Miracle-dz/UniFAR-FTUs huggingface dataset:
Constructing and Annotating GENES Database in KEGG

The KEGG (Kyoto Encyclopedia of Genes and Genomes) project is accumulating and computerizing vast knowledge of biochemistry and molecular biology. In addition to the PATHWAY database, the GENES database is a basic element of the KEGG system. It describes gene IDs, gene names, product names, chromosomal positions, gene classifications, EC numbers, codon frequencies, amino acid sequences and nucleotide sequences of over 20 species mainly with complete genomes. Since the GENES database provides links between genomes and pathways, it can be an important tool for functional genomics, where information of both genomes and pathways should be utilized. It can also be used for comparative genomics, where whole genomes from several species are analyzed at a time. A major problem in such analyses is that there is no standard nomenclature for representing genes and gene products. The names of the genes and gene products are often different between species even if the products have the same function. The discrepancies are conspicuous when the genomes are sequenced by different organizations. The construction of the GENES database is an effort to fill the gap and to provide a standardized resource for functional and comparative genomics. Last year, we reported main concepts of the GENES database [4]. This paper focuses on how the GENES database is constructed and how gene annotations are made to maintain consistent information among species.
Social Connectedness, Self-Efficacy, and Mental Health Outcomes Among Homeless Youth

Homeless youth frequently meet diagnosis criteria for depressive and/or substance use disorder(s). Although prior research has established that both social connectedness and self-efficacy buffer vulnerable youth’s adverse health outcomes, few studies have compared the potential of these protective factors on homeless youth’s mental well-being. The current study analyzes comparative effects of social connectedness and self-efficacy on meeting criteria for major depressive disorder, substance use disorder, and the co-occurrence of both disorders among a sample of 601 service-seeking homeless youth in Austin, Denver, and Los Angeles. Hierarchical logistic regressions indicate that while both social connectedness and self-efficacy constructs are valuable protective factors, social connectedness may offer greater utility, particularly in buffering against more complex mental health outcomes, such as the co-occurrence of depressive and substance use disorders. Accordingly, resource-strapped homeless youth service providers and researchers may benefit from tailoring mental health intervention strategies to further emphasize social connectedness in future efforts.
A pattern-based residual vector quantization (PBRVQ) algorithm for compressing images

We develop and test a new, two-stage, residual vector quantization algorithm using variable bit-rate encoding. In the first stage, we partition the input image into non-overlapping blocks, vector-quantize and code them by a small codebook using the well-known K-means algorithm. The novelty in this method is the use of high eigen-valued blocks as initial seeds which serve as good distributors in the formation of clusters and fast convergence. We compute the residual vectors and classify them based on threshold values of distortion and variance. Vectors above the given threshold require second-stage coding. In the second stage, we partition the residual vectors further into small sub blocks and scalar-quantize each sub block to form number patterns instead of performing Direct Vector Quantization (DVQ). These number patterns, which form the secondary codebook, are easily generated without complex calculations by applying basic ideas from combinatorics. Both the intra-block and inter-block correlation properties have been exploited to enhance the compression rate. This method offers several advantages: 1) the computational complexity is greatly reduced; 2) exhaustive comparisons in DVQ are carried out more efficiently; 3) the picture quality of the reconstructed image is not compromised; and, 4) a reduced bit-rate is achieved.
Observations of the neutral gas and dust in the radio galaxy 3C 305

