Miracle-dz/UniFAR-FTUs huggingface dataset:
STABILIZED 1 Modulates Pre-mRNA Splicing for Thermotolerance 1 [ OPEN ]

High-temperature stress often leads to differential RNA splicing, thus accumulating different types and/or amounts of mature mRNAs in eukaryotic cells. However, regulatory mechanisms underlying plant precursor mRNA (pre-mRNA) splicing in the environmental stress conditions remain elusive. Herein, we describe that a U5-snRNP-interacting protein homolog STABILIZED1 (STA1) has pre-mRNA splicing activity for heat-inducible transcripts including HEAT STRESS TRANSCRIPTION FACTORs and various HEAT SHOCK PROTEINs for the establishment of heat stress tolerance in Arabidopsis (Arabidopsis thaliana). Our cell-based splicing reporter assay demonstrated STA1 acts on pre-mRNA splicing for specific subsets of stressrelated genes. Cellular reconstitution of heat-inducible transcription cascades supported the view that STA1-dependent premRNA splicing plays a role in DREB2A-dependent HSFA3 expression for heat-responsive gene expression. Further genetic analysis with a loss-of-function mutant sta1-1, STA1-expressing transgenic plants in Col background, and STA1-expressing transgenic plants in the sta1-1 background verified that STA1 is essential in expression of necessary genes including HSFA3 for two-step heat stress tolerance in plants. However, constitutive overexpression of the cDNA version of HSFA3 in the sta1-1 background is unable to execute plant heat stress tolerance in sta1-1. Consistently our global target analysis of STA1 showed that its splicing activity modulates a rather broad range of gene expression in response to heat treatment. The findings of this study reveal that heat-inducible STA1 activity for pre-mRNA splicing serves as a molecular regulatory mechanism underlying the plant stress tolerance to high-temperature stress.
HBVPathDB: a database of HBV infection-related molecular interaction network.

AIM To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection. METHODS The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML). RESULTS We present the first version of HBVPathDB, which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1 050 molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search, unitized search-are supported by the search engine of the database. The database is freely available at http://www.bio-inf.net/HBVPathDB/HBV/. CONCLUSION The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing, visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.
IgG, IgA and IgE Reactivities to Sperm Antigens in Infertile Women

Abstract * Corresponding author. e-mail: andrea.brazdova@vscht.cz. Nowadays, World Health Organization (WHO) appoints infertility as a disease. Still more couples are diagnosed with unexplained infertility, it reaches almost 20 % of all cases. Immune system plays an important role: isounization of -immwomen is possible by human sperm cells. For better understanding, it is necessary to detect and characterize antigens recognized by women immune system. Our study is focused on female infertility and is based on the ejaculate sample from four healthy donors. Antigens analyzed by sodium dodecyl sulphate polyacrylamide gel electrophoresis and isoelectric focusing (followed by IgG, IgA and IgE immunoblotting) were detected by forty-five sera from women who were diagnosed with fertility failure. Ten children’s sera were used as negative controls. The immunodominant sperm antigens detected by IgG antibodies were 68 and 123 kDa proteins with pI from 6.60 to 6.62, respectively. Concerning mucosal immunity the most frequently recognized sperm IgA-binding protein reached 130 kDa and pI 6.9, 7.4, 9.5. This study did not prove theassociation of IgE antibodies with unexplained infertility in women.
Relation Of Gait Analysis To Gross Motor Function In Cerebral Palsy

The Gross Motor Function Measure (GMFM) and computerized gait analysis are commonly used to assess patients with cerebral palsy (CP). The authors investigated correlations between the GMFM and gait parameters in 32 children aged 3 to 18 (mean 8.9) years with spastic CP. Of the gait parameters, cadence and normalized velocity correlated most strongly with the GMFM score, and hip and knee excursion and percentage single support also correlated directly with the GMFM. In a stepwise multiple regression, cadence alone was a significant predictor of GMFM score. Time and distance parameters, hip and knee excursion in the sagittal plane and GMFM values all moved consistently further from pediatric norms as functional severity increased. The study confirms that gait is representative of general motor status in CP and that the GMFM and gait analysis are complementary measures in the functional assessment of these children.
Motivational Orientation, Expectancies, and Vulnerability for Depression in Women

