairs with various baselines to obtain precise depth estimates without suffering from ambiguity. The stereo matching method uses multiple stereo pairs with different baselines generated by a lateral displacement of a camera. Matching is performed by computing the sum of squared-difference (SSD) values. The SSD functions for individual stereo pairs are represented with respect to the inverse depth (rather than the disparity, as is usually done), and then are simply added to produce the sum of SSDs. This resulting function is called the SSSD-in-inverse-depth. The authors define a stereo algorithm, based on the SSSD-in-inverse-depth and then present a mathematical analysis to show how the algorithm can remove ambiguity and increase precision. Experimental results for stereo images are presented to demonstrate the effectiveness of the algorithm. <<ETX>>
Experimental Epilepsy in the Mouse.∗

Summary Chronic epilepsy has been produced in the mouse by cerebral implantation of various powdered metals, notably cobalt and nickel. In addition to spontaneous focal and generalized seizures, epileptic status was evaluated by response to challenge injections of Metrazol and semicarbazide, as well as to electroshock. Addendum. Cobalt implanted intracerebrally, in the manner described for mice, has recently proved highly epileptogenic in the rat as evidenced by lowered convulsive threshold to Metrazol.
SR 16435 [1-(1-(Bicyclo[3.3.1]nonan-9-yl)piperidin-4-yl)indolin-2-one], a Novel Mixed Nociceptin/Orphanin FQ/μ-Opioid Receptor Partial Agonist: Analgesic and Rewarding Properties in Mice

We identified a novel nociceptin/orphanin FQ (NOP)/μ-opioid receptor agonist, SR 16435 [1-(1-(bicyclo[3.3.1]nonan-9-yl)piperidin-4-yl)indolin-2-one], with high binding affinity and partial agonist activity at both receptors. It was hypothesized that SR 16435 would produce antinociception and yet, unlike morphine, would have diminished rewarding properties and tolerance development. Antinociception was assessed in mice using the tail-flick assay, whereas behavioral and rewarding effects were assessed using the place conditioning (PC) paradigm. PC was established by pairing drug injections with a distinct compartment. Behavioral effects were measured after acute and repeated drug administration, and the test for PC was carried out 24 h after four drug- and vehicle-pairing sessions. SR 16435 produced an increase in tail-flick latency, but SR 16435-induced antinociception was lower than that observed with morphine. Given that naloxone blocked SR 16435-induced antinociception, it is highly likely that this effect was mediated by μ-opioid receptors. Compared with morphine, chronic SR 16435 treatment resulted in reduced development of tolerance to its antinociceptive effects. SR 16435-induced conditioned place preference (CPP) was evident, an effect that was probably mediated via μ-opioid receptors, as it was reversed by coadministration of naloxone. NOP agonist activity was also present, given that SR 16435 decreased global activity, and this effect was partially reversed with the selective NOP antagonist, SR 16430 [1-(cyclooctylmethyl)-4-(3-(trifluoromethyl)phenyl)piperidin-4-ol]. Naloxone, however, also reversed the SR 16435-induced decrease in activity, indicating that both opioid and NOP receptors mediate this behavior. In summary, the mixed NOP/μ-opioid partial agonist SR 16435 exhibited both NOP and μ-opioid receptor-mediated behaviors.
An examination of black/white differences in the rate of age-related mortality increase

BACKGROUND The rate of mortality increase with age among adults is typically used as a measure of the rate of functional decline associated with aging or senescence. While black and white populations differ in the level of mortality, mortality also rises less rapidly with age for blacks than for whites, leading to the well-known black/white mortality “crossover”. OBJECTIVE This paper investigates black/white differences in the rate of mortality increase with age for major causes of death in order to examine the factors responsible for the black/white crossover. METHODS The analysis considers two explanations for the crossover: selective survival and age misreporting. Mortality is modeled using a Gompertz model for 11 causes of death from ages 50–84 among blacks and whites by sex. RESULTS Mortality increases more rapidly with age for whites than for blacks for nearly all causes of death considered. The all-cause mortality rate of mortality increase is nearly two percentage points higher for whites. The analysis finds evidence for both selective survival and age misreporting, although age misreporting is a more prominent explanation among women. CONCLUSIONS The black/white mortality crossover reflects large differences in the rate of age-related mortality increase. Instead of reflecting the impact of specific causes of death, this pattern exists across many disparate disease conditions, indicating the need for a broad explanation.
Population-level analysis of gut microbiome variation