We present MERLIN and Hubble Space Telescope (HST) observations of the central region of the nearby radio galaxy 3C 305 and use them to study the gas and dust in this object. The MERLIN observations are of neutral hydrogen (H I) absorption against the strong non-thermal 20 cm continuum seen towards the central 4 kpc of 3C 305. Our ∼0.2 arcsec (160 pc) resolution observations show that the H I absorption is highly localized against the south-western radio-emission with column densities ∼1.9 x 10 2 1 cm - 2 . The absorption is broad (full width at half maximum, FWHM, of 145 ′ 26 km s - 1 ) and redshifted by 130 km s - 1 relative to the systemic velocity. The HST images in multiple optical and infrared filters (430 nm, 702 nm, [O III] 500.7 nm, [Fe II] 1.64 μm and K-band polarization) are presented. Evidence is seen for coincidence of the [Fe n] emission with the knot at the end of the radio jet, which is evidence for the presence of shocks. We compare the optical and radio images in order to investigate the relationship between the dust and neutral gas distributions. An unresolved (0.07 arcsec) nucleus is detected in H and K and its properties are consistent with a quasar reddened by A V > 4. We propose that the absorption arises in a region of neutral gas and dust. Its structure is complex but is broadly consistent with an inclined disc of gas and dust encircling, but not covering, the active galactic nucleus. A comparison of the neutral gas observations and previous emission-line observations suggests that both the neutral and ionized gas are undergoing galactic rotation towards the observer in the north-east and away from the observer in the south-west. We propose that the outflow giving rise to the radio emission has a component towards the observer in the north-east and away from the observer in the south-west. Unfortunately, as we do not detect radio emission from the compact nucleus, we cannot set limits to neutral hydrogen absorption from a circumnuclear obscuring torus.
The life cycle of early skill formation

This thesis focuses on two dimensions of the child production function - the technology of human capital formation and the role of speci�fic family inputs into human capital. The �first two chapters explore the technology by which inputs produce child human capital. Speci�fically, for given parental lifetime income, these ask whether the timing of income matters for later outcomes of the children. Two methodologies estimate the effect at different margins. Firstly in a fully flexible model, the relationship between parental income at child ages 0-5, 6-11 and 12-17 and subsequent child outcomes is estimated nonparametrically, allowing for complementarity across periods. Income aged 0-5 is as important in general as income at age 6-11 for child human capital formation. Complementarities exist between 0-5 and 6-11 for households with low permanent income, which are those likely to be credit constrained. Similarly, very strong complementarities are found between early years income and income during adolescence (age 12-17) for the group of poor parents. Chapter 3 analyses the role of permanent and transitory income shocks at different ages, upon adolescent human capital. Empirical results suggest the effect of permanent shocks declines across age. This is intuitive, given that a permanent shock changes household wealth and hence a shock at age 1 drives more future income realisations than a later shock. Transitory shocks on the other hand, have an increasing effect upon child outcomes across child age. Further, there is evidence of intrahousehold insurance against paternal transitory income shocks. The fi�nal two chapters of the thesis look at parental inputs in the production function. Chapter 4 allows the life cycle of skill formation to begin pre-birth, by estimating the role of maternal smoking during pregnancy upon birth outcomes. Results suggest a large proportion of the correlation is explained by a maternal fi�xed effect. Finally, chapter 5 offers a cross country comparison of the similarities in child test score gaps, by a range of measures of family inequality. Despite wide institutional differences, this chapter estimates homogeneous correlates for maternal education, family size and child gender upon child achievement, but differences in the covariates of lone parenthood and ethnicity.
A modular system architecture for sensor data processing of ADAS applications

In this article a modular system architecture for fusion of data from environment sensors for advanced driver-assistance systems (ADAS) is proposed. The architecture allows different applications to have access to the fused sensor data by processing the data with respect to specific demands of different application groups. In the article the growing interconnection of functions is illustrated by two examples and the most relevant consequences of this trend are given. The question, if an application independent processing of sensor data is feasible is discussed and the most important aspects for the design of the system architecture are given. This provides the basis for the explanation of the system architecture.
Analysis and Implementation for Physical-Layer Network Coding with Carrier Frequency Offset

