Miracle-dz/UniFAR-FTUs huggingface dataset:
Semantic Segmentation of a Point Clouds of an Urban Scene

Semantic segmentation of images is a challenging task in computer vision. In our paper we present an algorithm for segmentation of images of urban scenes, acquired by methods of structure from motion. Our approach is based on extracting of depth and color features into a reduced parameter space. Our key contribution is a model of scene segmentation based on a k-nearest neighbor classifier in reduced color-depth space. Parameter space reduction is provided by splitting a parameter space on a regular grid in each major axis direction. Then we train kNN classifier to label pixels of input images as one of three categories: plants, roads and buildings.
Digitization and search: A non-traditional use of HPC

Automated search of handwritten content is a highly interesting and applicative subject, especially important today due to the public availability of large digitized document collections. We describe our efforts with the National Archives (NARA) to provide searchable access to the 1940 Census data and discuss the HPC resources needed to implement the suggested framework. Instead of trying to recognize the handwritten text, a still very difficult task, we use a content based image retrieval technique known as Word Spotting. Through this paradigm, the system is queried by the use of handwritten text images instead of ASCII text and ranked groups of similar looking images are presented to the user. A significant amount of computing power is needed to accomplish the pre-processing of the data so to make this search capability available on an archive. The required preprocessing steps and the open source framework developed are discussed focusing specifically on HPC considerations that are relevant when preparing to provide searchable access to sizeable collections, such as the US Census. Having processed the state of North Carolina from the 1930 Census using 98,000 SUs we estimate the processing of the entire country for 1940 could require up to 2.5 million SUs. The proposed framework can be used to provide an alternative to costly manual transcriptions for a variety of digitized paper archives.
Effect of Persian and almond gums as fat replacers on the physicochemical, rheological, and microstructural attributes of low‐fat Iranian White cheese

Abstract The effect of Persian and almond gums (0, 0.1 and 0.2% (w/w)) as fat replacers and milk fat (0.4, 0.9, and 1.4% (w/w)) on physicochemical and rheological characteristics and microstructure of low‐fat Iranian White cheese was studied. Persian and almond gums both effectively increased moisture‐to‐protein (M:P) ratio of low‐fat cheese samples which in turn led to a significant reduction in the hardness parameters fracture stress and Young's and storage (G’) moduli (p < .05); however, the effect of Persian gum was more pronounced (p < .01). Gum addition promoted cheese yield and proteolysis rate (p < .05). Response surface optimization described that supplementation of cheese milk containing 0.9% fat with 0.2% Persian gum and 0.12% almond gum would result in a low‐fat cheese with textural properties similar to its full‐fat counterpart. Scanning electron microscopy revealed that the fat replacers produced full‐fat‐like structure in the low‐fat Iranian White cheese, when incorporated at the optimum levels.
The Textual Semantic Lens

People often feel the limitation of time to read the continuously increasing articles they need to read. It is a grand challenge to handle the explosion of articles. To understand how humans read articles and get the meaning is the basis of improving the efficiency of reading articles. The underlying semantic links between language units of different granularities reflect some basic semantics. Sentence is the basic language unit for accurately indicating semantics. By defining concepts and the dependent set of sentences, and constructing the semantic link network of dependent sentences and semantic link network of concepts, this paper proposes the textual semantic lens with a set of functions for helping people comprehend articles. Integrating with the semantic link networks of articles, the semantic lens can help people efficiently read large-scale articles.
IKKβ slows Huntington’s disease progression in R6/1 mice

