Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical parameters including serum pepsinogen level and management strategy in patients with premalignant gastric dysplasia

Objective Surgical or endoscopic resection is recommended for the management of gastric high-grade dysplasia (HGD). However, there are no proper guidelines for the management of gastric low-grade dysplasia (LGD). We evaluated clinical parameters, histological results, and endoscopic follow-up to find a management strategy of LGD. Methods A total of 590 patients with LGD, HGD, functional dyspepsia (FD), and early or advanced gastric cancer (EGC or AGC, respectively) were consecutively enrolled. We examined the association of clinical parameters including low serum pepsinogen (PG) I/II ratio of 3.0 or less with the disease phenotypes. Histological results between initial forceps biopsy and final endoscopic mucosal resection (EMR) or endoscopic submucosal dissection (ESD) specimens were compared. Complications and recurrence were evaluated after EMR or ESD. Results The PG I/II ratio in FD was 4.2±1.7 (mean±SD), but was significantly lower in LGD (2.8±1.6, P<0.0001). The PG I/II ratio was not any lower in the HGD, EGC, and AGC groups. In patients with FD having a PG I/II ratio of 3.0 or less, multiple logistic regression analysis showed smoking habits and high salt intake were independent risk factors for gastric dysplasia or gastric cancer. About 11% (n=8/70) of LGD lesions were upgraded to HGD (6/70) or EGC (2/70) after EMR or ESD. Neither serious complications nor recurrence at the primary site after EMR or ESD were found in LGD. Conclusion It is proposed that endoscopic resection followed by endoscopic surveillance might be a beneficial strategy for patients with LGD having a PG I/II ratio of 3.0 or less.
3D Rendering of American Sign Language Finger-Spelling: A Comparative Study of Two Animation Techniques

— In this paper we report a study aimed at determining the most effective animation technique for representing ASL (American Sign Language) finger-spelling. Specifically, in the study we compare two commonly used 3D computer animation methods (keyframe animation and motion capture) in order to ascertain which technique produces the most ‘accurate’, ‘readable’, and ‘close to actual signing’ (i.e. realistic) rendering of ASL finger-spelling. To accomplish this goal we have developed 20 animated clips of fingerspelled words and we have designed an experiment consisting of a web survey with rating questions. 71 subjects ages 19-45 participated in the study. Results showed that recognition of the words was correlated with the method used to animate the signs. In particular, keyframe technique produced the most accurate representation of the signs (i.e., participants were more likely to identify the words correctly in keyframed sequences rather than in motion captured ones). Further, findings showed that the animation method had an effect on the reported scores for readability and closeness to actual signing; the estimated marginal mean readability and closeness was greater for keyframed signs than for motion captured signs. To our knowledge, this is the first study aimed at measuring and comparing accuracy, readability and realism of ASL animations produced with different techniques.
PET probes beyond 18F-FDG

Abstract During the past several decades, positron emission tomography (PET) has been one of the rapidly growing areas of medical imaging; particularly, its applications in routine oncological practice have been widely recognized. At present, 18F-fluorodeoxyglucose (18F-FDG) is the most broadly used PET probe. However, 18F-FDG also suffers many limitations. Thus, scientists and clinicians are greatly interested in exploring and developing new PET imaging probes with high affinity and specificity. In this review, we briefly summarize the representative PET probes beyond 18F-FDG that are available for patients imaging in three major clinical areas (oncology, neurology and cardiology), and we also discuss the feasibility and trends in developing new PET probes for personalized medicine.
Tissue-Driven Hypothesis of Transcriptome Evolution: An Update

In past decade, many reports have demonstrated that tissues in multi-cellular organisms may play important roles to shape the pattern of genome evolution. The tissue-driven hypothesis was then coined, claiming that tissue-specific factor as the common resource of functional constrain may underlie the positive correlations between tissue expression divergence, sequence divergence, or the expression tolerance of duplication divergence. However, the original version of tissue-driven hypothesis cannot rule out the tissue-specific effect of mutational variance. In this perspective, we solve this problem by modifying the evolutionary model that underlies the tissue expression evolution. Reanalysis of the microarray data reanalysis has revealed the relative importancebetween tissue-specific functional constraints and mutational variances in the tissue evolution. Finally, we outline how to utilize RNA-seq technology to further investigate the tissue expression evolution in the case of multiple tissues and species.
A source function for a dynamic bilateral brittle shear fracture

A two-dimensional brittle bilateral shear crack was numerically simulated to form and stop in an elastic isotropic medium. The crack surface remained a straight line but underwent rotation that was attributed partially to the starting of the crack and partially to the stopping of the crack. If the crack did not stop, the magnitude of rotation would be about half of the value obtained for this study. The largest displacement was parallel to the fracture and near the line of nucleation. The largest displacement perpendicular to the fracture occurred near the crack tips. Symmetric points across the fracture surface were found to have asymmetric displacements. The percentage of difference among the displacements was largest beyond the crack tips, but the magnitude of the displacement difference was larger near the crack tips. The results of the study are displayed graphically.
Stimulation of neovascularization by the anti-angiogenic factor PEDF.

