Miracle-dz/UniFAR-FTUs huggingface dataset:
Entamoeba histolytica Encodes Unique Formins, a Subset of Which Regulates DNA Content and Cell Division

ABSTRACT The formin family of proteins mediates dynamic changes in actin assembly in eukaryotes, and therefore it is important to understand the function of these proteins in Entamoeba histolytica, where actin forms the major cytoskeletal network. In this study we have identified the formin homologs encoded in the E. histolytica genome based on sequence analysis. Using multiple tools, we have analyzed the primary sequences of the eight E. histolytica formins and discovered three subsets: (i) E. histolytica formin-1 to -3 (Ehformin-1 to -3), (ii) Ehformin-4, and (iii) Ehformin-5 to -8. Two of these subsets (Ehformin-1 to -3 and Ehformin-4) showed significant sequence differences from their closest homologs, while Ehformin-5 to -8 were unique among all known formins. Since Ehformin-1 to -3 showed important sequence differences from Diaphanous-related formins (DRFs), we have studied the functions of Ehformin-1 and -2 in E. histolytica transformants. Like other DRFs, Ehformin-1 and -2 associated with F-actin in response to serum factors, in pseudopodia, in pinocytic and phagocytic vesicles, and at cell division sites. Ehformin-1 and -2 also localized with the microtubular assembly in the nucleus, indicating their involvement in genome segregation. While increased expression of Ehformin-1 and -2 did not affect phagocytosis or motility, it clearly showed an increase in the number of binucleated cells, the number of nuclei in multinucleated cells, and the average DNA content of each nucleus, suggesting that these proteins regulate both mitosis and cytokinesis in E. histolytica.
Exchange interactions and frustrated magnetism in single-side hydrogenated and fluorinated graphene

Magnetism in single-side hydrogenated (C$_2$H) and fluorinated (C$_2$F) graphene is analyzed in terms of the Heisenberg model with parameters determined from first principles. We predict a frustrated ground state for both systems, which means the instability of collinear spin structures and sheds light on the absence of a conventional magnetic ordering in defective graphene demonstrated in recent experiments. Moreover, our findings suggest a highly correlated magnetic behavior at low temperatures offering the possibility of a spin-liquid state.
A Modified TILLING Method for Wheat Breeding

The large genome and polyploidy of wheat (Triticum aestivum L.) makes it difficult to identify desirable genetic changes based on phenotypic screening due to gene redundancy. Forward genetics is, therefore, more difficult in wheat than in diploid plants. A modified TILLING (Targeting Induced Local Lesions IN Genomes) method including the harvest of five heads per M1 plant, storage of M2 seeds, using unlabeled primers and agarose gels for mutation detection, and crossing of useful mutants for desired grain quality was explored in this report. A soft wheat cultivar, QAL2000, and a hard wheat cultivar, Ventura, were mutagenized with ethyl methanesulfonate (EMS). Screening of the waxy genes Wx‐A1 and Wx‐D1 in 2348 EMS‐treated M2 plants allowed identification of 121 mutants, including silent, missense, and knockout (truncation) mutations. A complete waxy wheat was successfully bred in 18 mo by crossing two truncation mutants (Wx‐A1‐truncation and Wx‐D1‐truncation; Wx‐B1 is naturally null in both mutants). Screening of two puroindoline genes (Pina and Pinb) in QAL2000 identified 19 mutants. A hard grain variant of a soft cultivar was identified due to a mutation in Pinb caused by a premature stop codon. Background mutations were observed and further self‐fertilization or crossing with a wild type was performed to eliminate deleterious mutations. With the rapid accumulation of wheat genomics information, many potential target genes of interest can be screened for mutations in these TILLING populations.
Living Donor Liver Transplantation for Hepatocellular Carcinoma Living Donor Liver Transplantation for Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a major worldwide health problem, which is expected to increase steadily due to different underlying liver diseases. Surgical treatment modalities including liver transplantation (LT) or liver resection (LR) are the mainstay options for early cases of HCC. Liver transplantation for well‐selected cases provides excellent survival outcomes comparable to nonmalignant indications of LT. Living donor liver transplantation (LDLT) is an alternative option or even the sole one in the current era of organ shortage problem and in some Asian countries where deceased organ donation is markedly reduced due to various reasons. The adoption of LDLT for HCC treatment elicited many dynamic changes and debates to the dilemma of LT as a whole. In this chapter, we focus on different perspectives of LDLT for HCC, including selection criteria evolution, controversial topics, ethical considerations, operative highlights, and other points.
Familles de jeunes enfants présentant des incapacités intellectuelles : étude des besoins et du sentiment d’appropriation du pouvoir

