Miracle-dz/UniFAR-FTUs huggingface dataset:
A nucleus-basal body connector in Chlamydomonas reinhardtii that may function in basal body localization or segregation

We have isolated a nucleus-basal body complex from Chlamydomonas reinhardtii. The complex is strongly immunoreactive to an antibody generated against a major protein constituent of isolated Tetraselmis striata flagellar roots (Salisbury, J. L., A. Baron, B. Surek, and M. Melkonian, J. Cell Biol., 99:962-970). Electrophoretic and immunoelectrophoretic analysis indicates that, like the Tetraselmis protein, the Chlamydomonas antigen consists of two acidic isoforms of approximately 20 kD. Indirect immunofluorescent staining of nucleus- basal body complexes reveals two major fibers in the connector region, one between each basal body and the nucleus. The nucleus is also strongly immunoreactive, with staining radiating around much of the nucleus from a region of greatest concentration at the connector pole. Calcium treatment causes shortening of the connector fibers and also movement of nuclear DNA towards the connector pole. Electron microscopic observation of negatively stained nucleus-basal body complexes reveals a cluster of approximately 6-nm filaments, suspected to represent the connector, between the basal bodies and nuclei. A mutant with a variable number of flagella, vfl-2-220, is defective with respect to the nucleus-basal body association. This observation encourages us to speculate that the nucleus-basal body union is important for accurate basal body localization within the cell and/or for accurate segregation of parental and daughter basal bodies at cell division. A physical association between nuclei and basal bodies or centrioles has been observed in a variety of algal, protozoan, and metazoan cells, although the nature of the association, in terms of both structure and function, has been obscure. We believe it likely that fibrous connectors homologous to those described here for Chlamydomonas are general features of centriole-bearing eucaryotic cells.
Bonobos Respond to Distress in Others: Consolation across the Age Spectrum

How animals respond to conflict provides key insights into the evolution of socio-cognitive and emotional capacities. Evidence from apes has shown that, after social conflicts, bystanders approach victims of aggression to offer stress-alleviating contact behavior, a phenomenon known as consolation. This other-orientated behavior depends on sensitivity to the other's emotional state, whereby the consoler acts to ameliorate the other's situation. We examined post-conflict interactions in bonobos (Pan paniscus) to identify the determinants of consolation and reconciliation. Thirty-six semi-free bonobos of all ages were observed at the Lola ya Bonobo Sanctuary, DR Congo, using standardized Post-conflict/Matched Control methods. Across age and sex classes, bonobos consoled victims and reconciled after conflicts using a suite of affiliative and socio-sexual behaviors including embracing, touching, and mounting. Juveniles were more likely to console than adults, challenging the assumption that comfort-giving rests on advanced cognitive mechanisms that emerge only with age. Mother-reared individuals were more likely to console than orphans, highlighting the role of rearing in emotional development. Consistent with previous studies, bystanders were more likely to console relatives or closely bonded partners. Effects of kinship, affiliation and rearing were similarly indicated in patterns of reconciliation. Nearby bystanders were significantly more likely to contact victims than more distal ones, and consolation was more likely in non-food contexts than during feeding. The results did not provide convincing evidence that bystander contacts served for self-protection or as substitutes for reconciliation. Overall, results indicate that a suite of social, developmental and contextual factors underlie consolation and reconciliation in bonobos and that a sensitivity to the emotions of others and the ability to provide appropriate consolatory behaviors emerges early in development.
PROMPT: Algorithm and Tool for Automated Ontology Merging and Alignment

Researchers in the ontology-design field have developed the content for ontologies in many domain areas. Recently, ontologies have become increasingly common on the WorldWide Web where they provide semantics for annotations in Web pages. This distributed nature of ontology development has led to a large number of ontologies covering overlapping domains. In order for these ontologies to be reused, they first need to be merged or aligned to one another. The processes of ontology alignment and merging are usually handled manually and often constitute a large and tedious portion of the sharing process. We have developed and implemented PROMPT, an algorithm that provides a semi-automatic approach to ontology merging and alignment. PROMPT performs some tasks automatically and guides the user in performing other tasks for which his intervention is required. PROMPT also determines possible inconsistencies in the state of the ontology, which result from the user’s actions, and suggests ways to remedy these inconsistencies. PROMPT is based on an extremely general knowledge model and therefore can be applied across various platforms. Our formative evaluation showed that a human expert followed 90% of the suggestions that PROMPT generated and that 74% of the total knowledge-base operations invoked by the user were suggested by PROMPT.
Lysophosphatidic acid receptor gene vzg‐1/lpA1/edg‐2 is expressed by mature oligodendrocytes during myelination in the postnatal murine brain