Significance Huntington’s disease (HD) is a devastating neurodegenerative disorder caused by expansion of a polyglutamine repeat within the huntingtin (HTT) protein. A normal function of HTT is that of a scaffold for selective autophagy, a mechanism of protein and organelle degradation by the lysosome required for neuronal health. Here, we show that the inflammatory IκB kinase (IKK) kinase subunit IKKβ may function in vivo to regulate autophagy through direct phosphorylation of HTT at serine 13 and through the activation of autophagy gene expression. IKKβ is required to slow HD behavioral progression and to suppress neurodegeneration and microglial activation in HD transgenic mice. Our work suggests that the early activation of IKK may be protective to activate autophagy, thereby slowing HD progression. Neuroinflammation is an important contributor to neuronal pathology and death in neurodegenerative diseases and neuronal injury. Therapeutic interventions blocking the activity of the inflammatory kinase IKKβ, a key regulator of neuroinflammatory pathways, is protective in several animal models of neurodegenerative disease and neuronal injury. In Huntington’s disease (HD), however, significant questions exist as to the impact of blocking or diminishing the activity of IKKβ on HD pathology given its potential role in Huntingtin (HTT) degradation. In cell culture, IKKβ phosphorylates HTT serine (S) 13 and activates HTT degradation, a process that becomes impaired with polyQ expansion. To investigate the in vivo relationship of IKKβ to HTT S13 phosphorylation and HD progression, we crossed conditional tamoxifen-inducible IKKβ knockout mice with R6/1 HD mice. Behavioral assays in these mice showed a significant worsening of HD pathological phenotypes. The increased behavioral pathology correlated with reduced levels of endogenous mouse full-length phospho-S13 HTT, supporting the importance of IKKβ in the phosphorylation of HTT S13 in vivo. Notably, many striatal autophagy genes were up-regulated in HD vs. control mice; however, IKKβ knockout partially reduced this up-regulation in HD, increased striatal neurodegeneration, and enhanced an activated microglial response. We propose that IKKβ is protective in striatal neurons early in HD progression via phosphorylation of HTT S13. As IKKβ is also required for up-regulation of some autophagy genes and HTT is a scaffold for selective autophagy, IKKβ may influence autophagy through multiple mechanisms to maintain healthy striatal function, thereby reducing neuronal degeneration to slow HD onset.
Coherent multidimensional spectroscopy in the gas phase

Recent work applying multidimentional coherent electronic spectroscopy at dilute samples in the gas phase is reviewed. The development of refined phase cycling approaches with improved sensitivity has opened up new opportunities to probe even dilute gas-phase samples. In this context, first results of two-dimensional spectroscopy performed at doped helium droplets reveal the femtosecond dynamics upon the electronic excitation of cold, weakly-bound molecules, and even the induced dynamics from the interaction with the helium environment. Such experiments, offering well-defined conditions at low temperatures, are potentially enabling the isolation of fundamental processes in the excitation and charge transfer dynamics of molecular structures which so far have been masked in complex bulk environments.
Professional's Information Link (PiL): a web-based asynchronous consultation service

Despite the massive growth of on-line information resources, many clinicians still prefer to obtain information from other clinicians, particularly those to whom they refer patients. Based on this notion and an information needs assessment, we developed the Professional's Information Link (PiL), a Web-based asynchronous consultation service to facilitate question answering between rural clinicians and an academic medical center. The system aims to provide answers to questions within two working days. It also includes patient handouts and continuing medical education resources. Our preliminary evaluation demonstrates modest but enthusiastic use of the system.
BMP and FGF‐2 regulate neurogenin‐2 expression and the differentiation of sensory neurons and glia

We have examined the effects of signaling molecules and Notch signaling on the mechanisms regulating neurogenin (ngn) ‐2 expression. This ngn‐2 is a transcription factor that is essential for the specification of early differentiating sensory neurons in the dorsal root ganglia. In the presence of bone morphogenetic protein (BMP), anti–ngn‐2‐positive cells appeared in mouse trunk neural crest cell cultures, and they expressed Brn3, indicating that ngn‐2–expressing cells are sensory neurons. These cells did not differentiate after fibroblast growth factor (FGF) ‐2 treatment or after Notch activation. The suppression of ngn‐2 expression by FGF‐2 was recovered by treatment with a Notch signaling inhibitor. Thus, FGF‐2 may prevent ngn‐2 expression through Notch activation. Whereas BMP‐4 inhibited glial differentiation, FGF‐2 promoted gliogenesis by means of Notch activation. Our data suggest that BMP and FGF‐2 act as positive and negative regulators in ngn‐2 expression, respectively, and that these signaling molecules regulate the differentiation of sensory neurons and glia. Developmental Dynamics 235:646–655, 2006. © 2006 Wiley‐Liss, Inc.
Study on voltage stability of island grid supplied by large grid with long submarine cables considering different load patterns

