Miracle-dz/UniFAR-FTUs huggingface dataset:
Alternative Splice Variants in TIM Barrel Proteins from Human Genome Correlate with the Structural and Evolutionary Modularity of this Versatile Protein Fold

After the surprisingly low number of genes identified in the human genome, alternative splicing emerged as a major mechanism to generate protein diversity in higher eukaryotes. However, it is still not known if its prevalence along the genome evolution has contributed to the overall functional protein diversity or if it simply reflects splicing noise. The (βα)8 barrel or TIM barrel is one of the most frequent, versatile, and ancient fold encountered among enzymes. Here, we analyze the structural modifications present in TIM barrel proteins from the human genome product of alternative splicing events. We found that 87% of all splicing events involved deletions; most of these events resulted in protein fragments that corresponded to the (βα)2, (βα)4, (βα)5, (βα)6, and (βα)7 subdomains of TIM barrels. Because approximately 7% of all the splicing events involved internal β-strand substitutions, we decided, based on the genomic data, to design β-strand and α-helix substitutions in a well-studied TIM barrel enzyme. The biochemical characterization of one of the chimeric variants suggests that some of the splice variants in the human genome with β-strand substitutions may be evolving novel functions via either the oligomeric state or substrate specificity. We provide results of how the splice variants represent subdomains that correlate with the independently folding and evolving structural units previously reported. This work is the first to observe a link between the structural features of the barrel and a recurrent genetic mechanism. Our results suggest that it is reasonable to expect that a sizeable fraction of splice variants found in the human genome represent structurally viable functional proteins. Our data provide additional support for the hypothesis of the origin of the TIM barrel fold through the assembly of smaller subdomains. We suggest a model of how nature explores new proteins through alternative splicing as a mechanism to diversify the proteins encoded in the human genome.
Integration of Reduplicated Multiword Expressions and Named Entities in a Phrase Based Statistical Machine Translation System

The language specific Multiword expressions (MWEs) play important roles in many natural language processing (NLP) tasks. Integrating reduplicated multiword expressions (RMWEs) into the Phrase Based Statistical Machine Translation (PBSMT) to improve translation quality is reported in the present work between Manipuri, a highly agglutinative Tibeto-Burman language and English. In addition, Multiword Named Entities (MNEs) coupled with Transliterated non-named entities (non-NE) between Manipuri and English phrase based SMT system are also integrated. The tighter integration of RMWEs and NEs into the PBSMT is carried out after automatic extraction using SVM based machine learning technique followed by automatic bilingual RMWE and MNE extraction using GIZA++ alignment. Our experimental results show improvement in the PBSMT system BLEU and NIST scores over the baseline system. Subjective evaluation indicates the improvement in the adequacy.
Computerised segmentation of suspicious lesions in the digital mammograms

In this paper, a robust marker-controlled watershed method is proposed to yield more accurate segmentation results to delineate the masses in mammograms. The proposed method consists of three main steps: pre-processing, marker extraction and the final segmentation. In the first step, pre-processing algorithm is developed using top-hat morphological filter, wavelet transform followed by a noise smoothing anisotropic diffusion filter. In the second step, a novel technique is developed for the extraction of robust markers to locate the accurate position of the suspicious lesions. Finally, the extracted markers are used within the watershed algorithm to allow the reliable segmentation and quantification of masses in mammograms. The developed computer method was quantitatively evaluated using the area overlap metric (AOM), average minimum Euclidean distance (AMED) and Hausdorff distance (HD). The mean ± standard deviation values of AOM, AMED and HD for our method are 0.83 ± 0.10, 1.49 ± 1.20 mm and 4.62 ± 0.80.
Thermoplastic shape-memory polyurethanes based on natural oils

A new family of segmented thermoplastic polyurethanes with thermally activated shape-memory properties was synthesized and characterized. Polyols derived from castor oil with different molecular weights but similar chemical structures and a corn-sugar-based chain extender (propanediol) were used as starting materials in order to maximize the content of carbon from renewable resources in the new materials. The composition was systematically varied to establish a structure–property map and identify compositions with desirable shape-memory properties. The thermal characterization of the new polyurethanes revealed a microphase separated structure, where both the soft (by convention the high molecular weight diol) and the hard phases were highly crystalline. Cyclic thermo-mechanical tensile tests showed that these polymers are excellent candidates for use as thermally activated shape-memory polymers, in which the crystalline soft segments promote high shape fixity values (close to 100%) and the hard segment crystallites ensure high shape recovery values (80–100%, depending on the hard segment content). The high proportion of components from renewable resources used in the polyurethane formulation leads to the synthesis of bio-based polyurethanes with shape-memory properties.
Fusion of TOF and TDOA for 3GPP positioning