Afin de mieux connaitre la realite des familles ayant un jeune enfant avec des incapacites intellectuelles et de soutenir des interventions qui soient centrees sur leurs besoins, 71 parents ont ete rencontres. Ils recevaient tous les services d’un centre de readaptation pour personnes presentant une deficience intellectuelle et etaient parents d’un enfant âge de moins de six ans. Les outils utilises dans cette etude sont les traductions francophones du Parent Needs Survey (Seligman & Darling, 1989) et de la Family Empowerment Scale (Koren, Dechillo, & Friesen, 1992). L’etude permet de faire ressortir un profil des besoins communs et prioritaires pour differentes familles, notamment en lien avec l’acces a l’information et avec l’intervention pour favoriser le developpement du jeune enfant ayant des incapacites. Par ailleurs, d’autres besoins semblent moins prioritaires, comme le fait d’etre aide dans la gestion des tâches familiales quotidiennes ou encore dans les relations au sein de la famille. Le sentiment d’appropriation de pouvoir tel que percu par les parents que ce soit a l’egard des membres de leur famille, des services offerts ou encore par rapport a la communaute, est egalement examine.
Recommendations for the Development of a Mobile HIV Prevention Intervention for Men Who Have Sex With Men and Hijras in Mumbai: Qualitative Study

Background As Internet and mobile phone use expands in India, there is an opportunity to develop mobile health (mHealth) interventions for marginalized populations, including men who have sex with men (MSM) and hijras (transgender women), hesitant to access traditional health care systems. Objective The purpose of this study was to determine if an mHealth intervention was acceptable to MSM and hijras living in Mumbai, and if so, what features would be useful in targeting the prevention of HIV acquisition and to increase the quality of life among persons living with HIV/AIDS. Methods Data from 4 focus groups with MSM and interviews with 4 hijras, 10 health service providers, and 8 mHealth developers were thematically analyzed. Results Once the need for an mHealth intervention was confirmed, comments about features were organized into 3 themes: content, interface, and retention. Content subthemes included providing sex education for younger community members, providing information about STIs, and providing information and social support for persons living with HIV. Interface subthemes included presenting content using pictures; using videos to present stories of role models; using push notifications for testing, appointment, and medication reminders; using geolocation to link to just-in-time services; and using telemedicine to increase access to health service providers and community services. The 5 retention subthemes included keeping it fun, using gaming mechanics, developing content in regional languages, protecting confidentiality, and linking to social networking apps. Conclusions These findings may help inform mHealth development in India.
Leveraging External Knowledge for Phrase-Based Topic Modeling