PURPOSE Examine the effect of (pigment epithelium-derived growth factor; PEDF) on laser-induced choroidal neovascularization (CNV). METHODS Adult C57Bl/6 mice were anesthetized and four laser spots were placed in each quadrant of the fundus with a krypton red laser (614 nm, 50 microm, 0.05 second, 200 mW). Animals were treated with various doses of PEDF administered with miniosmotic pumps implanted subcutaneously. Seven days after laser treatment, mice were perfused with 3% FITC high-molecular-weight dextran, the eyes enucleated, and neovascularization analyzed by confocal microscopy. Data were recorded as the volume of the neovascular complex. The effect of PEDF on endothelial cell migration, vascular tube formation in synthetic basement membrane, and VEGF production was also determined. RESULTS Mice receiving a lower dose of PEDF (90 microg/mL) had significantly decreased areas of CNV. A high dose of PEDF (360 microg/mL) significantly increased CNV, whereas an intermediate dose (180 microg/mL) of PEDF had no effect. PEDF inhibited endothelial cell migration and vascular tube formation at lower doses (0.5-5 microg/mL). High doses of PEDF (25-50 microg/mL) stimulated endothelial cell migration, enhanced vascular tube formation in vitro, and stimulated VEGF production from endothelial cells. Neutralizing anti-VEGF antibody completely reversed the stimulatory effects of high doses of PEDF on CNV in vivo. CONCLUSIONS PEDF demonstrates opposing effects on CNV and endothelial cell function. Whereas low doses are inhibitory, high doses can augment the development of the neovasculature. These results suggest that the effects of PEDF on neovascularization are more complex than originally believed and that caution should be exercised when PEDF therapies are considered.
Shortening Ocular Pain Duration following Intravitreal Injections

Purpose. To determine ocular pain duration after routine in-office intravitreal injection and to determine whether topical eyedrops are beneficial in increasing patient comfort. Methods. Forty injection-naïve patients receiving routine intravitreal injections of bevacizumab for age-related macular degeneration were randomized into 3 groups: group 1 (control, no drops), group 2 (generic artificial tears), and group 3 (ketorolac tromethamine 0.4% eyedrops). Those who received topical medications were given a Visual Analog Pain score survey and asked to record their pain on a scale from 0 (no distress) to 10 (unbearable distress) daily until a score of 0 was achieved, at which point they were instructed to discontinue use of their given drops. Self-reported pain scores were assessed. Results. Pain after routine intravitreal injection lasts on average between 3 and 7 days. Patients receiving topical ketorolac eyedrops reported the fewest average number of pain days (2.25±1.22) vs patients receiving artificial tears (3.54±1.13) or those who received no postprocedure eyedrops (5.13±1.25); p<0.05. At most, patients receiving ketorolac eyedrops reported 3 days of recordable pain. Those who received artificial tears reported at most 5 days of recordable pain, and patients who did not receive any postprocedure eyedrops reported at most 7 days of recordable pain. Conclusions. Pain after intravitreal injection is generally mild, may be reduced by postinjection topical ketorolac eyedrops, and lasts less than 1 week.
How does graphotactic knowledge influence children's learning of new spellings?

Two experiments investigated whether and how the learning of spellings by French third graders is influenced by two graphotactic patterns: consonants cannot double in word-initial position (Experiment 1) and consonants cannot double after single consonants (Experiment 2). Children silently read meaningful texts that contained three types of novel spellings: no doublet (e.g., mupile, guprane), doublet in a legal position (e.g., muppile, gupprane), and doublet in an illegal position (e.g., mmupile, guprrane). Orthographic learning was assessed with a task of spelling to dictation. In both experiments, children recalled items without doublets better than items with doublets. In Experiment 1, children recalled spellings with a doublet in illegal word-initial position better than spellings with a doublet in legal word-medial position, and almost all misspellings involved the omission of the doublet. The fact that the graphotactic violation in an item like mmupile was in the salient initial position may explain why children often remembered both the presence and the position of the doublet. In Experiment 2, children recalled non-words with a doublet before a single consonant (legal, e.g., gupprane) better than those with a doublet after a single consonant (illegal, e.g., guprrane). Omission of the doublet was the most frequent error for both types of items. Children also made some transposition errors on items with a doublet after a single consonant, recalling for example gupprane instead of guprrane. These results suggest that, when a doublet is in the hard-to-remember medial position, children sometimes remember that an item contains a doublet but not which letter is doubled. Their knowledge that double consonants can occur before but not after single consonants leads to transposition errors on items like guprrane. These results shed new light on the conditions under which children use general knowledge about the graphotactic patterns of their writing system to reconstruct spellings.
Chemical and Isotopic Study of Lab-formed Carbonates Under Cryogenic and Hydrothermal Conditions

