Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Behavior of Salmonella-Induced Membrane Tubules in Epithelial Cells

Salmonella Typhimurium is a facultative intracellular pathogen that causes acute gastroenteritis in man. Intracellular Salmonella survive and replicate within a modified phagosome known as the Salmonella‐containing vacuole (SCV). The onset of intracellular replication is accompanied by the appearance of membrane tubules, called Salmonella‐induced filaments (Sifs), extending from the SCV. Sifs are enriched in late endosomal/lysosomal membrane proteins such as lysosome‐associated membrane protein 1, but their formation and ability to interact with endosomal compartments are not characterized. In this study, we use live cell imaging techniques to define the dynamics of Sif formation in infected epithelial cells. At early time‐points, Sifs are simple tubules extending from the surface of SCVs. These tubules are highly dynamic and exhibit bidirectional, microtubule‐dependent movement. At the distal ends of individual Sif tubules, furthest from the SCV, a distinct ‘leader’ domain was often observed. At later times, Sifs develop into highly complex tubular networks that extend throughout the cell and appear less dynamic than nascent Sifs; however, individual tubules continue to display bidirectional dynamics. Sifs can acquire endocytic content by fusion, indicating a sustained interaction with the endocytic pathway. Together, these results show that these Salmonella‐induced tubules form a highly dynamic network that involves both microtubule‐dependent motility and interactions with endosomal compartments.
Characterizing Process Variation in Nanometer CMOS

The correlation of a statistical analysis tool to hardware depends on the accuracy of underlying variation models. The models should represent actual process behavior as measured in silicon. In this paper, we present an overview of test structures for characterizing statistical variation of process parameters. We discuss the test structure design and characterization strategy for calibrating random and layout dependent systematic components of process variation. We also show measurement results from several fabricated structures in 65-nm CMOS technologies.
The Xenopus Amygdala Mediates Socially Appropriate Vocal Communication Signals

Social interaction requires that relevant sensory information is collected, classified, and distributed to the motor areas that initiate an appropriate behavioral response. Vocal exchanges, in particular, depend on linking auditory processing to an appropriate motor expression. Because of its role in integrating sensory information for the purpose of action selection, the amygdala has been implicated in social behavior in many mammalian species. Here, we show that two nuclei of the extended amygdala play essential roles in vocal communication in the African clawed frog, Xenopus laevis. Transport of fluorescent dextran amines identifies the X. laevis central amygdala (CeA) as a target for ascending auditory information from the central thalamic nucleus and as a major afferent to the vocal pattern generator of the hindbrain. In the isolated (ex vivo) brain, electrical stimulation of the CeA, or the neighboring bed nucleus of the stria terminalis (BNST), initiates bouts of fictive calling. In vivo, lesioning the CeA of males disrupts the production of appropriate vocal responses to females and to broadcasts of female calls. Lesioning the BNST in males produces an overall decrease in calling behavior. Together, these results suggest that the anuran CeA evaluates the valence of acoustic cues and initiates socially appropriate vocal responses to communication signals, whereas the BNST plays a role in the initiation of vocalizations.
API Usage Change Rules Mining based on Fine-grained Call Dependency Analysis

Software frameworks are widely used in application development. But APIs of a framework may change when it evolves to accommodate new feature requests or to fix bugs. Those changes may break existing client programs of the framework, so client programs need to be migrated to the updated release when the framework evolves. Some technologies (e.g. call dependency analysis) have been proposed to find replacement APIs between the old and new framework releases. However, existing approaches based on call dependency analysis take whole method body as an analysis unit. The context in which a method is called is ignored. In this paper, we present a fine-grained approach named AUC-Miner to infer API usage change rules between two releases of the framework. To take method invocation context into consideration, we propose an approach to get more precise call relationship changes by code splitting. We also analyze indirect method invocations to re-fine call dependency analysis. After elaborating API usage change transactions, we adopt frequent item-set mining to generate API replacement rules. Text similarity and some heuristics to identify evolution of root methods are also applied in the mining progress. The evaluation of AUC-Miner on three popular frameworks shows that its precision is higher than basic call dependency analysis and another API replacement recommendation tool named AURA.
GRP78 Protein Expression in Ovarian Cancer Patients and Perspectives for a Drug-Targeting Approach