The growth‐factor–like phospholipid lysophosphatidic acid (LPA) mediates a wide variety of biological functions. We recently reported the cloning of the first G‐protein–coupled receptor for LPA, called ventricular zone gene‐1 (vzg‐1/lpA1/edg‐2) because its embryonic central nervous system (CNS) expression is restricted to the neocortical ventricular zone (Hecht et al. [1996] J. Cell Biol. 135:1071–1083). Vzg‐1 neural expression diminishes at the end of the cortical neurogenetic period, just before birth. Here, we have investigated the subsequent reappearance of vzg‐1 expression in the postnatal murine brain, by using in situ hybridization and northern blot analyses. Vzg‐1 expression was undetectable by in situ hybridization at birth, but reappeared in the hindbrain during the 1st postnatal week. Subsequently, expression expanded from caudal to rostral, with peak expression observed around postnatal day 18. At all postnatal ages, vzg‐1 expression was concentrated in and around developing white matter tracts, and its expansion, peak, and subsequent downregulation closely paralleled the progress of myelination. Double‐label in situ hybridization studies demonstrated that vzg‐1–expressing cells co‐expressed mRNA encoding proteolipid protein (PLP), a mature oligodendrocyte marker, but not glial fibrillary acidic protein (GFAP), an astrocyte marker. Consistent with this, vzg‐1 mRNA expression was reduced by 40% in the brains of jimpy mice, which exhibit aberrant oligodendrocyte differentiation and cell death. Together with our characterization of vzg‐1 during cortical neurogenesis, these data suggest distinct pre‐ and postnatal roles for LPA in the development of neurons and oligodendrocytes and implicate lysophospholipid signaling as a potential regulator of myelination. J. Comp. Neurol. 398:587–598, 1998. © 1998 Wiley‐Liss, Inc.
Nonfunctional requirements: from elicitation to conceptual models

Nonfunctional requirements (NFRs) have been frequently neglected or forgotten in software design. They have been presented as a second or even third class type of requirement, frequently hidden inside notes. We tackle this problem by treating NFRs as first class requirements. We present a process to elicit NFRs, analyze their interdependencies, and trace them to functional conceptual models. We focus our attention on conceptual models expressed using UML (Unified Modeling Language). Extensions to UML are proposed to allow NFRs to be expressed. We show how to integrate NFRs into the class, sequence, and collaboration diagrams. We also show how use cases and scenarios can be adapted to deal with NFRs. This work was used in three case studies and their results suggest that by using our proposal we can improve the quality of the resulting conceptual models.
The Short-Stature Homeobox-Containing Gene (shox/SHOX) Is Required for the Regulation of Cell Proliferation and Bone Differentiation in Zebrafish Embryo and Human Mesenchymal Stem Cells

The short-stature homeobox-containing gene (SHOX) was originally discovered as one of genes responsible for idiopathic short-stature syndromes in humans. Previous studies in animal models have shown the evolutionarily conserved link between this gene and skeletal formation in early embryogenesis. Here, we characterized developmental roles of shox/SHOX in zebrafish embryos and human mesenchymal stem cells (hMSCs) using loss-of-function approaches. Morpholino oligo-mediated knockdown of zebrafish shox markedly hindered cell proliferation in the anterior region of the pharyngula embryos, which was accompanied by reduction in the dlx2 expression at mesenchymal core sites for future pharyngeal bones. In addition, the impaired shox expression transiently increased expression levels of skeletal differentiation genes in early larval stage. In cell culture studies, we found that hMSCs expressed SHOX; the siRNA-mediated blockade of SHOX expression significantly blunted cell proliferation in undifferentiated hMSCs but the loss of SHOX expression did augment the expressions of subsets of early osteogenic genes during early osteoblast differentiation. These data suggest that shox/SHOX maintains the population of embryonic bone progenitor cells by keeping its proliferative status and by repressing the onset of early osteogenic gene expression. The current study for the first time shows cellular and developmental responses caused by shox/SHOX deficiency in zebrafish embryos and hMSCs, and it expands our understanding of the role of this gene in early stages of skeletal growth.
Comprehensive Feature-Based Robust Video Fingerprinting Using Tensor Model