Topic modeling has been widely used for extracting the major topics from a corpus. Each discovered topic contains a set of related individual words that describe the topic itself. The discovered topics summarize the major themes of the corpus. Recently, a few phrase-based topic models have been proposed, which simultaneously model phrases and topics. The topics discovered by these models consist of phrases besides individual words, as phrases are typically more meaningful. However, these models typically require large amounts of data to provide reliable statistics for phrase-based topic modeling, thus limiting their performance in scenarios with limited data. To address this limitation, we propose a knowledge-based topic model that incorporates two types of pre-identified external knowledge for topical phrase discovery: Phrase knowledge, and phrase correlation knowledge. Phrase knowledge guides the discovery of meaningful phrases by leveraging a set of pre-identified exemplary phrases; Phrase correlation knowledge guides the discovery of meaningful topics by exploiting a set of pre-identified pairs of related phrases. Experimental results show that our method outperforms the state-of-the-art baseline on both small and large datasets, extracting more meaningful phrases and coherent topics.
Cloning of Mouse DAN cDNA and Its Down‐regulation in Transformed Cells

Recently, we have demonstrated that DAN gene product exhibits a tumor‐suppressive activity in vitro. We report here the cloning and sequencing of a mouse DAN cDNA that contains the entire coding region. Sequence analysis revealed that mouse DAN cDNA is 1691 nucleotides in length and contains an open reading frame of 178 amino acids. The deduced mouse DAN protein sequence shows 96% and 93% identity with the counterparts isolated from rat 3Y1 fibroblasts and normal human lung, respectively. Genomic Southern blot hybridization indicated that DAN gene exists as a single copy in the mouse genome. The expression of DAN gene was suppressed in a variety of transformed NIH3T3 cells when compared with that in the parental NIH3T3 cells.
21 2 Skeletal Muscle Plasticity

Skeletal muscle is a highly organized tissue designed to produce force for postural control, movement, and even breathing. Various architectural designs, varying amounts of muscle proteins (e.g., enzymes or myosin), and different isoforms of many muscle proteins provide for a wide range of force-producing, biochemical, and metabolic characteristics. Additionally, the ability of skeletal muscle to adapt to the demands placed upon it, such as increased mitochondrial volume associated with endurance training or increased muscle fi ber crosssectional area as a result of strength training, demonstrates a tremendous plasticity. For the sports nutritionist, a fundamental understanding of the structure and function of skeletal muscle is important inasmuch as the adaptive response to various contractile and nutritional perturbations are manifest in this tissue. It should be noted that there is a large variation among individuals with regard to the magnitude of muscle adaptability to various types of training. Differing muscle characteristics, such as muscle pennation and fi ber type, and variation in degree of adaptability among individuals partially explain the wide range of differences in aspects of exercise performance, such as muscular endurance or strength.
A novel mutation (c.T3816 > C) in the androgen receptor gene in a 46,XY female patient with androgen insensitivity syndrome.

INTRODUCTION Androgen receptor (AR) gene mutations are the most frequent cause of 46,XY disorders of sex development (DSD), and are associated with a variety of phenotypes ranging from phenotypic women (Complete Androgen Insensitivity Syndrome or CAIS) to milder degrees of undervirilisation (Partial Androgen Insensitivity Syndrome or PAIS) or men with infertility only (Mild Androgen Insensitivity Syndrome or MAIS). In this paper, we present the results of clinical, endocrine and molecular trials in a patient hospitalised because of primary amenorrhoea with typical phenotype of CAIS. MATERIAL AND METHODS The main objective of this study was to determine the molecular cause of androgen insensitivity syndrome in a 46,XY female patient. Molecular analysis of the AR gene was conducted using MSSCP (Multitemperature Single Strand Conformation Polymorphism) and sequencing methods. RESULTS MSSCP analysis showed changes in electrophoretic mobility in exon 8 of the AR gene. Sequencing analysis revealed a missense mutation which has not been previously described. This is a c.T3816 > C transition mutation which causes a S901P substitution in the amino acid chain (based on the latest NCBI reference sequence NM 000044.2). CONCLUSIONS The identified c.T3816 > C mutation in AR gene provides further evidence for the correlation between specific AR mutations and phenotype corresponding to androgen insensitivity.
Source-side Dependency Tree Reordering Models with Subtree Movements and Constraints