Glucose-regulated protein of 78 kD (GRP78) is a chaperone protein mainly located in the endoplasmic reticulum (ER). This protein is normally present at low levels in adult cells but its expression is triggered by ER stress including glucose deprivation and hypoxia. In tumor cells, it is overexpressed with fraction of protein found at the cell surface. This paper presents the physiology of GRP78 in the context of ovarian cancer and its potential use as drug delivery systems targeting ovarian cancer cell.
Gene regulatory factors in pancreatic development

The intensity of research on pancreatic development has increased markedly in the past 5 years, primarily for two reasons: we now know that the insulin‐producing β‐cells normally arise from an endodermally derived, pancreas‐specified precursor cell, and successful transplants of islet cells have been performed, relieving patients with type I diabetes of symptoms for extended periods after transplantation. Combining in vitro β‐cell formation from a pancreatic biopsy of a diabetic patient or from other stem‐cell sources followed by endocrine cell transplantation may be the most beneficial route for a future diabetes therapy. However, to achieve this, a thorough understanding of the genetic components regulating the development of β‐cells is required. The following review discusses our current understanding of the transcription factor networks necessary for pancreatic development and how several genetic interactions coming into play at the earliest stages of endodermal development gradually help to build the pancreatic organ. Developmental Dynamics 229:176–200, 2004. © 2003 Wiley‐Liss, Inc.
Understanding the Technology and Organizational Elements of Customer Relationship Management Systems

To build a clear understanding of the management of the technology and organizational elements of CRM systems, this research tries to form propositions based on literature findings and experts’ experiences to explain (1) the elements of the technology and organizational sides of a CRM system, and (2) how the technology and organizational elements interrelate to create effective CRM operation. The goal is to build in-depth knowledge of the dynamics of CRM systems and to suggest lasting organizational capabilities that are adaptive to environmental changes. Adopting the socio-technical view, the technology and organizational elements of CRM are closely interrelated in the operation of a business. The technology elements of an enterprise-wide CRM system can be organized into three parts: communicational CRM that coordinates all channels of customer contacts, execution CRM that consists of all value chain activities that execute customer relationship establishment and maintenance, and intelligent CRM that consolidates business intelligence about customers. The three interrelated elements provide a technical structure for customer value-generation activities. While the organizational resources including structure, processes, culture, and user abilities are elements that need to be aligned and coordinated with CRM technologies. Management of a CRM system, therefore, can be considered as managing an organism that requires interdependent elements to work together to maintain a continuous capability of creating and sustaining customer relationships.
Validation of self-reported periodontal measures among health professionals.

OBJECTIVE The objective of this study was to determine the validity of self-reported periodontal measures among nondentist health professionals. Valid self-reported measures could provide a time- and cost-efficient alternative for large epidemiologic studies. METHODS A subsample of 212 male nondentists sampled on the basis of their reported periodontal severity from the Health Professional Follow-up Study (HPFS) provided dental radiographs and completed questionnaires assessing self-reported oral health. Alveolar bone loss was evaluated from the radiographs at 32 posterior sites and used as the standard measure of cumulative periodontal disease. RESULTS The self-reported ordinal periodontal measure had a linear relationship with mean radiographic bone loss (r = .61). The positive and negative predictive values of the dichotomized self-reported periodontal measures were 83 percent and 69 percent. Self-reported history of periodontal surgery was also a good surrogate for bone loss (predictive value positive 78 percent and negative 71 percent). CONCLUSIONS Self-reports can provide discrimination and ranking information of cumulative periodontal disease among health professionals and can be used to provide valid results in etiologic studies in health professionals' populations.
Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages

