Miracle-dz/UniFAR-FTUs huggingface dataset:
Beyond KernelBoost

In this Technical Report we propose a set of improvements with respect to the KernelBoost classifier presented in [3]. We start with a scheme inspired by Auto-Context, but that is suitable in situations where the lack of large training sets poses a potential problem of overfitting. The aim is to capture the interactions between neighboring image pixels to better regularize the boundaries of segmented regions. As in AutoContext [32] the segmentation process is iterative and, at each iteration, the segmentation results for the previous iterations are taken into account in conjunction with the image itself. However, unlike in [32], we organize our recursion so that the classifiers can progressively focus on difficultto-classify locations. This lets us exploit the power of the decision-tree paradigm while avoiding over-fitting. In the context of this architecture, KernelBoost represents a powerful building block due to its ability to learn on the score maps coming from previous iterations. We first introduce two important mechanisms to empower the KernelBoost classifier, namely pooling and the clustering of positive samples based on the appearance of the corresponding groundtruth. These operations significantly contribute to increase the effectiveness of the system on biomedical images, where texture plays a major role in the recognition of the different image components. We then present some other techniques that can be easily integrated in the KernelBoost framework to further improve the accuracy of the final segmentation. We show extensive results on different medical image datasets, including some multi-label tasks, on which our method is shown to outperform state-of-the-art approaches. The resulting segmentations display high accuracy, neat contours, and reduced noise.
Speedy eye movements in multiple sclerosis: Association with performance on visual and nonvisual cognitive tests

Objective: Eye movement difficulties in multiple sclerosis (MS) are common and may influence performance on cognitive tests. The following studies examined associations between a new measure of speedy eye movement speed and visual/nonvisual cognitive tests. Method: In Experiment 1, MS patients (N = 71) were administered cognitive tests and the Speedy Eyes Test (SET) as a measure of purposeful speedy eye movements under timed conditions. Experiment 2 was composed of MS patients (n = 60) and a neurologically healthy comparison group (n = 31) and examined group differences in an abbreviated version of the SET. Results: In both studies, slower eye movements were significantly associated with poorer performance on cognitive tests with a large effect size in Experiment 1 and a medium effect size in Experiment 2. Analyses in Experiment 2 also revealed significant group differences in an abbreviated measure of the SET, where MS patients had slower eye movements than the comparison group. Conclusions: Pending further research, the SET, a brief, inexpensive, and nontechnical measure of speedy eye movement, may serve as a visual/oculomotor indicator of cognitive impairment in multiple sclerosis.
Differential Association Between HDL Subclasses and the Development of Type 2 Diabetes in a Prospective Study of Japanese Americans

OBJECTIVE Recent studies have suggested that HDL cholesterol is inversely associated with the development of type 2 diabetes. However, little is known about the association between different HDL subclasses and the risk for future type 2 diabetes. RESEARCH DESIGN AND METHODS The study enrolled 406 Japanese Americans (51% male) without diabetes, aged 34–75 years. Oral glucose tolerance tests were performed to determine type 2 diabetes status at baseline, 2.5 years, 5 years, and 10 years after enrollment. HDL2, HDL3, total HDL cholesterol, and visceral adipose tissue (VAT) area by computed tomography were measured at baseline. RESULTS In univariate analysis, total HDL and HDL2 cholesterol were inversely associated with the incidence of type 2 diabetes, but HDL3 cholesterol was not. In multivariate analysis, total HDL cholesterol (odds ratio per 1-SD increment, 0.72 [95% CI 0.52–0.995], P = 0.047) and HDL2 cholesterol (odds ratio per 1-SD increment, 0.64 [95% CI 0.44–0.93], P = 0.018) were inversely associated with the risk for type 2 diabetes independent of age, sex, BMI, waist circumference, family history of diabetes, lifestyle factors, systolic blood pressure, lipid-lowering medication use, triglyceride level, HOMA-insulin resistance, and 2-h glucose; however, HDL3 cholesterol was not associated with diabetes risk. The association between diabetes risk and total HDL and HDL2 cholesterol became insignificant after adjustment for VAT area. CONCLUSIONS Subjects with higher HDL2 cholesterol were at lower risk for incident type 2 diabetes, but this association was confounded by and not independent of VAT. Higher HDL3 cholesterol was not associated with diabetes risk.
Explorer Edinburgh System Description for the 2005 IWSLT Speech Translation Evaluation