“Normal” for the gut microbiota For the benefit of future clinical studies, it is critical to establish what constitutes a “normal” gut microbiome, if it exists at all. Through fecal samples and questionnaires, Falony et al. and Zhernakova et al. targeted general populations in Belgium and the Netherlands, respectively. Gut microbiota composition correlated with a range of factors including diet, use of medication, red blood cell counts, fecal chromogranin A, and stool consistency. The data give some hints for possible biomarkers of normal gut communities. Science, this issue pp. 560 and 565 Two large-scale studies in Western Europe establish environment-diet-microbe-host interactions. Fecal microbiome variation in the average, healthy population has remained under-investigated. Here, we analyzed two independent, extensively phenotyped cohorts: the Belgian Flemish Gut Flora Project (FGFP; discovery cohort; N = 1106) and the Dutch LifeLines-DEEP study (LLDeep; replication; N = 1135). Integration with global data sets (N combined = 3948) revealed a 14-genera core microbiota, but the 664 identified genera still underexplore total gut diversity. Sixty-nine clinical and questionnaire-based covariates were found associated to microbiota compositional variation with a 92% replication rate. Stool consistency showed the largest effect size, whereas medication explained largest total variance and interacted with other covariate-microbiota associations. Early-life events such as birth mode were not reflected in adult microbiota composition. Finally, we found that proposed disease marker genera associated to host covariates, urging inclusion of the latter in study design.
Scheduling Product Line Features for Effective Roadmapping

Large industrial product lines may produce tens of thousands of variants each year. Each variant typically contains both reusable assets as well as product specific code created by different organizational units. To produce this vast number of variants the organizational resources must be used efficiently. For roadmapping this means an ability to schedule production of reusable assets so that all variants can be completed according to their requirements. When aiming for centralized variability management, roadmapping requires effective management of product line feature dependences and priorities. In this paper, we first introduce the problems haunting feature roadmapping in industrial product lines. Then we investigate how these problems can be solved using a novel approach for organizing product lines based on our practical experiences. Finally, we discuss our experiences and compare our approach with results by other researchers.
IL‐1β Promotes Malignant Transformation and Tumor Aggressiveness in Oral Cancer

Chronic inflammation, coupled with alcohol, betel quid, and cigarette consumption, is associated with oral squamous cell carcinoma (OSCC). Interleukin‐1 beta (IL‐1β) is a critical mediator of chronic inflammation and implicated in many cancers. In this study, we showed that increased pro‐IL‐1β expression was associated with the severity of oral malignant transformation in a mouse OSCC model induced by 4‐Nitroquinolin‐1‐oxide (4‐NQO) and arecoline, two carcinogens related to tobacco and betel quid, respectively. Using microarray and quantitative PCR assay, we showed that pro‐IL‐1β was upregulated in human OSCC tumors associated with tobacco and betel quid consumption. In a human OSCC cell line TW2.6, we demonstrated nicotine‐derived nitrosamine ketone (NNK) and arecoline stimulated IL‐1β secretion in an inflammasome‐dependent manner. IL‐1β treatment significantly increased the proliferation and dysregulated the Akt signaling pathways of dysplastic oral keratinocytes (DOKs). Using cytokine antibodies and inflammation cytometric bead arrays, we found that DOK and OSCC cells secreted high levels of IL‐6, IL‐8, and growth‐regulated oncogene‐α following IL‐1β stimulation. The conditioned medium of IL‐1β‐treated OSCC cells exerted significant proangiogenic effects. Crucially, IL‐1β increased the invasiveness of OSCC cells through the epithelial‐mesenchymal transition (EMT), characterized by downregulation of E‐cadherin, upregulation of Snail, Slug, and Vimentin, and alterations in morphology. These findings provide novel insights into the mechanism underlying OSCC tumorigenesis. Our study suggested that IL‐1β can be induced by tobacco and betel quid‐related carcinogens, and participates in the early and late stages of oral carcinogenesis by increasing the proliferation of dysplasia oral cells, stimulating oncogenic cytokines, and promoting aggressiveness of OSCC. J. Cell. Physiol. 230: 875–884, 2015. © 2014 The Authors. Journal of Cellular Physiology Published by Wiley Periodicals, Inc.
Multiple Primary Tumors in Patients Diagnosed with Hypopharyngeal Cancer