We propose a novel source-side dependency tree re-ordering model for statistical machine translation, in which subtree movements and constraints are represented as reordering events associated with the widely used lexicalized reordering models. This model allows us to not only efﬁciently capture the statistical distribution of the subtree-to-subtree transitions in training data, but also utilize it directly at the decoding time to guide the search process. Using subtree movements and constraints as features in a log-linear model, we are able to help the reordering models make better selections. It also allows the subtle importance of monolingual syntactic movements to be learned alongside other reordering features. We show improvements in translation quality in English → Spanish and English → Iraqi translation tasks.
Automated FES for Upper Limb Rehabilitation Following Stroke and Spinal Cord Injury

Neurorehabilitation aims to induce beneficial neural plasticity in order to restore function following injury to the nervous system. There is an increasing evidence that appropriately timed functional electrical stimulation (FES) can promote associative plasticity, but the dosage is critical for lasting functional benefits. Here, we present a novel approach to closed-loop control of muscle stimulation for the rehabilitation of reach-to-grasp movements following stroke and spinal cord injury (SCI). We developed a simple, low-cost device to deliver assistive stimulation contingent on users’ self-initiated movements. The device allows repeated practice with minimal input by a therapist, and is potentially suitable for home use. Pilot data demonstrate usability by people with upper limb weakness following SCI and stroke, and participant feedback was positive. Moreover, repeated training with the device over 1–2 weeks led to functional benefits on a general object manipulation assessment. Thus, automated FES delivered by this novel device may provide a promising and readily translatable therapy for upper limb rehabilitation for people with stroke and SCI.
Learning visibility of landmarks for vision-based localization

We aim to perform robust and fast vision-based localization using a pre-existing large map of the scene. A key step in localization is associating the features extracted from the image with the map elements at the current location. Although the problem of data association has greatly benefited from recent advances in appearance-based matching methods, less attention has been paid to the effective use of the geometric relations between the 3D map and the camera in the matching process. In this paper we propose to exploit the geometric relationship between the 3D map and the camera pose to determine the visibility of the features. In our approach, we model the visibility of every map feature with respect to the camera pose using a non-parametric distribution model. We learn these non-parametric distributions during the 3D reconstruction process, and develop efficient algorithms to predict the visibility of features during localization. With this approach, the matching process only uses those map features with the highest visibility score, yielding a much faster algorithm and superior localization results. We demonstrate an integrated system based on the proposed idea and highlight its potential benefits for the localization in large and cluttered environments
Prominent effects and neural correlates of visual crowding in a neurodegenerative disease population

Visual crowding is a perceptual phenomenon whereby recognition of a stimulus is disrupted by the presence of flanker stimuli. Yong et al. observe excessive crowding in individuals with a neurodegenerative condition (posterior cortical atrophy) and identify associations between prominent crowding and lower grey matter volume in the right collateral sulcus.
Autosomal Ichthyosis with Hypotrichosis Syndrome Displays Low Matriptase Proteolytic Activity and Is Phenocopied in ST14 Hypomorphic Mice*

Human autosomal recessive ichthyosis with hypotrichosis (ARIH) is an inherited disorder recently linked to homozygosity for a point mutation in the ST14 gene that causes a G827R mutation in the matriptase serine protease domain (G216 in chymotrypsin numbering). Here we show that human G827R matriptase has strongly reduced proteolytic activity toward small molecule substrates, as well as toward its candidate epidermal target, prostasin. To further investigate the possible contribution of low matriptase activity to ARIH, we generated an ST14 hypomorphic mouse strain that displays a 100-fold reduction in epidermal matriptase mRNA levels. Interestingly, unlike ST14 null mice, ST14 hypomorphic mice were viable and fertile but displayed a spectrum of abnormalities that strikingly resembled ARIH. Thus, ST14 hypomorphic mice developed hyperproliferative and retention ichthyosis with impaired desquamation, hypotrichosis with brittle, thin, uneven, and sparse hair, and tooth defects. Biochemical analysis of ST14 hypomorphic epidermis revealed reduced prostasin proteolytic activation and profilaggrin proteolytic processing, compatible with a primary role of matriptase in this process. This work strongly indicates that reduced activity of a matriptase-prostasin proteolytic cascade is the etiological origin of human ARIH and provides an important mouse model for the exploration of matriptase function in ARIH, as well as multiple other physiological and pathological processes.
The Emotional Valence of Information Experience: Relation to Personality and Approach to Studying