Abstract In this study, motivational components in me personal styles of sociotropy and autonomy were examined in a sample of 284 women. One hypothesis was that self-validation needs would account for the vulnerability for depressive symptoms in these personal styles. A second hypothesis was that the association of these personal styles with depressive symptoms would be moderated by expectations and perceptions of how likely these validation needs would be met. As predicted, it was found that validation seeking mediated the association of sociotropy and autonomy with depressive symptoms in these women. Another finding was that expectancies moderated the effects of sociotropy and autonomy to predict depressive symptoms. Negative expectancies in women high on these personal styles together further increased the level of depressive symptoms. These findings are compatible with theories emphasizing the importance of situational factors in the onset and maintenance of depression in women.
STABILITY-INDICATING HIGH PERFORMANCE LIQUID CHROMATOGRAPHIC DETERMINATION OF FLUCONAZOLE IN THE PRESENCE OF ITS OXIDATIVE DEGRADATION PRODUCT - KINETIC AND STRESS STUDY

A simple, specific, accurate, and stability-indicating high performance liquid chromatographic method (HPLC) method has been established for analysis of fluconazole (FLZ) in the presence of its degradation products generated in the stress degradation study. FLZ was subjected to stress conditions of acid, alkali, and neutral hydrolysis, oxidation, photolysis, and thermal decomposition. Extensive degradation was found to occur in oxidative medium under thermal stress. Successful separation of drug from degradation products was achieved on a C-18 column using phosphoric acid 0.5% v/v: acetonitrile (80:20% v/v) as the mobile phase. The flow rate was 1.5 mL min−1 and the detector was set at 261 nm. The retention times of FLZ and its main oxidative degradation product were found to be 5.389 min and 2.729 min, respectively. Linearity was established for fluconazole in the range of 0.5–50 µg/ml. The percentage recovery of fluconazole was found to be 99.91 ± 0.74. Because the method effectively separates fluconazole from its oxidative degradation products, it can be used as stability-indicating method. The proposed method was also used to study the kinetics of fluconazole oxidative degradation that was found to follow a zero-order reaction. The t1/2 was 21.66 min while k (reaction rate constant) was 2.91 × 10−8 mole/min.
Wearable fluid power composed of transformed flat tube actuators

This paper presents a novel approach of driving the human joints by means of a fluid control system with flexibility just like clothes, which leads to a cyborg amplifying the human motor function. Former actuators for body mounting were not always designed from the point of clothing comfort. Thus, in the first part of this paper, a clothing comfort index is introduced so as to evaluate the desirability of the actuator mounted on the body. Then, pneumatic tube actuators with a novel structure are systematically proposed to increase the comfort index. By using the actuators, an efficient driving method of both the arm and the leg is shown to realize "Wearable Fluid Power" so as to assist the disabled to walk or to improve their sporting skill.
Using scenarios in deficiency-driven requirements engineering

A process is described for generating and validating specifications, together with an automated tool which supports this approach. The input to the process is a set of client objectives, expressed as transitions between states. These transitions fall into two classes: those which should be supported, and those which should be prevented. The output is a specification of a target artifact, expressed as a set of capabilities. A valid specification is a set of artifact capabilities that can be used to achieve all desired transitions but cannot be used to achieve any undesirable transitions. An automated system is used for reasoning about scenarios (sequences of actions) to generate and evaluate specifications. Scenarios are employed to identify missing capabilities that would enable artifact users to achieve their goals, and to determine whether a particular capability set will allow prohibited transitions. <<ETX>>
Activation of CAAT Enhancer-binding Protein δ (C/EBPδ) by Interleukin-1 Negatively Influences Apolipoprotein C-III Expression*

Tissue-specific transcription of the apolipoprotein C-III (apoC-III) gene is mainly regulated by synergistic interactions between the liver-enriched transcription factor HNF-4, which binds to the proximal promoter, and ubiquitous factors, which bind to the upstream enhancer region. Here we show that apoC-III expression in HepG2 cells is negatively regulated in response to interleukin-1 (IL-1), and this inhibition is mainly due to transcriptional repression. CAAT enhancer-binding protein δ (C/EBPδ) was found to be the main mediator of IL-1-induced suppression. Analysis of the apoC-III promoter revealed two IL-1 response elements. The first is located in the proximal promoter region D and the second in the distal enhancer region I. Proximal element D is a high affinity binding site for C/EBPδ, while the enhancer element I is not directly recognized by this transcription factor. Functional analysis of different combinations of homologous and heterologous promoter constructs revealed that indirect interaction of C/EBPδ with site I, in the context of the full promoter, leads to repression. C/EBPδ is activated by phosphorylation during IL-1-induced signal transduction pathway. This modification is important for both DNA binding activity and indirect transrepression of the apoC-III promoter.
Practical Shape Analysis