Positioning in cellular networks is often based on mobile-assisted measurements of serving and neighboring base stations. Traditionally, positioning is considered to be enabled when the mobile provides measurements of three different base stations. In this paper, we additionally investigate positioning based on time series of Time Of Flight (TOF) and Time Difference of Arrival (TDOA) measurements gathered from two base stations with known positions, where the specific base stations involved depend on the trajectory of the mobile station. The set of two base stations is different along the trajectory. Each report contains TOF for the serving base station, and one TDOA measurement for the most favorable neighboring base station relative the serving base station. We derive explicit analytical solution related to the intersection of the absolute distance circle (from TOF) and relative distance hyperbola (from TDOA). We consider both geometric noise-free problem and the more realistic problem with additive noise as delivered in the 3rd Generation Partnership Project (3GPP) Long-Term Evolution (LTE). Positioning performance is evaluated using the Cramér-Rao lower bound.
Multiple human detection in images based on differential evolution and HOG-LBP

In this paper a method for multiple human detection in the image has been presented. This method uses differential evolution (DE) algorithm to improve window position detection speed and HOG-LBP algorithm for feature extraction. Fitness function for DE algorithm is SVM and in the final state, a postprocessing on detected windows by DE algorithm is performed. This method has been tested on INRIA datasets and its precision for detecting humans in the image is 92% which is better than state of the art methods.
Exploration of the Direct Use of Anodized Alumina as a Mold for Nanoimprint Lithography to Fabricate Magnetic Nanostructure over Large Area

We have explored the direct use of anodized alumina (AAO) fabricated on an Si wafer as a mold for the nanoimprint lithography (NIL). The AAO mold has been fabricated over more than 10 cm2 area with two different pore diameters of nm and nm. One of the key challenges of the lack of bonding between the antisticking self-assembled monolayer (SAM) and the AAO has been overcome by modifying the surface chemistry of the fabricated AAO mold by coating it with thin SiO2 layer. Then we have applied the commonly used silane-based self-assembled monolayer (SAM) on these SiO2-coated AAO molds and achieved successful imprinting of resist pillars with feature size of nm by using the mold with a pore diameter of nm. Finally, we have achieved (001) oriented L10 FePt patterned structure with a dot diameter of nm by using a AAO mold with a pore diameter of nm. The perpendicular Hc of the unpatterned and patterned FePt is about 3.3 kOe and 12 kOe, respectively. These results indicate that AAO mold can potentially be used in NIL for fabricating patterned nanostructures over large area.
A 3-D Depth Information Based Human Motion Pose Tracking Algorithms

Tracking human pose is the critical step of recognizing and analyzing the human motion on 3-D stereo vision, and it has great value and potential for applications of the machine vision. However, due to the complexity of human motion and background, most of the existing tracking methods for 3-D human motion gesture will add some extra restrictions on acquiring the human motion, and the tracking algorithms are often hard to obtain a robust algorithm performance. In this paper, a new human motion tracking method based on 3-D depth information is presented aiming to improve the tracking method quality. The algorithm makes a determination for the human body contour through analyzing the depth image information at first. Then the special skeletal points are estimated and tracked based on the 3-D depth vision images. Finally, the motion estimation is executed by using the three-step search algorithm, and the tracking pose is achieved naturally. Experimental results show the effectiveness of the algorithm, and it also has verified this method is feasibility and superiority on the aspect of acquiring human motion gestures and tracking compare to the similar method. Copyright © 2014 IFSA Publishing, S. L.
Utility of Skin Biopsy in Diabetic Neuropathy

Skin biopsy is receiving increased recognition as a useful diagnostic procedure for disorders of the peripheral nervous system. The purpose of this article is to discuss the relationship of skin biopsy to other diagnostic methods for diabetic neuropathy, the methods used to visualize the variety of nerves in skin, and some abnormalities that have been observed in skin biopsies from patients with diabetes. The diagnosis of diabetic neuropathy by neurologic history and examination, supplemented by neurophysiologic and quantitative sensory testing, is efficient and reliable. Therapy centers about maintenance of tight glycemic control to slow advancement. ' The increasing availability of additional putative treatments for diabetic neuropathy, such as islet or whole pancreas transplantation (PTx), aldose reductase inhibitors, myoinositol, and trophic substances accentuates the need to search for additional means to demonstrate patient benefit related to treatment. The methods should provide quantitative comparison of function or morphology of peripheral and autonomic nerves before and after therapy.
A Pluggable Tool for Measuring Software Metrics from Source Code

This paper proposes a new mechanism to measure a variety of source code metrics at low cost. The proposed mechanism is very promising because it realizes to add new metrics as necessary. Users do not need to use multiple measurement tools for measuring multiple metrics. The proposed mechanism has been implemented as an actual software tool MASU. This paper shows how using MASU makes it easy and less costly to develop plugins of the CK metrics suite.
Bereaved caregivers' descriptions of sleep: impact on daily life and the bereavement process.