Content-based near-duplicate video detection (NDVD) is essential for effective search and retrieval, and robust video fingerprinting is a good solution for NDVD. Most existing video fingerprinting methods use a single feature or concatenate different features to generate video fingerprints, and show good performance under single-mode modifications such as noise addition and blurring. However, when they suffer combined modifications, the performance is degraded to a certain extent because such features cannot characterize the video content completely. By contrast, the assistance and consensus among different features can improve the performance of video fingerprinting. Therefore, in the present study, we mine the assistance and consensus among different features based on a tensor model, and we present a new comprehensive feature to fully use them in the proposed video fingerprinting framework. We also analyze what the comprehensive feature really is for representing the original video. In this framework, the video is initially set as a high-order tensor that consists of different features, and the video tensor is decomposed via the Tucker model with a solution that determines the number of components. Subsequently, the comprehensive feature is generated by the low-order tensor obtained from tensor decomposition. Finally, the video fingerprint is computed using this feature. A matching strategy used for narrowing the search is also proposed based on the core tensor. The robust video fingerprinting framework is resistant not only to single-mode modifications but also to their combination.
Fhl-1, a New Key Protein in Pulmonary Hypertension

Background— Pulmonary hypertension (PH) is a severe disease with a poor prognosis. Different forms of PH are characterized by pronounced vascular remodeling, resulting in increased vascular resistance and subsequent right heart failure. The molecular pathways triggering the remodeling process are poorly understood. We hypothesized that underlying key factors can be identified at the onset of the disease. Thus, we screened for alterations to protein expression in lung tissue at the onset of PH in a mouse model of hypoxia-induced PH. Methods and Results— Using 2-dimensional polyacrylamide gel electrophoresis in combination with matrix-assisted laser desorption/ionization time-of-flight analysis, we identified 36 proteins that exhibited significantly altered expression after short-term hypoxic exposure. Among these, Fhl-1, which is known to be involved in muscle development, was one of the most prominently upregulated proteins. Further analysis by immunohistochemistry, Western blot, and laser-assisted microdissection followed by quantitative polymerase chain reaction confirmed the upregulation of Fhl-1, particularly in the pulmonary vasculature. Comparable upregulation was confirmed (1) after full establishment of hypoxia-induced PH, (2) in 2 rat models of PH (monocrotaline-treated and hypoxic rats treated with the vascular endothelial growth factor receptor antagonist SU5416), and (3) in lungs from patients with idiopathic pulmonary arterial hypertension. Furthermore, we demonstrated that regulation of Fhl-1 was hypoxia-inducible transcription factor dependent. Abrogation of Fhl-1 expression in primary human pulmonary artery smooth muscle cells by small-interfering RNA suppressed, whereas Fhl-1 overexpression increased, migration and proliferation. Coimmunoprecipitation experiments identified Talin1 as a new interacting partner of Fhl-1. Conclusions— Protein screening identified Fhl-1 as a novel protein regulated in various forms of PH, including idiopathic pulmonary arterial hypertension.
Tolerating Malicious Device Drivers in Linux