Our participation in the IWSLT 2005 speech translation task is our first effort to work on limited domain speech data. We adapted our statistical machine translation system that performed successfully in previous DARPA competitions on open domain text translations. We participated in the supplied corpora transcription track. We achieved the highest BLEU score in 2 out of 5 language pairs and had competitive results for the other language pairs.
Influence of genotype and diet on steer performance, manure odor, and carriage of pathogenic and other fecal bacteria. II. Pathogenic and other fecal bacteria.

This study assessed the influence of cattle genotype and diet on the carriage and shedding of zoonotic bacterial pathogens and levels of generic Escherichia coli in feces and ruminal contents of beef cattle during the growing and finishing periods. Fifty-one steers of varying proportions of Brahman and MARC III [0 (15), 1/4 (20), 1/2 (7), and 3/4 Brahman (9)] genotypes were divided among 8 pens, such that each breed type was represented in each pen. Four pens each were assigned to 1 of 2 diets [100% chopped bromegrass hay or a diet composed primarily of corn silage (87%)] that were individually fed for a 119-d growing period, at which time the steers were switched to the same high-concentrate, corn-based finishing diet and fed to a target weight of 560 kg. Feces or ruminal fluid were collected and analyzed at alternating intervals of 14 d or less. Generic E. coli concentrations in feces or ruminal fluid did not differ (P > 0.10) by genotype or by growing diet in the growing or finishing periods. However, the concentrations in both feces and ruminal fluid increased in all cattle when switched to the same high-corn diet in the finishing period. There was no effect (P > 0.25) of diet or genotype during either period on E. coli O157 shedding in feces. Forty-one percent of the steers were positive for Campylobacter spp. at least once during the study, and repeated isolations of Campylobacter spp. from the same steer were common. These repeated isolations from the same animals may be responsible for the apparent diet (P = 0.05) and genotype effects (P = 0.02) on Campylobacter in feces in the finishing period. Cells bearing stx genes were detected frequently in both feces (22.5%) and ruminal fluid (19.6%). The number of stx-positive fecal samples was greater (P < 0.05) for 1/2 Brahman steers (42.9%) than for 1/4 Brahman (25.0%) or 3/4 Brahman steers (22.2%), but were not different compared with MARC III steers (38.3%). The greater feed consumption of 1/2 Brahman and MARC III steers may have resulted in greater starch passage into the colon, accompanied by an increase in fecal bacterial populations, which may have further improved the ability to detect stx genes in these cattle. There was no correlation between either ADG or daily DMI and the number of positive samples of E. coli O157, Campylobacter spp. , or stx genes, which agrees with our current understanding that these microorganisms occur commonly in, and with no measurable detriment to, healthy cattle.
SHARING KNOWLEDGE IN VOLUNTARY SERVICE NOT-FOR-PROFIT ORGANIZATIONS

Knowledge sharing has shown itself to be a phenomenon of great interest to both academics and practitioners. However, literature from both communities seems to have neglected a crucial part of our society: the non-profit sector. This study examines the factors that potentially influence knowledge sharing in voluntary service not-for-profit organizations (VSNFPs). Its examination of survey responses from members of Canadian VSNFPs reveals that, although there are many similarities, there are important differences between the two archetypes such as the impact of self-perceived expertise.
Measurement of the Forward‐Backward Charge Asymmetry in Top‐Quark Pair Production in Proton‐Antiproton Collisions at DO/

A measurement of the forward‐backward charge asymmetry in top‐antitop (tt) pair production in proton‐antiproton (pp) collisions is presented. The asymmetry is measured for different jet multiplicities in the lepton+jets final state on 0.9 fb−1 of data collected by the DO/ experiment at the Fermilab Tevatron Collider. The result is sensitive to new physics, which is demonstrated by setting an upper limit on tt production via heavy neutral gauge bosons (Z′).
Knockout of ATG5 leads to malignant cell transformation and resistance to Src family kinase inhibitor PP2