The voltage response characteristics considered different load patterns are studied in the paper. The effects of on-load tap changer (OLTC), over-excitation limiter (OLE), and high voltage direct current (HVDC) link on voltage stability are also analyzed. In which, the converter terminals of HVDC link are considered as a constant real and reactive power load under steady state and the effects of HVDC control modes on voltage stability are also studied. A practical system of larger grid (Taiwan grid) connecting to a smaller island grid (Peng-Hu grid) via two circuits of long submarine cables is used to study. The strategies for improving voltage stability include reactive power support and under-voltage load shedding (UVLS) are proposed. Based on the simulation results, it shows that the voltage response characteristics are affected significantly by different load patterns. The OLTC plays an important role during the load voltage restoration. The reactive power support devices and UVLS can improve the short-term voltage stability, which makes the power system achieve voltage stability operation. However, the interactions between OLTC and OEL under HVDC link connected operation would lead the power system to voltage instability. The constant current control mode of HVDC link has better effect on voltage stability. All of these studies are performed by software package, namely power system simulation for engineering (PSS/E) in this paper.
Impaired SIRT1 activity leads to diminution in glomerular endowment without accelerating age‐associated GFR decline

Glomerular filtration rate (GFR) declines with age such that the prevalence of chronic kidney disease is much higher in the elderly. SIRT1 is the leading member of the sirtuin family of NAD+‐dependent lysine deacetylases that mediate the health span extending properties of caloric restriction. Since reduction in energy intake has also been shown to decrease age‐related kidney disease in rodents, we hypothesized that a diminution in SIRT1 activity would accelerate the GFR decline and structural injury with age. To test this hypothesis, we compared changes in the kidney structure and function in control mice and mice that carry a point mutation at a conserved histidine (H355Y) of SIRT1 that renders the enzyme catalytically inactive. Taking advantage of this mouse model along with the disector/fractionator technique for glomerular counting and direct measurements of GFR by inulin clearance, we assessed the impact of SIRT1 inactivity on kidney aging. At 14 months of age, SIRT1 catalytically inactive (Sirt1Y/Y) mice had lower GFRs and fewer glomeruli than their wild‐type (Sirt1+/+) counterparts. This was not, however, due to either accelerated GFR decline or increased glomerulosclerosis and loss, but rather to reduced glomerular endowment in Sirt1Y/Y mice. Moreover, the compensatory glomerular hypertrophy and elevated single nephron GFR that customarily accompany reduction in nephron number were absent in Sirt1Y/Y mice. These findings suggest a role for SIRT1 not only in determining nephron endowment but also in orchestrating the response to it.
A new anchor word selection method for the separable topic discovery

Separable nonnegative matrix factorization (SNMF) is an important method for topic modeling, where “separable” assumes every topic contains at least one anchor word, defined as a word that has non‐zero probability only on that topic. SNMF focuses on the word co‐occurrence patterns to reveal topics by two steps: anchor word selection and topic recovery. The quality of the anchor words strongly influences the quality of the extracted topics. Existing anchor word selection algorithm is to greedily find an approximate convex hull in a high‐dimensional word co‐occurrence space. In this work, we propose a new method for the anchor word selection by associating the word co‐occurrence probability with the words similarity and assuming that the most different words on semantic are potential candidates for the anchor words. Therefore, if the similarity of a word‐pair is very low, the two words are very likely to be the anchor words. According to the statistical information of text corpora, we can get the similarity of all word‐pairs. We build the word similarity graph where the nodes correspond to words and weights on edges stand for the word‐pair similarity. Following this way, we design a greedy method to find a minimum edge‐weight anchor clique of a given size in the graph for the anchor word selection. Extensive experiments on real‐world corpus demonstrate the effectiveness of the proposed anchor word selection method that outperforms the common convex hull‐based methods on the revealed topic quality. Meanwhile, our method is much faster than typical SNMF‐based method.
Genome‐wide association studies of alcohol dependence, DSM‐IV criterion count and individual criteria