Shape analysis is a program analysis technique used to prove that imperative programs using manual memory management will not crash. In the past, shape analysis has been applied to data structures like linked lists and binary trees. It has also been used on simplified versions of Windows device drivers. We describe techniques that allow us to apply shape analysis to data structures that occur commonly in systems code. These data structures often use arrays, hash tables, C strings, and buffers of a known size. Sometimes, memory in these data structures is managed by manual reference counting. Analyzing such code is difficult or impossible with existing shape analyses. Most difficult of all, many data structures use several of these patterns at the same time, such as a hash table pointing to reference counted objects through which a doubly linked list threads. We describe an analysis capable of handling these data structures easily and efficiently. Our technique uses abstract interpretation over the combination of two abstract domains. One, based on three-valued logic, is used for analyzing the heap. The other domain reasons about integers and set cardinality. The key feature of the combined domain is that quantified facts can be shared between the integer and heap domains. The precision we achieve is significantly greater than if either domain were used independently. Besides improvements in precision, we also describe changes that make both domains more scalable and efficient. We present the results of experiments analyzing the cache data structure of the thttpd web server, which uses a hash table, linked lists, and reference counting in a single data structure. We successfully prove the absence of memory errors in about two minutes.
Application-specific protocol architectures for wireless networks

In recent years, advances in energy-efficient design and wireless technologies have enabled exciting new applications for wireless devices. These applications span a wide range, including real-time and streaming video and audio delivery, remote monitoring using networked microsensors, personal medical monitoring, and home networking of everyday appliances. While these applications require high performance from the network, they suffer from resource constraints that do not appear in more traditional wired computing environments. In particular, wireless spectrum is scarce, often limiting the bandwidth available to applications and making the channel error-prone, and the nodes are battery-operated, often limiting available energy. My thesis is that this harsh environment with severe resource constraints requires an application-specific protocol architecture, rather than the traditional layered approach, to obtain the best possible performance. This dissertation supports this claim using detailed case studies on microsensor networks and wireless video delivery. The first study develops LEACH (Low-Energy Adaptive Clustering Hierarchy), an architecture for remote microsensor networks that combines the ideas of energy-efficient cluster-based routing and media access together with application-specific data aggregation to achieve good performance in terms of system lifetime, latency, and application-perceived quality. This approach improves system lifetime by an order of magnitude compared to general-purpose approaches when the node energy is limited. The second study develops an unequal error protection scheme for MPEG-4 compressed video delivery that adapts the level of protection applied to portions of a packet to the degree of importance of the corresponding bits. This approach obtains better application-perceived performance than current approaches for the same amount of transmission bandwidth. These two systems show that application-specific protocol architectures achieve the energy and latency efficiency and error robustness needed for wireless networks. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
A Comparative Method for Both Discrete and Continuous Characters Using the Threshold Model

The threshold model developed by Sewall Wright in 1934 can be used to model the evolution of two-state discrete characters along a phylogeny. The model assumes that there is a quantitative character, called liability, that is unobserved and that determines the discrete character according to whether the liability exceeds a threshold value. A Markov chain Monte Carlo algorithm is used to infer the evolutionary covariances of the liabilities for discrete characters, sampling liability values consistent with the phylogeny and with the observed data. The same approach can also be used for continuous characters by assuming that the tip species have values that have been observed. In this way, one can make a comparative-methods analysis that combines both discrete and continuous characters. Simulations are presented showing that the covariances of the liabilities are successfully estimated, although precision can be achieved only by using a large number of species, and we must always worry whether the covariances and the model apply throughout the group. An advantage of the threshold model is that the model can be straightforwardly extended to accommodate within-species phenotypic variation and allows an interface with quantitative-genetics models.
A Primary Care Focus on the Diagnosis and Treatment of Major Depressive Disorder in Adults