In this paper we consider physical-layer network coding (PLNC) in OFDM-based two-way relaying systems. Practically, a key impairment for the application of PLNC is the carrier frequency offset (CFO) mismatch between the sources and the relay, which can not be compensated completely in the multiple-access (MA) phase. As this CFO mismatch results in inter-carrier interference (ICI) for OFDM transmissions, practical CFO compensation and ICI cancelation strategies are investigated to mitigate the impairment for a-posterior probability (APP) based PLNC decoders at the relay. Furthermore, we perform hardware implementation of the two-way relaying network employing an long term evolution (LTE) near parametrization adapted to PLNC. The APP-based decoding schemes with CFO compensation and ICI cancelation are applied on this real-time transmission platform to verify the analytical results.
Endonuclease G promotes mitochondrial genome cleavage and replication

Endonuclease G (EndoG) is a nuclear-encoded endonuclease, mostly localised in mitochondria. In the nucleus EndoG participates in site-specific cleavage during replication stress and genome-wide DNA degradation during apoptosis. However, the impact of EndoG on mitochondrial DNA (mtDNA) metabolism is poorly understood. Here, we investigated whether EndoG is involved in the regulation of mtDNA replication and removal of aberrant copies. We applied the single-cell mitochondrial Transcription and Replication Imaging Protocol (mTRIP) and PCR-based strategies on human cells after knockdown/knockout and re-expression of EndoG. Our analysis revealed that EndoG stimulates both mtDNA replication initiation and mtDNA depletion, the two events being interlinked and dependent on EndoG's nuclease activity. Stimulation of mtDNA replication by EndoG was independent of 7S DNA processing at the replication origin. Importantly, both mtDNA-directed activities of EndoG were promoted by oxidative stress. Inhibition of base excision repair (BER) that repairs oxidative stress-induced DNA damage unveiled a pronounced effect of EndoG on mtDNA removal, reminiscent of recently discovered links between EndoG and BER in the nucleus. Altogether with the downstream effects on mitochondrial transcription, protein expression, redox status and morphology, this study demonstrates that removal of damaged mtDNA by EndoG and compensatory replication play a critical role in mitochondria homeostasis.
Aerogels-Airy Materials: Chemistry, Structure, and Properties.

Air, air, air…︁ and some solid skeleton; this is the basis for an interesting class of materials-the aerogels (shown schematically on the right). Can one therefore speak of "simple" chemistry? The design of such a filigrane network requires the very careful control of chemical parameters. The reward is an assortment of different property profiles owing to the richness of possible variations.
Navigation and robot-aided surgery in the spine: historical review and state of the art

Spinal anatomy is complex and in close vicinity of vulnerable anatomical structures, such as nerve roots, spinal cord, and blood vessels, requiring high precision in surgical procedures, while the surgical exposure is limited and even more limited in percutaneous procedures. A high risk of misplaced implants and/or high intraoperative radiation exposure are the consequences. Spinal navigation techniques have been introduced to alleviate these problems. The majority of reports on navigation document its role in increasing implant-placement accuracy and reduc- ing intraoperative radiation. The technology is increasingly finding acceptance amongst spinal surgeons. This however does not yet present the end of the road. Robotic applications could be regarded as a coherent continuation of spinal navigation. We reviewed the literature pertaining to spinal navigation, as well as novel and upcoming robotic applications for spinal surgery. For this purpose, a Medline search using the terms "robot" and "spine" and extensive cross-reference analysis (using Medline, Ovid, and Web of Science data banks) were performed. The goal was to provide an overview of present achievements and novel developments in this fast-growing research area. While a number of robotic techniques are under investigation, mainly to aid navigated screw placement, the SpineAssist/Renaissance system has cleared US Food and Drug Administration approval and is in relatively wide clinical use. Another robotic system, the da Vinci, is currently applied in an increasing number of cases under research protocols.
Contextual Design in Industrial Settings: Experiences and Recommendations