Genome‐wide association studies (GWAS) of alcohol dependence (AD) have reliably identified variation within alcohol metabolizing genes (eg, ADH1B) but have inconsistently located other signals, which may be partially attributable to symptom heterogeneity underlying the disorder. We conducted GWAS of DSM‐IV AD (primary analysis), DSM‐IV AD criterion count (secondary analysis), and individual dependence criteria (tertiary analysis) among 7418 (1121 families) European American (EA) individuals from the Collaborative Study on the Genetics of Alcoholism (COGA). Trans‐ancestral meta‐analyses combined these results with data from 3175 (585 families) African‐American (AA) individuals from COGA. In the EA GWAS, three loci were genome‐wide significant: rs1229984 in ADH1B for AD criterion count (P = 4.16E−11) and Desire to cut drinking (P = 1.21E−11); rs188227250 (chromosome 8, Drinking more than intended, P = 6.72E−09); rs1912461 (chromosome 15, Time spent drinking, P = 1.77E−08). In the trans‐ancestral meta‐analysis, rs1229984 was associated with multiple phenotypes and two additional loci were genome‐wide significant: rs61826952 (chromosome 1, DSM‐IV AD, P = 8.42E−11); rs7597960 (chromosome 2, Time spent drinking, P = 1.22E−08). Associations with rs1229984 and rs18822750 were replicated in independent datasets. Polygenic risk scores derived from the EA GWAS of AD predicted AD in two EA datasets (P < .01; 0.61%‐1.82% of variance). Identified novel variants (ie, rs1912461, rs61826952) were associated with differential central evoked theta power (loss − gain; P = .0037) and reward‐related ventral striatum reactivity (P = .008), respectively. This study suggests that studying individual criteria may unveil new insights into the genetic etiology of AD liability.
Conformational resolution of nucleotide cycling and effector interactions for multiple small GTPases determined in parallel

Small GTPases alternatively bind GDP/GTP guanine nucleotides to gate signaling pathways that direct most cellular processes. Numerous GTPases are implicated in oncogenesis, particularly the three RAS isoforms HRAS, KRAS, and NRAS and the RHO family GTPase RAC1. Signaling networks comprising small GTPases are highly connected, and there is some evidence of direct biochemical cross-talk between their functional G-domains. The activation potential of a given GTPase is contingent on a codependent interaction with the nucleotide and a Mg2+ ion, which bind to individual variants with distinct affinities coordinated by residues in the GTPase nucleotide-binding pocket. Here, we utilized a selective-labeling strategy coupled with real-time NMR spectroscopy to monitor nucleotide exchange, GTP hydrolysis, and effector interactions of multiple small GTPases in a single complex system. We provide insight into nucleotide preference and the role of Mg2+ in activating both WT and oncogenic mutant enzymes. Multiplexing revealed guanine nucleotide exchange factor (GEF), GTPase-activating protein (GAP), and effector-binding specificities in mixtures of GTPases and resolved that the three related RAS isoforms are biochemically equivalent. This work establishes that direct quantitation of the nucleotide-bound conformation is required to accurately determine an activation potential for any given GTPase, as small GTPases such as RAS-like proto-oncogene A (RALA) or the G12C mutant of KRAS display fast exchange kinetics but have a high affinity for GDP. Furthermore, we propose that the G-domains of small GTPases behave autonomously in solution and that nucleotide cycling proceeds independently of protein concentration but is highly impacted by Mg2+ abundance.
Comparing the Superficial Vasculature of the Central Nervous System in Six Laboratory Animals: A Hypothesis About the Role of the “Circle of Willis”