Comparative phage genomics can retrace part of the evolutionary history of phage modules encoding phage‐specific functions such as capsid building or establishment of the lysogenic state. The diagnosis of relatedness is not based exclusively on sequence similarity, but includes topological considerations of genome organization. The gene maps from the λ‐, ψM2‐, L5‐, Sfi21‐, Sfi11‐, φC31‐, sk1‐ and TM4‐like phages showed a remarkable synteny of their structural genes defining a λ supergroup within Siphoviridae (Caudovirales with long non‐contractile tails). A hierarchy of relatedness within the λ supergroup suggested elements of vertical evolution in the capsid module of Siphoviridae. Links to P22‐like Podoviridae and P2‐like Myoviridae were also detected. Numerous cases of horizontal gene transfer were observed, but recent transfers were limited to interbreeding phage populations. We suggest that tailed phages are the result of both vertical and horizontal evolution and are thus a good model system for web‐like phylogenies.
Molecular cloning and sequence of the thdF gene, which is involved in thiophene and furan oxidation by Escherichia coli

Our previous work resulted in the isolation of mutant strains of Escherichia coli K-12 which were able to oxidize furans and thiophenes as a result of mutations in several novel genes. Some of the genes involved in thiophene oxidation were cloned into the multicopy vector pUC19. The plasmid pKA10 carries a 3.8-kb chromosomal fragment which encodes a previously undiscovered gene involved in thiophene oxidation. Three proteins with approximate molecular sizes of 48, 30, and 26 kDa were overproduced by cells carrying pKA10. Maxicell experiments and DNA sequence analysis indicated that the 48- and 26-kDa proteins are encoded by pKA10, whereas the 30-kDa protein is apparently chromosomally derived. A cassette specifying kanamycin resistance was inserted into various sites on pKA10. An insertion which abolished the 48-kDa protein also abolished thiophene oxidation. Chromosomal integration of pKA10::Kan allowed us to locate the chromosomal insert of pKA10 at 84 min on the E. coli genetic map by transduction. Since no previously identified genes involved in thiophene metabolism are located in this region, we designated the gene for the 48-kDa protein as thdF. Sequencing of the 3.8-kb insert revealed an overlap of several hundred bases with the regulatory and structural regions of the tnaA gene, which is also located at 84 min. The 26-kDa protein is probably truncated tnaA protein. An open reading frame corresponding to the 48-kDa thdF protein was located next to the tnaA gene, which encodes tryptophanase, but was transcribed in the opposite sense.
Alphaherpesviral US3 Kinase Induces Cofilin Dephosphorylation To Reorganize the Actin Cytoskeleton

ABSTRACT The conserved alphaherpesviral serine/threonine kinase US3 causes dramatic actin rearrangements, associated with increased viral spread. Here, we show that US3 of pseudorabies virus (PRV) leads to activation (dephosphorylation) of the central actin regulator cofilin. A mutation that impairs US3 kinase activity and the group I p21-activated kinase inhibitor IPA-3 inhibited US3-mediated cofilin activation. Additionally, expression of phosphomimetic S3D cofilin significantly suppressed the ability of US3 to cause cell projections and cell rounding. In conclusion, the US3 kinase of PRV leads to activation (dephosphorylation) of cofilin, and cofilin contributes to US3-mediated actin rearrangements.
Konsekwencje doświadczanych negatywnych wydarzeń życiowych — objawy stresu pourazowego i potraumatyczny wzrost

Introduction. People experience various negative life events, which may result both negative (posttraumatic stress disorder [PTSD]) and positive (posttraumatic growth [PTG]) outcomes. Growth and distress seem to be two separate independent dimensions of the traumatic events, so they may coexist. The purpose of the study was to assess what consequences occur people who experienced negative life event and to investigate the relationship between PTSD and PTG. Materials and methods. The study group comprised of 63 cardiological patients, who experienced surgery of heart transplantation, implantation of by-pass or artificial heart valve. 58.7% were men, 41.3% women. The mean age was 51.2 (SD = 8.02). The Impact of Event Scale — Revised (IES-R) and the Posttraumatic Growth Inventory (PTGI) were used in the study. Results. All persons participating in the study experienced positive changes following trauma event; 30% on a high level. However 52% of them also revealed PTSD symptoms, which positively correlate with better relations to others, increased appreciation of life and spiritual changes. Conclusions. Revealed associations between PTSD and PTG contribute to the understanding the mechanisms of experiencing negative life events and indicate that PTG represents both coping effort coexisting with distress and outcome of coping success.
TALPID3 controls centrosome and cell polarity and the human ortholog KIAA0586 is mutated in Joubert syndrome (JBTS23)