PURPOSE/OBJECTIVES To describe how sleep and bereavement may be related in family caregivers. DESIGN Descriptive and qualitative. SETTING Participants' homes. SAMPLE 9 adults with no previous diagnoses of clinical depression or sleep disorders who had been providing care to family members who died in the previous six months. METHODS Participants provided narrative accounts of sleep quality, bereavement, and daily functioning since the death of their family members. Participants' sleep quality and depressive symptoms also were measured with the Pittsburgh Sleep Quality Index (PSQI) and Center for Epidemiological Studies-Depression Scale (CES-D). MAIN RESEARCH VARIABLES Sleep quality, depressive symptoms, bereavement, and daily functioning. FINDINGS Narratives revealed five themes: nightmares, wake after sleep onset, scheduling, daily life, and bereavement. Participants scored high on the PSQI and CES-D. CONCLUSIONS Sleep quality appears to affect bereavement and daily functioning. Participants reported severe levels of sleep disturbance and depressive symptoms. IMPLICATIONS FOR NURSING Studies are needed to explore sleep quality in bereaved caregivers and to examine the relationship between sleep quality and an individual's ability to accomplish the tasks of bereavement.
A novel device for measuring long-term oxygen therapy adherence: a preliminary validation.

INTRODUCTION Current methods for measuring patient adherence to long-term oxygen therapy fail to measure the actual amount of time the patient is inhaling oxygen and the pattern of oxygen use within the day. We have developed a novel oxygen-adherence monitor to address these limitations, and this report introduces the monitor and provides preliminary data validating its use. METHODS This battery-powered monitor attaches to the oxygen source and detects respiratory-related pressure fluctuations transmitted through the nasal cannula. The monitor takes a measurement over a 25-second period, at 4-min intervals. It detects and stores data on 4 different states that describe the patient's actual use of the oxygen source and nasal cannula: source-off/cannula-off, source-off/cannula-on, source-on/cannula-off, and source-on/cannula-on. We studied the monitor's performance with 10 patients with chronic obstructive pulmonary disease, during a directly-observed sequence of using and not using supplemental oxygen via nasal cannula, while sitting and walking. RESULTS The monitor correctly detected 122 out of 129 measurements among all participants, yielding a 95\% detection accuracy. CONCLUSION A monitor that objectively measures oxygen inhalation, rather than oxygen expenditure, may help improve the management of patients on long-term oxygen therapy.
Linearized models of calcium dynamics: formal equivalence to the cable equation

The dynamics of calcium and other diffusible second messengers play an important role in intracellular signaling. We show here the conditions under which nonlinear equations governing the diffusion, extrusion, and buffering of calcium can be linearized. Because the resulting partial differential equation is formally identical to the one-dimensional cable equation, quantities analogous to the input resistance, space constant, and time constant--familiar from the study of passive electrical propagation--can be defined. Using simulated calcium dynamics in an infinite cable and in a dendritic spine as examples, we bound the errors due to the linearization, and show that parameter uncertainty is so large that most nonlinearities can usually be ignored: robust phenomena in the nonlinear model are also present in the linear model.
Customizing a Lexicon to Better Suit a Computational Task

We discuss a method for augmenting and rearranging a structured lexicon in order to make it more suitable for a topic labefing task, by making use of lexical association information from a large text corpus. We first describe an algorithm for converting the hierarchical structure of WordNet [13] into a set of flat categories. We then use lexical cooccurrence statistics in combination with these categories to classify proper names, assign more specific senses to broadly defined terms, and classify new words into existing categories. We also describe how to use these statistics to assign schema-like information to the categories and show how the new categories improve a text-labeling algorithm. In effect, we provide a mechanism for successfully combining a hand-built lexicon with knowledge-free, statistically-derived information. 1 I n t r o d u c t i o n Much effort is being appl ied to the creation of lexicons and the acquisi t ion of semant ic and syntact ic a t t r ibu tes of the lexical i tems tha t comprise them, e.g, [1], [4],[7],[8], [11], [16], [18], [20]. However, a lexicon as given may not suit the requirements of a par t icu la r computa t iona l task. Because lexicons are expensive to build, ra ther than create new ones from scratch, i t is preferable to ad jus t existing ones to meet an appl ica t ion ' s needs. In this paper we describe such an effort: we add associat ional informat ion to a hierarchical ly s t ructured lexicon in order to bet ter serve a text labeling task. An a lgor i thm for par t i t ion ing a full-length exposi tory text into a sequence of subtopiea l discussions is described in [9]. Once the par t i t ioning is done, we need to assign labels 1 indicat ing what the subtopical discussions are about , for the purposes of informat ion retr ieval and hyper tex t navigat ion. One way to label texts, when working within a l imited domain of discourse, is to s t a r t with a pre-defined set of topics and specify the word contexts tha t indicate the topics of interest (e.g., [10]). Another way, assuming tha t a large collection of prelabeled texts exists, is to use s tat is t ics to au tomat i ca l ly infer which lexical i tems indicate which labels (e.g., [12]). In contrast , we are interested in assigning labels to general, domainindependent text , wi thout benefit of pre-classified texts. In all three cases, a lexicon tha t specifies which lexical i tems correspond to which topics is required. The topic label ing method we use is s ta t is t ica l and thus requires a large number of representat ive lexical i tems for each category. The s ta r t ing point for our lexicon is WordNet [13], which is readi ly available online and provides a large reposi tory of English lexical i tems. WordNet 2 is composed of synse t s , 1 The terms "label" and "topic" are used interchangeably in this paper. 2 All work described here pertains to Version 1.3 of WordNet.
User-centred and driven knowledge-based systems for clinical support using ripple down rules