We provide images of the entire central nervous system vasculature, and compare the anatomical findings in six different laboratory animals. A detailed understanding of the specific anatomy for each is important in the design of experimental modeling and for understanding the specific function of each target organ. Six different types of animals, the Korean wild mouse, C57BL/6J mouse, F344 rat, mongolian gerbil, Syrian hamsters, and guinea pigs, were included. To stain the blood vessels in each of the animals, Alcian blue reagent was used to perfuse each species. The bifurcation and anastomotic patterns of the anterior cerebral arteries differed in each species. The vascular supply to the olfactory nerve was visualized as a single artery supplying both olfactory nerves, and arteries supplying the lateral portion of the olfactory nerves originating from the olfactory bulb area. The posterior communicating arteries of the six animals demonstrated unique morphologies. The shape of the hypophyseal portal system varied by species. Most animals used in this study had a hexagonal Circle of Willis, except for the Korean wild mouse. Using this approach, we successfully mapped the brain vascular system in six different species of animals. This information and the images created can guide other researchers as they design research studies and create experimental models for new surgical procedures and approaches. Anat Rec, 2019. © 2019 Wiley Periodicals, Inc. Anat Rec, 302:2049–2061, 2019. © 2019 American Association for Anatomy
Blood Pressure Lowering With Nilvadipine in Patients With Mild‐to‐Moderate Alzheimer Disease Does Not Increase the Prevalence of Orthostatic Hypotension

Background Hypertension is common among patients with Alzheimer disease. Because this group has been excluded from hypertension trials, evidence regarding safety of treatment is lacking. This secondary analysis of a randomized controlled trial assessed whether antihypertensive treatment increases the prevalence of orthostatic hypotension (OH) in patients with Alzheimer disease. Methods and Results Four hundred seventy‐seven patients with mild‐to‐moderate Alzheimer disease were randomized to the calcium‐channel blocker nilvadipine 8 mg/day or placebo for 78 weeks. Presence of OH (blood pressure drop ≥20/≥10 mm Hg after 1 minute of standing) and OH‐related adverse events (dizziness, syncope, falls, and fractures) was determined at 7 follow‐up visits. Mean age of the study population was 72.2±8.2 years and mean Mini‐Mental State Examination score was 20.4±3.8. Baseline blood pressure was 137.8±14.0/77.0±8.6 mm Hg. Grade I hypertension was present in 53.4% (n=255). After 13 weeks, blood pressure had fallen by −7.8/−3.9 mm Hg for nilvadipine and by −0.4/−0.8 mm Hg for placebo (P<0.001). Across the 78‐week intervention period, there was no difference between groups in the proportion of patients with OH at a study visit (odds ratio [95% CI]=1.1 [0.8–1.5], P=0.62), nor in the proportion of visits where a patient met criteria for OH, corrected for number of visits (7.7±13.8% versus 7.3±11.6%). OH‐related adverse events were not more often reported in the intervention group compared with placebo. Results were similar for those with baseline hypertension. Conclusions This study suggests that initiation of a low dose of antihypertensive treatment does not significantly increase the risk of OH in patients with mild‐to‐moderate Alzheimer disease. Clinical Trial Registration URL: https://www.clinicaltrials. gov. Unique identifier: NCT02017340.
People with schizophrenia show enhanced cognitive costs of maintaining a single item in working memory

Abstract Background Working memory (WM) deficits are seen as a core deficit in schizophrenia, implicated in the broad cognitive impairment seen in the illness. Here we examine the impact of WM storage of a single item on the operation of other cognitive systems. Methods We studied 37 healthy controls (HCS) and 43 people with schizophrenia (PSZ). Each trial consisted of a sequence of two potential target stimuli, T1 and T2. T1 was a letter presented for 100 ms. After delays of 100–800 ms, T2 was presented. T2 was a 1 or a 2 and required a speeded response. In one condition, subjects were instructed to ignore T1 but respond to T2. In another condition, they were required to report T1 after making their speeded response to T2 (i.e. to make a speeded T2 response while holding T1 in WM). Results PSZ were dramatically slowed at responding to T2 when T1 was held in WM. A repeated measures ANOVA yielded main effects of group, delay, and condition with a group by condition interaction (p's < 0.001). Across delays, the slowing of the T2 response when required to hold T1 in memory, relative to ignoring T1, was nearly 3 times higher in PSZ than HCS (633 v. 219 ms). Conclusions Whereas previous studies have focused on reduced storage capacity, the present study found that PSZ are impaired at performing tasks while they are successfully maintaining a single item in WM. This may play a role in the broad cognitive impairment seen in PSZ.