OBJECTIVE: There have been few series to report on the incidence of multiple primary tumors associated with hypopharyngeal cancer. A unique consecutive patient group in a closed community who were treated by a single surgeon was available. The incidence and effect of multiple primary tumors were unknown. STUDY DESIGN: We sought to assess (1) the incidence of multiple primary tumors among patients with hypopharyngeal cancer who were treated at a tertiary center, (2) the incidence of synchronous and metachronous tumors, and (3) the location of these multiple primary tumors and their effect on patient survival. METHODS: We conducted a retrospective study of case notes of 150 consecutive patients with hypopharyngeal malignancy treated by a single surgeon between 1983 and 1998. Information was compiled from the patients' medical records and death data from the Family Health Services Authority. RESULTS: Thirty-four patients had multiple primary tumors (22.6%). There were 22 men and 12 women; piriform fossa tumor was seen in 21 men and 6 women, and postcricoid space tumor was seen in 6 women and 1 man. Second primary tumors were synchronous in 7 patients, subsequent to hypopharyngeal tumor in 5 patients, and antecedent to hypopharyngeal tumor in 14 patients. Eight patients had 2 primary tumors, of which 4 were synchronous, 4 were subsequent, and 8 were antecedent to hypopharyngeal malignancy. On the last review (2001), 3 patients were alive, and 31 had died: 17 had died from primary malignancy, 11 from another malignancy, and 3 from unrelated causes. CONCLUSION: The presence of second primary tumors in hypopharyngeal cancer is higher than previously reported, and their presence had a significant effect on the patients' survival.
Transcriptional Regulation of Multi-Drug Tolerance and Antibiotic-Induced Responses by the Histone-Like Protein Lsr2 in M. tuberculosis

Multi-drug tolerance is a key phenotypic property that complicates the sterilization of mammals infected with Mycobacterium tuberculosis. Previous studies have established that iniBAC, an operon that confers multi-drug tolerance to M. bovis BCG through an associated pump-like activity, is induced by the antibiotics isoniazid (INH) and ethambutol (EMB). An improved understanding of the functional role of antibiotic-induced genes and the regulation of drug tolerance may be gained by studying the factors that regulate antibiotic-mediated gene expression. An M. smegmatis strain containing a lacZ gene fused to the promoter of M. tuberculosis iniBAC (PiniBAC) was subjected to transposon mutagenesis. Mutants with constitutive expression and increased EMB-mediated induction of PiniBAC::lacZ mapped to the lsr2 gene (MSMEG6065), a small basic protein of unknown function that is highly conserved among mycobacteria. These mutants had a marked change in colony morphology and generated a new polar lipid. Complementation with multi-copy M. tuberculosis lsr2 (Rv3597c) returned PiniBAC expression to baseline, reversed the observed morphological and lipid changes, and repressed PiniBAC induction by EMB to below that of the control M. smegmatis strain. Microarray analysis of an lsr2 knockout confirmed upregulation of M. smegmatis iniA and demonstrated upregulation of genes involved in cell wall and metabolic functions. Fully 121 of 584 genes induced by EMB treatment in wild-type M. smegmatis were upregulated (“hyperinduced”) to even higher levels by EMB in the M. smegmatis lsr2 knockout. The most highly upregulated genes and gene clusters had adenine-thymine (AT)–rich 5-prime untranslated regions. In M. tuberculosis, overexpression of lsr2 repressed INH-mediated induction of all three iniBAC genes, as well as another annotated pump, efpA. The low molecular weight and basic properties of Lsr2 (pI 10.69) suggested that it was a histone-like protein, although it did not exhibit sequence homology with other proteins in this class. Consistent with other histone-like proteins, Lsr2 bound DNA with a preference for circular DNA, forming large oligomers, inhibited DNase I activity, and introduced a modest degree of supercoiling into relaxed plasmids. Lsr2 also inhibited in vitro transcription and topoisomerase I activity. Lsr2 represents a novel class of histone-like proteins that inhibit a wide variety of DNA-interacting enzymes. Lsr2 appears to regulate several important pathways in mycobacteria by preferentially binding to AT-rich sequences, including genes induced by antibiotics and those associated with inducible multi-drug tolerance. An improved understanding of the role of lsr2 may provide important insights into the mechanisms of action of antibiotics and the way that mycobacteria adapt to stresses such as antibiotic treatment.
Real-time fault diagnosis and fault-tolerant control