Joubert syndrome (JBTS) is a severe recessive neurodevelopmental ciliopathy which can affect several organ systems. Mutations in known JBTS genes account for approximately half of the cases. By homozygosity mapping and whole-exome sequencing, we identified a novel locus, JBTS23, with a homozygous splice site mutation in KIAA0586 (alias TALPID3), a known lethal ciliopathy locus in model organisms. Truncating KIAA0586 mutations were identified in two additional patients with JBTS. One mutation, c.428delG (p.Arg143Lysfs*4), is unexpectedly common in the general population and may be a major contributor to JBTS. We demonstrate KIAA0586 protein localization at the basal body in human and mouse photoreceptors, as is common for JBTS proteins, and also in pericentriolar locations. We show that loss of TALPID3 (KIAA0586) function in animal models causes abnormal tissue polarity, centrosome length and orientation, and centriolar satellites. We propose that JBTS and other ciliopathies may in part result from cell polarity defects. DOI: http://dx.doi. org/10.7554/eLife.08077. 001
Resistive and reactive changes to the impedance of intracortical microelectrodes can be mitigated with polyethylene glycol under acute in vitro and in vivo settings

The reactive response of brain tissue to implantable intracortical microelectrodes is thought to negatively affect their recordable signal quality and impedance, resulting in unreliable longitudinal performance. The relationship between the progression of the reactive tissue into a glial scar and the decline in device performance is unclear. We show that exposure to a model protein solution in vitro and acute implantation result in both resistive and capacitive changes to electrode impedance, rather than purely resistive changes. We also show that applying 4000 MW polyethylene glycol (PEG) prevents impedance increases in vitro, and reduces the percent change in impedance in vivo following implantation. Our results highlight the importance of considering the contributions of non-cellular components to the decline in neural microelectrode performance, and present a proof of concept for using a simple dip-coated PEG film to modulate changes in microelectrode impedance.
How Do Market Failures Justify Interventions in Rural Credit Markets

Understanding of the economic causes and consequences of market failure in credit markets has progressed a great deal in recent years. This article draws on these developments to appraise the case for government intervention in rural financial markets in developing countries and to discover whether the theoretical findings can be used to identify directives for policy. Before debating the when and how of intervention, the article defines market failure, emphasizing the need to consider the full array of constraints that combine to make a market work imperfectly. The various reasons for market failure are discussed and set in the context in which credit markets function in developing countries. The article then looks at recurrent problems that may be cited as failures of the market justifying intervention. Among these problems are enforcement; imperfect information, especially adverse selection and moral hazard; the risk of bank runs; and the need for safeguards against the monopoly power of some lenders. The review concludes with a discussion of interventions, focusing on the learning process that must take place for financial markets to operate effectively.
EFFECT OF CREATINE PHOSPHATE SUPPLEMENTATION ON ANAEROBIC WORKING CAPACITY AND BODY WEIGHT AFTER TWO AND SIX DAYS OF LOADING IN MEN AND WOMEN

The purpose of this study was to determine the effects of 2 and 6 days of creatine phosphate loading on anaerobic working capacity (AWC) and body weight (BW) in men and women. Sixty-one men (n = 31) and women (n = 30) randomly received 1 of 3 treatments (4 3 5 g·d-1 X 6 days) using a double blind design: (a) 18 g dextrose as placebo (PL); (b) 5.0 g Cr + 20 g dextrose (Cr); or (c) 5.0 g Cr + 18 g dextrose + 4 g of sodium and potassium phosphates (CrP). AWC was determined at baseline and following 2 and 6 days of supplementation using the Critical Power Test. BW increased significantly over time, and the mean value for the men was significantly greater compared to that for women, but there were no interactions (p > 0.05). There were gender-specific responses for AWC expressed in both absolute values (kJ) and relative to BW (kJ· kg-1), with the women demonstrating no significant interactions. For the men, CrP loading significantly increased AWC following 2 days (23.8%) and 6 days (49.8%) of supplementation vs. PL (kJ and kJ·kg-1). Cr supplementation increased AWC 13–15% in both genders compared to PL (1.1%–3.0% decline); although this result was not statistically significant, it may have some practical significance.
PLGG1, a plastidic glycolate glycerate transporter, is required for photorespiration and defines a unique class of metabolite transporters