This paper presents SUD, a system for running existing Linux device drivers as untrusted user-space processes. Even if the device driver is controlled by a malicious adversary, it cannot compromise the rest of the system. One significant challenge of fully isolating a driver is to confine the actions of its hardware device. SUD relies on IOMMU hardware, PCI express bridges, and messagesignaled interrupts to confine hardware devices. SUD runs unmodified Linux device drivers, by emulating a Linux kernel environment in user-space. A prototype of SUD runs drivers for Gigabit Ethernet, 802.11 wireless, sound cards, USB host controllers, and USB devices, and it is easy to add a new device class. SUD achieves the same performance as an in-kernel driver on networking benchmarks, and can saturate a Gigabit Ethernet link. SUD incurs a CPU overhead comparable to existing runtime driver isolation techniques, while providing much stronger isolation guarantees for untrusted drivers. Finally, SUD requires minimal changes to the kernel--just two kernel modules comprising 4,000 lines of code--which may at last allow the adoption of these ideas in practice.
Poststroke Fatigue: An Emerging, Critical Issue in Stroke Medicine

Poststroke fatigue is a common and disabling condition. However, few studies on or therapeutic trials addressing poststroke fatigue have appeared in the literature. We aimed to review the prevalence, natural course, potential predisposing factors (physiological, psychocognitive, and organic), and pharmacological and nonpharmacological treatments of poststroke fatigue. Using PubMed CINAHL and PsycINFO, we reviewed all the available literature on poststroke fatigue and related issues. The prevalence of poststroke fatigue ranges from 23% to 75%, depending on the definition of fatigue and the characteristics of the patients included. Post-stroke fatigue seems to be of complex etiology. Predisposing factors were physiological ones including functional disability, prestroke fatigue, medical comorbidities, medication, sleep disturbances, and nutritional problems; psychocognitive ones including depression and cognitive dysfunction; and organic ones including damage to particular brain areas with consequent neurochemical alterations, perfusion deficit, and neuroinflammation. Poststroke fatigue is a persistent and debilitating symptom in some patients, and can have adverse affects on patient's neurological recovery, quality of life, and mortality. Few therapeutic trials have been reported, and the therapy was rarely successful, possibly because of the complex nature of poststroke fatigue. Poststroke fatigue is a common and frequently disabling problem of complex etiology. Further studies are urgently needed to improve our understanding of the pathophysiology of post-stroke fatigue and to develop better treatments for this condition.
Hepatocyte Nuclear Factor 4α (HNF4α) Is a Transcription Factor of Vertebrate Fatty Acyl Desaturase Gene as Identified in Marine Teleost Siganus canaliculatus

Rabbitfish Siganus canaliculatus was the first marine teleost demonstrated to have the capability of biosynthesizing long-chain polyunsaturated fatty acids (LC-PUFA) from C18 precursors, and to possess a Δ4 fatty acyl desaturase (Δ4 Fad) which was the first report in vertebrates, and is a good model for studying the regulatory mechanisms of LC-PUFA biosynthesis in teleosts. In order to understand regulatory mechanisms of transcription of Δ4 Fad, the gene promoter was cloned and characterized in the present study. An upstream sequence of 1859 bp from the initiation codon ATG was cloned as the promoter candidate. On the basis of bioinformatic analysis, several binding sites of transcription factors (TF) including GATA binding protein 2 (GATA-2), CCAAT enhancer binding protein (C/EBP), nuclear factor 1 (NF-1), nuclear factor Y (NF-Y), hepatocyte nuclear factor 4α (HNF4α) and sterol regulatory element (SRE), were identified in the promoter by site-directed mutation and functional assays. HNF4α and NF-1 were confirmed to interact with the core promoter of Δ4 Fad by gel shift assay and mass spectrometry. Moreover, over-expression of HNF4α increased promoter activity in HEK 293T cells and mRNA level of Δ4 Fad in rabbitfish primary hepatocytes, respectively. The results indicated that HNF4α is a TF of rabbitfish Δ4 Fad. To our knowledge, this is the first report on promoter structure of a Δ4 Fad, and also the first demonstration of HNF4α as a TF of vertebrate Fad gene involved in transcription regulation of LC-PUFA biosynthesis.
Highest Weight Categories Arising from Khovanov's Diagram Algebra I: Cellularity

This is the first of four articles studying some slight generalisations Hn m of Khovanov’s diagram algebra, as well as quasi-hereditary covers Kn m of these algebras in the sense of Rouquier, and certain infinite dimensional limiting versions K m , K m and K ∞ . In this article we prove that H n m is a cellular symmetric algebra and that Kn m is a cellular quasi-hereditary algebra. In subsequent articles, we relate Hn m , Kn m and K m to level two blocks of degenerate cyclotomic Hecke algebras, parabolic category O and the general linear supergroup, respectively.
Histopathologic retrieval analysis of clinically failed porous tantalum osteonecrosis implants.