Autophagy can either promote or inhibit cell death in different cellular contexts. In this study, we investigated the role of autophagy in ATG5 knockout (KO) cell line established using CRISPR/Cas9 system. In ATG5 KO cells, RT‐PCR and immunoblot of LC3 confirmed the functional gene knockout. We found that knockout of ATG5 significantly increased proliferation of NIH 3T3 cells. In particular, autophagy deficiency enhanced susceptibility to cellular transformation as determined by an in vitro clonogenic survival assay and a soft agar colony formation assay. We also found that ATG5 KO cells had a greater migration ability as compared to wild‐type (WT) cells. Moreover, ATG5 KO cells were more resistant to treatment with a Src family tyrosine kinase inhibitor (PP2) than WT cells were. Cyto‐ID Green autophagy assay revealed that PP2 failed to induce autophagy in ATG5 KO cells. PP2 treatment decreased the percentage of cells in the S and G2/M phases among WT cells but had no effect on cell cycle distribution of ATG5 KO cells, which showed a high percentage of cells in the S and G2/M phases. Additionally, the proportion of apoptotic cells significantly decreased after treatment of ATG5 KO cells with PP2 in comparison with WT cells. We found that expression levels of p53 were much higher in ATG5 KO cells. The ATG5 KO seems to lead to compensatory upregulation of the p53 protein because of a decreased apoptosis rate. Taken together, our results suggest that autophagy deficiency can lead to malignant cell transformation and resistance to PP2.
ROEDORES SIGMODONTINOS DEL SITIO ARQUEOLÓGICO "EL DIVISADERO MONTE 6" (HOLOCENO TARDÍO, BUENOS AIRES, ARGENTINA): TAXONOMÍA Y RECONSTRUCCIÓN AMBIENTAL

Sigmodontine rodents from "El Divisadero Monte 6" archaeological site (Late Holocene, Bue- nos Aires, Argentina): Taxonomy and enviromental reconstruction. We describe the assemblage of sigmo- dontine rodents from the archaeological site "El Divisadero Monte 6". This site is placed within the fringe of coastal wetlands of the Bahia de Samborombon (General Lavalle county, Buenos Aires province, Argentina). A radiocarbon date of 540 ± 60 years B.P. indicates a Late Holocene age for the studied sample. The studied sample is mostly composed by species still frequent in the area (e.g., Akodon azarae, Oligoryzomys flavescens , Holochilus brasiliensis) and other sigmodontines regionally extinct (e.g. Bibimys torresi, Pseudoryzomys simplex). The observed decrease both in richness and diversity in recent samples probably was triggered by human-made disturbances over the pampean region during the last centuries.
Role of the nitric oxide-cyclic GMP-K+ channel pathway in the antinociception induced by atrial natriuretic peptide (ANP) and diclofenac.

Diclofenac and indomethacin are non-steroidal antiinflammatory drugs (NSAIDs) with strong antiinflammatory and analgesic activity [1,2]. These drugs are effective in the treatment of rheumatic and non-rheumatic conditions [3]. It is accepted that some NSAIDs, besides inhibiting cyclo-oxygenase in vitro and in vivo [4-5], have additional mechanisms of action [6]. Some reports have demonstrated that inhibition of serotonergic transmission by pretreatment with methiothepin, ritanserin, pchlorophenylalanine or 5,7-dihydroxytryptamine reduce the antinociceptive effect of diclofenac [7], suggesting a direct relationship between central serotonergic mechanisms and the antinociceptive effect of diclofenac. In addition, diclofenac is able to block in a dose-dependent manner the hyperalgesia induced by intrathecal NMDA, but not that induced by intrathecal substance P or AMPA [7]. This effect is reversed by L-arginine, but not by Darginine. These results suggest that diclofenac is able to interfere with the pronociceptive activity of the nitric oxide (NO) system at the spinal level. Indomethacin-induced antinociception seems to be the
23-1 Waste Stabilization Ponds for Waste Water Treatment , Anaerobic Pond