This "Special Section on Real-Time Fault Diagnosis and Fault-Tolerant Control" of the IEEE Transactions on Industrial Electronics is motivated to provide a forum for academic and industrial communities to report recent theoretic/application results in real-time monitoring, diagnosis, and fault-tolerant design, and exchange the ideas about the emerging research direction in this field. Twenty-three papers were eventually selected through a strict peer-reviewed procedure, which represent the most recent progress on real-time fault diagnosis, fault-tolerant control design, and their applications. Twelve selected papers pay attention on fault diagnosis methods and applications, and the other eleven papers are concentrated on realtime fault-tolerant control and applications. We are going to overview the selected papers following fault diagnosis techniques and fault-tolerant control techniques, sequentially.
Post-Grouting Stability of Bentonite Suspensions within Sand Pores

Permeation grouting can be an effective way to deliver bentonite into porous media to control ground water flow. Bentonite slurries can be permeated into the porous media to reduce the hydraulic conductivity of the original soil. While some work has been done on the change in hydraulic conductivity of the soils when introducing bentonite, the stability of the bentonite within the pore space has not been significantly investigated. The current paper presents a study on the post-grouting stability of bentonite grouts within a porous media. The performance of bentonite grout in permeated sands was investigated by studying the rheological properties of bentonite suspensions (particularly, yield stress) and stability of the ground under in-situ hydraulic gradients. The rheological parameters of bentonite suspensions were measured at various bentonite concentrations (ranging from 6 to 16% bentonite to total weight) with and without sodium pyrophosphate (SPP) modifications (SPP percentage ranged from 1 to 11% by dry weight of bentonite). SPP is an ionic additive used to temporary control the rheological properties of the bentonite grouts. The stability of bentonite grout was inspected by studying the hydraulic conductivity of sand permeated with bentonite suspensions under increasing hydraulic gradients; when washing out occurs, it results in an increase in hydraulic conductivity. The critical hydraulic gradient at which washing out of bentonite suspensions is initiated was examined. Accordingly, a relation between the yield stress of bentonite suspensions and the critical hydraulic conductivity is developed.
Local activation of the nitric oxide/cyclic guanosine monophosphate pathway in growth cones regulates filopodial length via protein kinase G, cyclic ADP ribose and intracellular Ca2+ release

Nitric oxide (NO) is a gaseous messenger that has been shown to affect growth cone motility and neurite outgrowth in several model systems, but how NO brings about its effects is not understood. We have previously demonstrated that global and long‐term application of NO to Helisoma trivolvis B5 neurons results in a transient increase in filopodial length, decrease in filopodial number and decrease in neurite outgrowth, all of which are mediated via soluble guanylyl cyclase (sGC) and involve an increase in the intracellular Ca2+ concentration [S. Van Wagenen & V. Rehder (1999)Journal of Neurobiology, 39, 168–185; K.R. Trimm & V. Rehder (2004)European Journal of Neuroscience, 19, 809–818]. The goal of the current study was twofold: to investigate the effects of short‐term NO exposure on individual growth cones and to further elucidate the downstream pathway through which NO exerts its effects. Local application of the NO donor NOC‐7 for 10–20 ms via puffer micropipette resulted in a transient increase in filopodial length and a small decrease in filopodial number. We show evidence that these effects of NO are mediated via sGC, protein kinase G and cyclic ADP ribose, resulting in the release of Ca2+ from intracellular stores, probably of the ryanodine‐sensitive type. These results suggest that growth cones expressing sGC are highly sensitive to local and short‐term exposure to NO, which they may experience during pathfinding, and that the stereotyped response of transient filopodial elongation seen in B5 neurons in response to NO requires intracellular Ca2+ release.
STRING v9.1: protein-protein interaction networks, with increased coverage and integration