The Contextual Design (CD) methodology offers a framework for planning and implementing a user-centered design process throughout all project phases. It is team-based and was designed especially for interdisciplinary teams. The application of CD is particularly profitable in projects confronted with implicit requirements and hidden factors of influence. In contrast to many other design and evaluation methods such as focus groups or usability tests, CD does not take users out of their everyday setting and more easily reveals important design issues and contextual influences like users’ motivation, values, emotions or real-time interruptions. Despite these advantages, CD is often not used due to high costs in terms of time and effort. This paper provides a report on experiences with CD in two research projects in the industry domain. It is intended to help other researchers to plan and implement a CD process in industrial settings and benefit from our lessons learned.
Using a Hybrid Method for Formalizing Informal Stakeholder Decisions

Decisions are hard to make when available information is incomplete, inconsistent, and ambiguous. Moreover, good – sufficiently complete, consistent, traceable, and testable – requirements are a prerequisite for successful projects. Without understanding what the stakeholders really want and need and writing these requirements in a concise, understandable and testable manner, projects will not develop what the stakeholders wanted leading to either major late rework or project termination. During the development of the WinWin negotiation model and the EasyWinWin requirements negotiation method, we have gained considerable experience in capturing decisions made by stakeholders in over 100 projects. However, the transition from informal decisions to requirements specification is still a challenging problem. Based on our analysis of the projects to date, we have developed an integrated set of gap-bridging methods as a hybrid method to support stakeholders making better decisions in order to eliminate requirements related problems and ease the process of formality transition.
Tactile feedback in upper limb prosthetic devices using flexible textile force sensors

Many upper limb amputees are faced with the difficult challenge of using a prosthesis that lacks tactile sensing. State of the art research caliber prosthetic hands are often equipped with sophisticated sensors that provide valuable information regarding the prosthesis and its surrounding environment. Unfortunately, most commercial prosthetic hands do not contain any tactile sensing capabilities. In this paper, a textile based tactile sensor system was designed, built, and evaluated for use with upper limb prosthetic devices. Despite its simplicity, we demonstrate the ability of the sensors to determine object contact and perturbations due to slip during a grasping task with a prosthetic hand. This suggests the use of low-cost, customizable, textile sensors as part of a closed-loop tactile feedback system for monitoring grasping forces specifically in an upper limb prosthetic device.
A quantitative assessment of the importance of tone in mandarin speech recognition

How important is tone to Mandarin speech recognition? Because contextual information can resolve some lexical ambiguities, the question has been raised as to whether a strong language model obviates the need for explicit tone modeling. This letter addresses that question by evaluating the effect of tone information on word perplexity under different conditions, including knowledge of the correct tone sequence, perfect acoustic information, and imperfect syllable and tone information. Results show that conditioning on tone information can reduce word uncertainty in conversational speech by 11%-20%, depending on the accuracy of syllable and tone recognition.
Increased Feeding and Food Hoarding following Food Deprivation Are Associated with Activation of Dopamine and Orexin Neurons in Male Brandt's Voles

Small mammals usually face energetic challenges, such as food shortage, in the field. They have thus evolved species-specific adaptive strategies for survival and reproductive success. In the present study, we examined male Brandt's voles (Lasiopodomys brandtii) for their physiological, behavioral, and neuronal responses to food deprivation (FD) and subsequent re-feeding. Although 48 hr FD induced a decrease in body weight and the resting metabolic rate (RMR), such decreases did not reach statistical significance when compared to the control males that did not experience FD. During the first 2 hr of re-feeding following 48 hr FD, voles showed higher levels of feeding than controls. However, when permitted to hoard food, FD voles showed an increase in food hoarding, rather than feeding, compared to the controls. Further, both feeding and food hoarding induced an increase in neuronal activation, measured by Fos-ir, in a large number of brain areas examined. Interestingly, feeding and food hoarding also induced an increase in the percentage of tyrosine hydroxylase immunoreactive (TH-ir) cells that co-expressed Fos-ir in the ventral tegmental area (VTA), whereas both FD and feeding induced an increase in the percentage of orexin-ir cells that co-expressed Fos-ir in the lateral hypothalamus (LH). Food hoarding also increased orexin-ir/Fos-ir labeling in the LH. Together, our data indicate that food-deprived male Brandt's voles display enhanced feeding or food hoarding dependent upon an environmental setting. In addition, changes in central dopamine and orexin activities in selected brain areas are associated with feeding and hoarding behaviors following FD and subsequent re-feeding.
Mathematical Model for Thermal Environment and Broiler Chickens Performance Prediction in Acclimatized Housings