Waste stabilization ponds (WSP) have been used world-wide over the last 50 years for municipal and industrial wastewater. The waste water treatment system has been accepted and used to change the physical, chemical, or biological character of the waste. This article presents the characteristics, parameters, and examples of the waste stabilization ponds all over the world. This work was based on review of previous research, experiments and articles that discuss how the treatment is of great importance to humanity. Parasite removals were reduced 98% after using the treatment in several countries with 100 beds. There will be comparison and description of the WSPs in USA, Canada, Europe, and former Soviet Union. Experiments have shown how the treatment is effective due to the elimination of waste in water, improving water quality by a 95%. There are several types of waste stabilization ponds. They are: anaerobic, facultative, and maturation ponds. Approximately half of the solid waste left after primary treatment settles out in the oxidation ponds. The growth of algae in the oxidation ponds help water quality by increasing the oxygen and consuming Nitrogen and Phosphorous, two common nutrients that area found in waste water. Some pre-requisites may be used for efficiency of the process.
Basic FGF and TGF-/M influence commitment to melanogenesis in neural crest-derived cells of avian embryos

we showed that neural crest (NC)-derived from embryonic quail (DRG) and peripheral nerve (PN), which do not normally give rise to melanocytes, committed to following in the phorbol ester drug 12-O-tetradecanoyl phorbol-13-acetate (TPA). These and support the notion that melanocytes and Schwann cells are derived from a common bipotent intermediate in the neural crest lineage - the melanocyte/Schwann cell progenitor. In this study, we test the possibility that peptide growth factors found in the embryonic environment might act similarly to TPA to influence the fates of these cells. We found that When in the of a (TGF-/J1) These data that at least some NC-derived to and and that these growth factors may play an important role in the control of NC cell fate.
The enigma of embryonic diapause

Embryonic diapause – a period of embryonic suspension at the blastocyst stage – is a fascinating phenomenon that occurs in over 130 species of mammals, ranging from bears and badgers to mice and marsupials. It might even occur in humans. During diapause, there is minimal cell division and greatly reduced metabolism, and development is put on hold. Yet there are no ill effects for the pregnancy when it eventually continues. Multiple factors can induce diapause, including seasonal supplies of food, temperature, photoperiod and lactation. The successful reactivation and continuation of pregnancy then requires a viable embryo, a receptive uterus and effective molecular communication between the two. But how do the blastocysts survive and remain viable during this period of time, which can be up to a year in some cases? And what are the signals that bring it out of suspended animation? Here, we provide an overview of the process of diapause and address these questions, focussing on recent molecular data. Summary: This Primer discusses the complex embryo-uterine interactions that induce, maintain and reactivate the blastocyst from diapause, highlighting the roles of hormones, cytokines and growth factors across animal species.
Roman Copper Alloys: Analysis of Artefacts from Northern Britain

A survey of the range of Roman copper (Cu) alloys is offered. This is based primarily on the analysis of almost 1200 Roman artefacts from sites throughout northern Britain. This large body of data is examined from a number of different perspectives (e.g. typological, cultural, chronological). A full list of the data as an “interactive database” is to be published separately inInternet Archaeology.
Old Red Sandstone basins and alluvial systems of Midland Scotland

Abstract Old Red Sandstone rocks of the Midland Valley of Scotland record the amalgamation history of blocks widely separated from each other in Ordovician times. As a response to the lateral juxtaposition of the Midland Valley against the Highland block, the Midland Valley, weakened during its long history of igneous activity, was subjected to transtension and transpression, which opened and closed basins resulting in much recycling of sediment and the renewed development of intermittent and sometimes prolific volcanic activity. The Old Red Sandstone comprises two cycles of basin fill: the older (the Lower Old Red Sandstone) is separated by a major unconformity from the younger (the Upper Old Red Sandstone). Each cycle begins with conglomeratic sedimentation in pull-apart basins then fines and petrographically matures upward. The cycles, initiated by faulting, record the decline in tectonic influence and the concomitant reduction in source relief. The sediment source to the Old Red Sandstone is enigmatic. The Dalradian basement to the north and Southern Uplands to the south were, in many places, extensively eroded by Late Silurian-Early Devonian times. The thickest sequence of coarse sediment in the UK, if not in Europe, therefore has no obvious nearby uplift to provide both the sediment and the persistent, substantial slopes required to deliver sediment of that calibre to the basin. To the northeast, the Greenland-Baltica collision had created a major Silurian-Carboniferous (Scandian) uplift. Major river systems draining this mountain belt entered the Lower and Upper Old Red Sandstone basins at a late stage in their development when relief was lowered sufficiently to allow access to them.
From Protein-Protein Interaction to Molecular Event Extraction