Major depressive disorder (MDD), a highly prevalent psychiatric condition, is encountered in 1 of every 10 to 20 patients seen in the primary care setting. While awareness of MDD has increased, timely and accurate diagnosis and adequate treatment remain formidable challenges. Treatment options for patients with MDD should be individualized according to each patient's clinical and medication history, pharmacologic tolerability profile, and personal preferences, to maximize long-term adherence. The most robust and consistently maintained positive outcomes occur in patients who are administered effective treatment with recommended antidepressant pharmacotherapy, psychotherapy, or a combination of these treatment modalities. This manuscript reviews the epidemiology, biologic and clinical features, diagnosis, and treatment of patients with MDD. A focus is placed on guidelines and strategies that target the achievement of MDD symptom remission. The article also includes details on individualizing treatment selection and novel and emerging therapies. Primary care physicians must be prepared to adjust, substitute, or augment antidepressant treatments to optimize patient response and enhance the chances of achieving remission. Considerations that strongly influence long-term patient adherence, including tolerability and cost, are also reviewed. (Journal of Psychiatric Practice 2011;17:340–350)
Armored geckos: A histological investigation of osteoderm development in Tarentola (Phyllodactylidae) and Gekko (Gekkonidae) with comments on their regeneration and inferred function

Osteoderms are bone‐rich organs found in the dermis of many scleroglossan lizards sensu lato, but are only known for two genera of gekkotans (geckos): Tarentola and Gekko. Here, we investigate their sequence of appearance, mode of development, structural diversity and ability to regenerate following tail loss. Osteoderms were present in all species of Tarentola sampled (Tarentola annularis, T. mauritanica, T. americana, T. crombei, T. chazaliae) as well as Gekko gecko, but not G. smithii. Gekkotan osteoderms first appear within the integument dorsal to the frontal bone or within the supraocular scales. They then manifest as mineralized structures in other positions across the head. In Tarentola and G. gecko, discontinuous clusters subsequently form dorsal to the pelvis/base of the tail, and then dorsal to the pectoral apparatus. Gekkotan osteoderm formation begins once the dermis is fully formed. Early bone deposition appears to involve populations of fibroblast‐like cells, which are gradually replaced by more rounded osteoblasts. In T. annularis and T. mauritanica, an additional skeletal tissue is deposited across the superficial surface of the osteoderm. This tissue is vitreous, avascular, cell‐poor, lacks intrinsic collagen, and is herein identified as osteodermine. We also report that following tail loss, both T. annularis and T. mauritanica are capable of regenerating osteoderms, including osteodermine, in the regenerated part of the tail. We propose that osteoderms serve roles in defense against combative prey and intraspecific aggression, along with anti‐predation functions. J. Morphol. 276:1345–1357, 2015. © 2015 Wiley Periodicals, Inc.
The Link Between Hysterectomy and Depression

This paper reviews the current literature on the possible link between hysterectomy and depression. Psychological hypotheses for such a link are discussed. The literature is divided fairly evenly into those papers which support a definite association between hysterectomy and post-operative depression and those which refute any such link. A summary of these papers is given with a critical discussion of the various methodologies and operational definitions used. No clear-cut association can be found on review of these studies, but in those papers which do suggest an association, the risk factors of a history of pre-operative depression, no organic uterine pathology and hysterectomy in young women of child bearing age are common to most. The point is made that depression occurring after hysterectomy is more likely to be associated with the social and psychological consequences of organ removal than with the operative procedure itself, and therefore, one may not expect the condition to become clinically obvious for anywhere from six months to two years post-operatively. The authors conclude that care should be taken in performing hysterectomy where the indications are equivocal, especially if the above alleged risk factors are present. A plea is made for more research in this area to determine whether hysterectomy is a factor in the etiology of depression in some women, and if so, which women are at risk.
HIF Takes It Up a Notch

The interaction of the transcription factor HIF-α with the Notch receptor promotes cell fate specification and maintenance. Notch signaling is used to choose cell fates in many developmental contexts. New evidence shows that circulating blood cells in Drosophila, in the absence of Notch ligand provided by neighboring cells, activate Notch signaling through stabilization with the hypoxia-inducible factor–α (HIF-α) transcription factor. Although HIF-α is a key regulator of the low-oxygen stress response, here it acts without its HIF-β partner by interacting with and stabilizing the Notch receptor. These roles for HIF-α and Notch are atypical in multiple ways, from the activity of HIF-α under normal oxygen tensions and without its partner HIF-β to the ligand-independent activity of Notch, and serve as a challenge to identify other noncanonical uses of well-studied signaling pathways.