Aqueous environments on early Mars were probably relatively short-lived and localized, as evidenced by the lack of abundant secondary minerals detected by the TES instrument. In order to better understand the aqueous history of early Mars we need to be able to interpret the evidence preserved in secondary minerals formed during these aqueous events. Carbonate minerals, in particular, are important secondary minerals for interpreting past aqueous environments as illustrated by the carbonates preserved in ALH84001. Carbonates formed in short-lived, dynamic aqueous events often preserve kinetic rather than equilibrium chemical and isotopic processes, and predicting the behavior of such systems is facilitated by empirical data.
Prenatal nicotine exposure increases the strength of GABAA receptor‐mediated inhibition of respiratory rhythm in neonatal rats

Infants born to mothers that smoke while pregnant have a relatively high incidence of central respiratory control abnormalities. Recent studies have shown that prenatal nicotine exposure increases GABA release and the frequency of GABAergic currents, leading to an up‐regulation of GABAA receptors in central neurones. Activation of GABAA receptors inhibits ventilatory activity, with intense activation causing apnoea. These observations lead us to hypothesize that prenatal nicotine exposure alters GABAergic control of respiratory motor pattern in the early neonatal period. Osmotic minipumps were implanted in pregnant Sprague‐Dawley rats on the fifth day of gestation, and filled with nicotine (6 mg kg−1 day−1, 2.5 μl h−1) or physiological saline (2.5 μl h−1). Brainstem–spinal cord preparations from 1‐ to 3‐day‐old neonates were studied under in vitro conditions. Electrical activity was recorded from the fourth cervical ventral root (C4 VR), which contains the axons of phrenic motoneurones. Bath application of GABAA receptor agonists muscimol (250 μm) or pentobarbital sodium (60 μm) to the brainstem led to consistent, reversible and significant reductions in C4 VR burst frequency. In saline‐exposed animals, frequency (bursts min−1) fell from 6.8 ± 0.4 to a nadir of 2.8 ± 0.5 with muscimol, and from 6.5 ± 0.3 to a nadir of 2.9 ± 0.3 for pentobarbital; in nicotine‐exposed animals, frequency fell from 6.3 ± 0.4 to 1.0 ± 0.4 with muscimol and from 6.4 ± 0.2 to 1.7 ± 0.4 with pentobarbital (P < 0.05 in all cases). The decrease in C4 VR frequency was significantly greater in nicotine‐exposed compared to saline‐exposed preparations with both muscimol and pentobarbital (P < 0.001 for both). There were no changes in the amplitude of C4 VR bursts under any condition. The GABAA receptor antagonist bicuculline methiodide (8 μm) did not change C4 VR frequency or amplitude in either group, although it was effective in reversing the effects of muscimol. These experiments demonstrate that prenatal nicotine exposure alters the GABAergic regulation of respiratory rhythm in a reduced preparation. The results may lead to a better understanding of the perturbed breathing pattern observed in neonates that are exposed to nicotine in utero.
Texture contrast attracts overt visual attention in natural scenes

In natural vision, the central nervous system actively selects information for detailed processing through mechanisms of visual attention. It is widely held that simple stimulus features such as color, orientation and intensity contribute to the determination of visual salience and thus can act to guide the selection process in a bottom‐up fashion. Contrary to this view, Einhäuser, W. & König, P. [(2003) Eur. J. Neurosci. , 17, 1089–1097] conclude from their study of human eye movements that luminance contrast does not contribute to the calculation of stimulus salience and that top‐down, rather than bottom‐up, factors therefore determine attentional allocation in natural scenes. In this article, we dispute their conclusion and argue that the Einhäuser and König study has a number of methodological problems, the most prominent of which is the unintentional introduction of changes in texture contrast. We hypothesize that texture contrast, like luminance contrast, can contribute to the guidance of attention in a bottom‐up fashion, and that an appeal to top‐down factors is not necessary. To test this hypothesis, we implement a purely bottom‐up model of visual selective attention where salience is derived from both luminance and texture contrast. We find that the model can quantitatively account for Einhäuser and König's results and that texture contrast strongly influences attentional guidance in this particular paradigm. The significance of this result for attentional guidance in other paradigms is discussed.
Unsupervised abnormal crowd activity detection using interaction power model