Abstract This chapter discusses individual differences in information experiences, with particular focus on emotional aspects. It reports findings from two studies that explored K12 and mature students’ experiences of uncertainty in the information search process. These experiences were related to the respondents’ personality traits and approaches to studying. The studies found that intrinsic motivation and openness to experience increased the likelihood of a pleasant information experience in a study context, while extrinsic motivation and insecurity often resulted in a negative one. Conscientious and systematic searchers tended to be foremost goal-oriented, whereby the affective tone of a search depended on the amount of progress towards the goal. Patterns of explorative or systematic searching were found both during a specific inquiry process and as broader conceptions of regularly occurring information experiences.
Motion corrected photoacoustic difference imaging of fluorescent contrast agents

In fluorophores, such as exogenous dyes and genetically expressed proteins, the excited state lifetime can be modulated using pump-probe excitation at wavelengths corresponding to the absorption and fluorescence spectra. Simultaneous pump-probe pulses induce stimulated emission (SE) which, in turn, modulates the thermalized energy, and hence the photoacoustic (PA) signal amplitude. For time-delayed pulses, by contrast, SE is suppressed. Since this is not observed in endogenous chromophores, the location of the fluorophore can be determined by subtracting images acquired using simultaneous and time-delayed pump-probe excitation. This simple experimental approach exploits a fluorophorespecific contrast mechanism, and has the potential to enable deep-tissue molecular imaging at fluences below the MPE. In this study, some of the challenges to its in vivo implementation are addressed. First, the PA signal amplitude generated in fluorophores in vivo is often much smaller than that in blood. Second, tissue motion can give rise to artifacts that correspond to endogenous chromophores in the difference image. This would not allow the unambiguous detection of fluorophores. A method to suppress motion artifacts based on fast switching between simultaneous and time-delayed pump-probe excitation was developed. This enables the acquisition of PA signals using the two excitation modes with minimal time delay (20 ms), thus minimizing the effects of tissue motion. The feasibility of this method is demonstrated by visualizing a fluorophore (Atto680) in tissue phantoms, which were moved during the image acquisition to mimic tissue motion.
Distributed Matching Algorithms: Maximizing Secrecy in the Presence of Untrusted Relay

In this paper, we propose a secrecy sum-rate maximization based matching algorithm between primary trans-mitters and secondary cooperative jammers in the presence of an eavesdropper. More explicitly, we consider an untrusted relay scenario, where the relay is a potential eavesdropper. We ﬁrst show the achievable secrecy regions employing a friendly jammer in a cooperative scenario with employing an untrusted relay. Then, we provide results for the secrecy regions for two cases, one where we consider that there is no direct link between the source and the destination, for the second case we consider that in addition to the relay link we also have a direct link between the source and destination. Furthermore, a friendly jammer helps to send a noise signal during the ﬁrst phase of the cooperative transmission, for securing the information transmitted from the source. In our matching algorithm, the selected cooperative jammer or the secondary user, is rewarded with the spectrum allocation for a fraction of time slot from the source which is the primary user. The Conventional Distributed Algorithm (CDA) and the Pragmatic Distributed Algorithm (PDA), which were originally designed for maximising the user’s sum rate, are modiﬁed and adapted for maximizing the secrecy sum-rate for the primary user. Instead of assuming perfect modulation and/or perfect channel coding, we have also investigated our proposed schemes when practical channel coding and modulation schemes are invoked.