BACKGROUND An Osteonecrosis Intervention Implant made of porous tantalum was recently developed to provide structural support and a compatible surface for tissue ingrowth in osteonecrotic femoral heads. From an investigational device exemption study that comprised 113 implants, we carried out a retrieval analysis of clinically failed implants. METHODS Seventeen porous tantalum implants that had been used for the treatment of Steinberg stage-II osteonecrosis of the hip were retrieved at the time of conversion to a total hip arthroplasty. Fifteen implants that had been transected near the base of the femoral neck with the proximal portion left in situ within the femoral head underwent histopathologic analysis at an average of 13.4 months (range, three to thirty-six months) after implantation. RESULTS Residual osteonecrosis was present in fourteen of the fifteen specimens. Fracture of the subchondral bone of the femoral head was present in all instances, and collapse of the femoral head was present in nine instances (60%). Backscattered scanning electron microscopy confirmed the presence of bone ingrowth in thirteen (87%) of the fifteen specimens. The mean extent of bone ingrowth was 1.9% (range, 0% to 4.4%). CONCLUSIONS The retrieved implants were associated with little bone ingrowth and insufficient mechanical support of subchondral bone. The implant design, the surgical technique, its application, and the clinical characteristics of candidates for this procedure should continue to be monitored closely.
The Social Impact of Natural Language Processing

Medical sciences have long since established an ethics code for experiments, to minimize the risk of harm to subjects. Natural language processing (NLP) used to involve mostly anonymous corpora, with the goal of enriching linguistic analysis, and was therefore unlikely to raise ethical concerns. As NLP becomes increasingly wide-spread and uses more data from social media, however, the situation has changed: the outcome of NLP experiments and applications can now have a direct effect on individual users’ lives. Until now, the discourse on this topic in the ﬁeld has not followed the technological development, while public discourse was often focused on exaggerated dangers. This position paper tries to take back the initiative and start a discussion. We identify a number of social implications of NLP and discuss their ethical signiﬁcance, as well as ways to address them.
Scrub Typhus in Children at a Tertiary Hospital in North India: Clinical Profile and Complications

Objective: To study the clinical profile and complications of childhood scrub typhus. Methods: Prospective observational study of 66 children with scrub typhus, admitted to a tertiary hospital in north India, during the period between January 2011 and December 2012. The diagnosis was confirmed by serology. Findings : All children presented with fever. Other common symptoms were vomiting (56%), facial swelling (52%), cough (35%), abdominal pain (33%), breathlessness (29%) and decreased urine output (29%). High grade fever (>101 oF) was recorded in 91% of children. Other common signs were hepatomegaly, splenomegaly, edema, tender lymphadenopathy and hypotension, observed in 82%, 59%, 39%, 38% and 36% of cases, respectively. An eschar and a maculopapular rash each were observed in 20% of patients. Meningoencephalitis (30.3%), severe thrombocytopenia (27.2%), shock (25.8%), acute kidney injury (16.7%) and hepatitis (13.6%) were the most common complications observed in these children. Other common complications were acute respiratory distress syndrome, respiratory failure requiring ventilation, bronchopneumonia and myocarditis. Ninety percent of children became afebrile within 48 hours of initiating an appropriate antibiotic. Median time to defervescence was 22 hours. The overall mortality rate was 7.5%. Causes of death were refractory shock, meningoencephalitis, acute respiratory distress syndrome, bronchopneumonia, acute kidney injury and myocarditis. Conclusion: Pediatricians should keep a high index of suspicion for scrub typhus in any febrile child having a maculopapular rash, hepatosplenomegaly, tender lymphadenopathy, thrombocytopenia and features suggestive of capillary leak. Pending serological confirmation, empirical therapy with doxycycline or azithromycin should be started, as delay in treatment would result in life threatening complications.