Ripple down rules (RDR) are a case based reasoning technique that have been developed in answer to the need to provide a way of maintaining large KBS in domains where knowledge and practice are continually being reviewed. RDR are based on the view that knowledge is not an artifact but something that is "made-up" to fit a particular situation. In keeping with this, maintenance and context are key issues. RDR offer a number of features that make it particularly suitable for clinical support. These features are: knowledge is captured, changed and validated within the local context of cases; KA is simple and designed to be performed by the domain expert; and the use of cases, difference lists and the exception structure are intuitive and natural for experts. In medical domains, ownership and control of knowledge are seen as important issues and the ability to build a KBS without the need for a knowledge engineer is a real plus. The ease of developing and maintaining an RDR KBS means that it is feasible for individual pathology laboratories to customise the system to suit the local knowledge which they contain. The paper describes RDR, how they provide an environment for interacting with the knowledge according to the decision situation of the user and some results-to-date in the area of pathology.
QIP = PSPACE

We prove that the complexity class QIP, which consists of all problems having quantum interactive proof systems, is contained in PSPACE. This containment is proved by applying a parallelized form of the matrix multiplicative weights update method to a class of semidefinite programs that captures the computational power of quantum interactive proofs. As the containment of PSPACE in QIP follows immediately from the well-known equality IP = PSPACE, the equality QIP = PSPACE follows.
Network coded gossip with correlated data

We design and analyze gossip algorithms for networks with correlated data. In these networks, either the data to be distributed, the data already available at the nodes, or both, are correlated. Although coding schemes for correlated data have been studied extensively, the focus has been on characterizing the rate region in static memory-free networks. In a gossip-based scheme, however, nodes communicate among each other by continuously exchanging packets according to some underlying communication model. The main figure of merit in this setting is the stopping time - the time required until nodes can successfully decode. While Gossip schemes are practical, distributed and scalable, they have only been studied for uncorrelated data. We wish to close this gap by providing techniques to analyze network coded gossip in (dynamic) networks with correlated data. We give a clean framework for oblivious network models that applies to a multitude of network and communication scenarios, specify a general setting for distributed correlated data, and give tight bounds on the stopping times of network coded protocols in this wide range of scenarios.
Alu retrotransposons promote differentiation of human carcinoma cells through the aryl hydrocarbon receptor

Abstract Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, their role in gene regulation is poorly understood. Here, we show that the dioxin receptor (AHR) leads to differentiation of human carcinoma cells through the transcriptional upregulation of Alu retrotransposons, whose RNA transcripts can repress pluripotency genes. Despite the genome-wide presence of Alu elements, we provide evidences that those located at the NANOG and OCT4 promoters bind AHR, are transcribed by RNA polymerase-III and repress NANOG and OCT4 in differentiated cells. OCT4 and NANOG repression likely involves processing of Alu-derived transcripts through the miRNA machinery involving the Microprocessor and RISC. Consistently, stable AHR knockdown led to basal undifferentiation, impaired Alus transcription and blockade of OCT4 and NANOG repression. We suggest that transcripts produced from AHR-regulated Alu retrotransposons may control the expression of stemness genes OCT4 and NANOG during differentiation of carcinoma cells. The control of discrete Alu elements by specific transcription factors may have a dynamic role in genome regulation under physiological and diseased conditions.
A Scale to Measure the Cause of Life Events*

An increase in life event stress has been shown to occur prior to the onset of a number of psychiatric illnesses. This paper describes the construction of a scale to measure the cause of this increased life event experience. One hundred and five normal adults were asked to judge the extent to which any particular event might have occurred by pure chance, by one's own behaviour or by the behaviour of others. These three perceived causative factors are conceptually distinct and together comprehensive. Scalings on these three perceived causative factors for each of 67 life events were derived. The utility of such a scale is discussed.