Photorespiratory carbon flux reaches up to a third of photosynthetic flux, thus contributes massively to the global carbon cycle. The pathway recycles glycolate-2-phosphate, the most abundant byproduct of RubisCO reactions. This oxygenation reaction of RubisCO and subsequent photorespiration significantly limit the biomass gains of many crop plants. Although photorespiration is a compartmentalized process with enzymatic reactions in the chloroplast, the peroxisomes, the mitochondria, and the cytosol, no transporter required for the core photorespiratory cycle has been identified at the molecular level to date. Using transcript coexpression analyses, we identified Plastidal glycolate glycerate translocator 1 (PLGG1) as a candidate core photorespiratory transporter. Related genes are encoded in the genomes of archaea, bacteria, fungi, and all Archaeplastida and have previously been associated with a function in programmed cell-death. A mutant deficient in PLGG1 shows WT-like growth only in an elevated carbon dioxide atmosphere. The mutant accumulates glycolate and glycerate, leading to the hypothesis that PLGG1 is a glycolate/glycerate transporter. This hypothesis was tested and supported by in vivo and in vitro transport assays and 18O2-metabolic flux profiling. Our results indicate that PLGG1 is the chloroplastidic glycolate/glycerate transporter, which is required for the function of the photorespiratory cycle. Identification of the PLGG1 transport function will facilitate unraveling the role of similar proteins in bacteria, archaea, and fungi in the future.
Contemporary developments in family theory.

Ordinary Urban Families, London: Tavistock Publications, 1957. Mogey, John, "The Family and Community in Urban-Industrial Societies," in Handbook of Marriage and the Family, op. cit., pp. 501-535. Sussman, Marvin and Lee Burchinal, "Kin Family Networks: Unheralded Structures in Current Conceptualizations of Family Functioning," Marriage and Family Living, 24:3 (August 1962), pp. 320-332. 5. The Family and Personality Brim, Orville G. , Jr., Education for Child Rearing, New York: Russell Sage Foundation, 1959. Bronfenbrenner, Urie, "Socialization and Social Class Through Time and Space," in Readings in Social Psychology, ed. by Eleanor Maccoby et al., New York: Holt, 1958, pp. 400-425. Clausen, John A. and Judith R. Williams, "Sociological Correlates of Child Behavior: Family Structure and Socialization Processes," Sixty-Second Yearbook of the National Society for the Study of Education, Part I, Child Psychology, 1963, Chicago: U. of Chicago Press, 1963, pp. 62-107. Dager, Edmard Z. , "Socialization and Personality Development in the Child," in Handbook of Marriage and the Family, op. cit., pp. 740-782. Lennard, Henry I. , Maurice R. Beaulieu, and Nolen G. Embrey, "Interaction in Families with a Schizophrenic Child," Archives of General Psychiatry, 12 (February 1965), pp. 166-183. Spiegel, John P. and Norman W. Bell, "The Family of the Psychiatric Patient," in The American Handbook of Psychiatry, ed. by Sylvano Arieti, New York: Norton, 1959, Vol. I, pp. 114-149. 6. The Family and Social Structure Bardis, Panos D. , "Family Forms and Variations Historically Considered," in Handbook of Marriage and the Family, op. cit., pp. 403462.
Meta-Meta is better-better!

The increasing openness and heterogeneity of distributed computing systems requires the representation of meta-information in distributed environments. Most type management systems can only define types within particular type systems. In contrast, the DSTC’s Meta-Object Facility (MOF) first defines a type system as a set of meta-meta-objects, and then defines types as meta-objects which are described by those meta-meta-objects. This approach enables the definition of many type systems in one MOF, the composition of type systems, and the federation of type systems. This paper presents a conceptual framework for discussing metainformation and the meta-meta-objects that are the foundation of the DSTC’s MetaObject Facility (MOF), which is a tool for enabling heterogeneity, extensibility and openness.