This research aimed to develop and validate a mathematical model to predict thermal environment, main physiological responses, and productive performance of broiler chickens throughout acclimatized housing equipped with negative pressure tunnel ventilation systems associated with evaporative pad cooling, misting system, or both systems. Experimental results, used to validate the model showed that standard errors between simulated and measured values were smaller than or equal to 1.27, except for relative humidity, daily feed intake, and respiration rate, which were 5.43%, 1.77 g/day, and 2.15 breathes/min, respectively. It was concluded that the proposed mathematical model simulated satisfactorily all response variables modeled, allowing simulation of several production scenarios.
Definition of Scientific Hypothesis: A Generalization or a Causal Explanation?

This study reviewed and discussed the nature of scientific hypothesis described in philosophy, the philosophy of science, science, and science education. In these descriptions, a hypothesis was defined as one of five types: hypothesis as an assumption, hypothesis as a prediction, hypothesis as a tentative explanation, hypothesis as a tentative law, and hypothesis as a tentative causal explanation. Most scholars agreed that a hypothesis is a proposition or a set of propositions proposed as an explanation for an observed situation. In this view, a hypothesis is a possible answer to or an explanation of a question that accounts for all the observed facts. Also, it is a statement that explains why things happen in nature or an explanation for an observation that can be tested. In the five types of hypothesis meanings, a tentative explanation includes a tentative law and a tentative causal explanation. However, tentative laws are not explanation but description which are general statements drawn from specific experiences by way of a process known as induction. A number of studies also have distinguished hypothesis from assumption, tentative explanation, tentative law, and prediction. Therefore, a hypothesis is concluded to be a proposition or a set of propositions proposed as a tentative causal explanation for an observed situation.
Genome-wide association analysis and fine mapping of NT-proBNP level provide novel insight into the role of the MTHFR-CLCN6-NPPA-NPPB gene cluster

High blood concentration of the N-terminal cleavage product of the B-type natriuretic peptide (NT-proBNP) is strongly associated with cardiac dysfunction and is increasingly used for heart failure diagnosis. To identify genetic variants associated with NT-proBNP level, we performed a genome-wide association analysis in 1325 individuals from South Tyrol, Italy, and followed up the most significant results in 1746 individuals from two German population-based studies. A genome-wide significant signal in the MTHFR-CLCN6-NPPA-NPPB gene cluster was replicated, after correction for multiple testing (replication one-sided P-value = 8.4 × 10−10). A conditional regression analysis of 128 single-nucleotide polymorphisms in the region of interest identified novel variants in the CLCN6 gene as independently associated with NT-proBNP. In this locus, four haplotypes were associated with increased NT-proBNP levels (haplotype-specific combined P-values from 8.3 × 10−03 to 9.3 × 10−11). The observed increase in the NT-proBNP level was proportional to the number of haplotype copies present (i.e. dosage effect), with an increase associated with two copies that varied between 20 and 100 pg/ml across populations. The identification of novel variants in the MTHFR-CLCN6-NPPA-NPPB cluster provides new insights into the biological mechanisms of cardiac dysfunction.
Approach to Face Recognition Using Neural Networks

The paper describes the approach to automatic face recognition for access control application area using wavelet transform and neural network's ensemble. Wavelet transform implements the compression of the face images and thus accelerates the classifier's work, while neural network's ensemble with proposed decision rule provides low recognition error. Proposed ensemble's decision rule carries out a high level of unknown people's access rejection, which is the most significant requirement for the access control systems, and gives a good balance between known and unknown people's recognition errors.