Abnormal event detection in crowded scenes is one of the most challenging tasks in the video surveillance for the public security control. Different from previous work based on learning. We proposed an unsupervised Interaction Power model with an adaptive threshold strategy to detect abnormal group activity by analyzing the steady state of individuals’ behaviors in the crowed scene. Firstly, the optical flow field of the potential pedestrians is only calculated within the extracted foreground to reduce the computational cost. Secondly, each pedestrian can be divided into patches of the same size, and the interaction power of the pedestrians will be represented by the motion particles which describe the motion status at the center pixels of the patches. The motion status of each patch is computed by using the optical flows of the pixels within the patch. For each motion particle, its interaction power, defined as its steady state of the current behavior, is computed among all its neighboring motion particles. Finally, the dense crowds’ steady state can be represented as a collection of motion particles’ interaction power. Here, an adaptive threshold strategy is proposed to detect abnormal events by examining the frame power field which is a fixed-size random sampling of the interaction power of motion particles. Experimental results on the standard UMN dataset and online videos show that our method could detect the crowd anomalies and achieve a higher accuracy compared to the other competitive methods published recently.
Soil carbon pools in central Texas: Prairies, restored grasslands, and croplands

ABSTRACT: Establishment of perennial grasses on degraded soils has been suggested as a means to improve soil quality and sequester carbon in the soil. Particulate organic carbon may be an important component in the increased soil carbon content. We measured particulate organic carbon [defined as organic carbon in the 53 to 2000 μm (0.002 to 0.08 in) size fraction] and mineral associated organic carbon (defined as the less than 53 μm (0.002 in) size fraction) at three locations in central Texas. Each location had a never-tilled native grassland site, a long-term agricultural site and a restored grassland on a previously tilled site. Organic carbon pool sizes varied in the surface 40 cm (16 in) of native grassland, restored grasslands and agricultural soils. The native grasslands contained the largest amounts of total organic carbon, while the restored grasslands and agricultural soils contained similar amounts of total organic carbon. Both particulate organic carbon and mineral associated carbon pools were reduced beyond the depth of tillage in the restored grass and agricultural soils compared to the native grassland soils. The restored grassland soils had a larger particulate organic carbon content than the agricultural soils, but the increase in particulate organic carbon was limited to the surface 5 cm (2 in) of soil. Trends in particulate organic carbon accumulation over time from nine to 30 years were not significant in this study.
Detecting GPS information leakage in Android applications

Location Based Service(LBS) becomes very popular in mobile computing platforms, such as Android. However, it could also leak highly personal information about the phone owner if used by Malwares. It has been witnessed that an increased number of malicious Android applications use LBS to obtain users' locations and transmit them to attackers without users' acknowledgement, causing users' privacy breach. In this paper, we first discuss the common way in which privacy can be breached in Android applications, and then define a classification algorithm for GPS information leakage. Furthermore, we develop a location information leakage detection tool named Brox. Brox is based on dalvik-opcode specification, which uses data flow analysis framework equipped with flow-sensitive, context-sensitive, and inter-procedure techniques to detect potential information leakage path in Android malicious applications. Specifically, Brox uses inter-procedure analysis and dependency calculation to understand the intention for each sensitive operation; by using reachable analysis, connection between privacy access operation and leakage operation is established. More importantly, Brox confirms whether the sending out operation contains location information or not using static taint analysis. At last, we classify the detection results with the help of identification of interaction and non-user interaction entry points in order to discover stealthy leaks of GPS location. The extensive experiments results show that the proposed method can effectively detect privacy leakage in Android applications with a high accuracy rate.
Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems

MOTIVATION Partial order alignment (POA) has been proposed as a new approach to multiple sequence alignment (MSA), which can be combined with existing methods such as progressive alignment. This is important for addressing problems both in the original version of POA (such as order sensitivity) and in standard progressive alignment programs (such as information loss in complex alignments, especially surrounding gap regions). RESULTS We have developed a new Partial Order-Partial Order alignment algorithm that optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. Using this algorithm, we show the combined Progressive POA alignment method yields results comparable with the best available MSA programs (CLUSTALW, DIALIGN2, T-COFFEE) but is far faster. For example, depending on the level of sequence similarity, aligning 1000 sequences, each 500 amino acids long, took 15 min (at 90% average identity) to 44 min (at 30% identity) on a standard PC. For large alignments, Progressive POA was 10-30 times faster than the fastest of the three previous methods (CLUSTALW). These data suggest that POA-based methods can scale to much larger alignment problems than possible for previous methods. AVAILABILITY The POA source code is available at http://www.bioinformatics. ucla.edu/poa
Economics of coastal zone management in the Pacific

This publication synthesises a wide diversity of intofmration on economic pressures on the coastal sector, highlighting examples of impacts and providing a rationale for their responses, all from an economic perspective. It serves as an introduction to many aspects of coastal zone management as well as the various drivers and pressures to which coastal zones are exposed.