This document describes the methods and results for our participation in the BioNLP'09 Shared Task #1 on Event Extraction. It also contains some error analysis and a brief discussion of the results. Previous shared tasks in the BioNLP community have focused on extracting gene and protein names, and on finding (direct) protein-protein interactions (PPI). This year's task was slightly different, since the protein names were already manually annotated in the text. The new challenge was to extract biological events involving these given gene and gene products. We modified a publicly available system (AkanePPI) to apply it to this new, but similar, protein interaction task. AkanePPI has previously achieved state-of-the-art performance on all existing public PPI corpora, and only small changes were needed to achieve competitive results on this event extraction task. Our official result was an F-score of 36.9%, which was ranked as number six among submissions from 24 different groups. We later balanced the recall/precision by including more predictions than just the most confident one in ambiguous cases, and this raised the F-score on the test-set to 42.6%. The new Akane program can be used freely for academic purposes.
Noise performance of 0.35-/spl mu/m SOI CMOS devices and micropower preamplifier following 63-MeV, 1-mrad (Si) proton irradiation

Total dose and single-event radiation hardness, and operation over extreme temperatures make silicon-on-insulator (SOI) complementary metal oxide semiconductor (CMOS) processes leading contenders for space applications. This paper reports noise degradation of 0.35-/spl mu/m partially-depleted SOI CMOS devices and a micropower, low-noise preamplifier following 63-MeV proton irradiation to 1Mrad (Si). Proton irradiation, relevant for space mission environments, was considered since it induces both ionizing and displacement damage. Preamplifier input-referred white-noise voltage was minimized at low power consumption by operating input devices in moderate inversion for high transconductance efficiency. Flicker-noise, important for gyros and other mission sensors having low-frequency outputs, was minimized by large-area pMOS input devices and careful management of noninput devices. Measured 1-Hz gate-referred, flicker-noise voltage density increased 24 and 32% for pMOS and nMOS test devices respectively following 1 Mrad (Si) irradiation. Measured 1-Hz input-referred noise voltage density increased 22% between a nonirradiated and radiated preamplifier sample, which agrees closely with the 24% increase expected since noise is dominated by pMOS input devices. Device small-signal transconductance and white-noise were largely unchanged while output conductance appeared to increase over a factor-of-three. This suggests a modest design margin is required to maintain flicker noise performance, while substantial design margin may be required to maintain open-loop voltage gain.
The F-Box Protein Fbp1 Regulates Sexual Reproduction and Virulence in Cryptococcus neoformans

ABSTRACT Cryptococcus neoformans is the leading cause of fungal meningitis in immunocomprised populations. Although extensive studies have been conducted on signal transduction pathways important for fungal sexual reproduction and virulence, how fungal virulence is regulated during infection is still not understood. In this study, we identified the F-box protein Fbp1, which contains a putative F-box domain and 12 leucine-rich repeats (LRR). Although fbp1 mutants showed normal growth and produced normal major virulence factors, such as melanin and capsule, Fbp1 was found to be essential for fungal virulence, as fbp1 mutants were avirulent in a murine systemic-infection model. Fbp1 is also important for fungal sexual reproduction. Basidiospore production was blocked in bilateral mating between fbp1 mutants, even though normal dikaryotic hyphae were observed during mating. In vitro assays of stress responses revealed that fbp1 mutants are hypersensitive to SDS, but not calcofluor white (CFW) or Congo red, indicating that Fbp1 may regulate cell membrane integrity. Fbp1 physically interacts with Skp1 homologues in both Saccharomyces cerevisiae and C. neoformans via its F-box domain, suggesting it may function as part of an SCF (Skp1, Cullins, F-box proteins) E3 ligase. Overall, our study revealed that the F-box protein Fbp1 is essential for fungal sporulation and virulence in C. neoformans, which likely represents a conserved novel virulence control mechanism that involves the SCF E3 ubiquitin ligase-mediated proteolysis pathway.