Complete knowledge of all direct and indirect interactions between proteins in a given cell would represent an important milestone towards a comprehensive description of cellular mechanisms and functions. Although this goal is still elusive, considerable progress has been made—particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available interaction data is desirable, including lower-quality data and/or computational predictions. The STRING database (http://string-db.org/) aims to provide such a global perspective for as many organisms as feasible. Known and predicted associations are scored and integrated, resulting in comprehensive protein networks covering >1100 organisms. Here, we describe the update to version 9.1 of STRING, introducing several improvements: (i) we extend the automated mining of scientific texts for interaction information, to now also include full-text articles; (ii) we entirely re-designed the algorithm for transferring interactions from one model organism to the other; and (iii) we provide users with statistical information on any functional enrichment observed in their networks.
Artifacts in brain magnetic resonance imaging due to metallic dental objects.

OBJECTIVE Artifacts caused by metallic objects, such as dental crowns, dental implants and metallic orthodontic appliances, are a common problem in head and neck MRI. The aim of this retrospective study was to identify the main metal dental objects that produce artifacts on brain MRIs. STUDY DESIGN Imaged metallic artifacts and their sources were identified. Artifact image plane was rated on a score of 0 or 1 (0--distinguishable for diagnosis and 1--not distinguishable for diagnosis). RESULTS Seventy-eight percent of the artifacts appearing in images were caused by orthodontic appliances, followed by dental titanium implants (18%) and metallic crowns (4%). Orthodontic appliances obtained the highest scores in all planes. CONCLUSIONS We concluded that is difficult to avoid the effect of metallic artifacts in the maxillofacial regions on brain scan. Removing metallic parts of the orthodontic appliance should ensure diagnostically useful quality scans.
Differential Proteome Analysis of Chlamydomonas reinhardtii Response to Arsenic Exposure

The fresh water unicellular green alga Chlamydomonas reinhardtii was used to explore whether it could function as a model system to identify proteins that are differentially expressed in response to arsenate exposure. Cells were treated with different concentrations of arsenate ranging from 100 - 400 μM. When exposed to 200 μM arsenate, the amount of live cells started to lessen on the second day and continued to diminish, indicating a toxic effect of arsenate. Proteomic analysis was used to investigate if these cells showed a specific response to arsenic-induced stress. Fifteen proteins were found that were over-expressed in the 200 μM arsenate-treated samples and two proteins were found to be very strongly over-expressed in samples treated with 400 μM. These were selected for identification using liquid chromatography coupled with tandem mass spectrometry. Oxidative stress and protein damage were the major effects as shown by the up-regulation of Mn-superoxide dismutase, an oxygen-evolving enhancer protein, a chaperonin-like protein and a heat shock protein.
Effect of mechanical removal of pili on gliding motility of Myxococcus xanthus

Gliding motility of Myxococcus xanthus is governed by both the adventurous (A) and the social (S) motility gene systems. The presence of pili has previously been shown to be correlated with a genetically intact S-motility system (D. Kaiser, Proc. Natl. Acad. Sci. USA 76:5952-5956, 1979). The purpose of the present work was to study the direct effect of mechanical removal of pill on the social motility of M. xanthus. Depiliation resulted in (i) a loss of streaming motility of A- S+ mutants, i.e., strains which are able to move by virtue of the S-motility system only, (ii) no effect on motility in A+ S- mutants, i.e., strains capable of movement by the A-motility system only, and (iii) a retardation of streaming speed in the wild-type strain (A+ S+). Cell-cell cohesion, another characteristic of social behavior, was not affected by mechanical removal of pill. The observation that mechanical depiliation perturbed the motility of strains which rely on the S-motility system strongly supports a role for pili in social motility of M. xanthus.