Miracle-dz/UniFAR-FTUs huggingface dataset:
Invariant chain protects class II histocompatibility antigens from binding intact polypeptides in the endoplasmic reticulum.

Unlike class I histocompatibility (MHC) antigens, most newly synthesized MHC class II molecules fail to be loaded with peptides in the endoplasmic reticulum (ER), binding instead to the invariant chain glycoprotein (Ii). Ii blocks the class II peptide binding groove until the class II:Ii complexes are transported to endosomes where Ii is removed by proteolysis, thus permitting loading with endosomal short peptides (approximately 12–25 amino acids). Ligands from which the groove is protected by Ii have not yet been identified; theoretically they could be short peptides or longer polypeptides (or both), because the class II groove is open at both ends. Here we show that in Ii‐ deficient cells, but not in cells expressing large amounts of Ii, a substantial fraction of class II alpha beta dimers forms specific, SDS‐resistant 1:1 complexes with a variety of polypeptides. Different sets of polypeptides bound to H‐2Ak, Ek, Ed and HLA‐DR1 class II molecules; for Ak, a major species of Mr 50 kDa (p50) and further distinct 20 and 130 kDa polypeptides were detectable. Class II binding of p50 was characterized in detail. Point mutations within the Ak antigen binding groove destabilized the p50:class II complexes; a mutation outside the groove had no effect. A short segment of p50 was sufficient for association with Ak. The p50 polypeptide was synthesized endogenously, bound to Ak in a pre‐Golgi compartment, and was transported to the cell surface in association with Ak. Thus, Ii protects the class II groove from binding endogenous, possibly misfolded polypeptides in the ER. The possibility is discussed that polypeptide binding is an ancestral function of the MHC antigen binding domain.
Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli.

INTRODUCTION. 61 PROCESSING OF DAMAGED DNA . 61 SOS REGULATORY NETWORK . 61 Present Model for SOS Regulation . 62 SOS Responses . 62 Development of the Model for SOS Regulation . 64 Genetic studies of recA and lexA . 6.4i. 64 Deduction of the essential elements of SOS regulation . 65 Identification of genes in the SOS network. 66 Biochemical studies of SOS regulation. 67 SOS-Inducing Signal . 67 Central role of RecA activation . 67 Agents and treatments which cause SOS induction . 68 Indirect induction.6. 68 Role of DNA replication . 68 Involvement of small molecules . 68 Role of single-strand DNA-binding protein . 69 Fine Tuning in the Induction of the SOS System . 69 Intermediate states of induction.69 Factors influencing the extent of SOS induction . 70 Strategies for modulating individual genes within the SOS network. 70 INDUCTION OF HEAT SHOCK GENES BY DNA-DAMAGING AGENTS . 71 ADAPTIVE RESPONSE TO METHYLATING AND ETHYLATING AGENTS . 71 Biochemistry of the Adaptive Response . 72 06-Alkylguanine-DNA alkyltransferase . 72 3-Methyladenine-DNA glycosylase II. 72 Regulation of the Adaptive Network . 72 Effect of the Adaptive Response on Mutagenesis. 72 Comparison of the SOS, Heat Shock, and Adaptive Regulatory Systems . 73 ROLE OF SOS PROCESSING IN MUTAGENESIS . 73 Mutagenesis by UV and Most Chemicals Is Not a Passive Process . 73 Weigle reactivation and Weigle mutagenesis . 73 Bacterial mutagenesis . 74 Significance of umuD and umuC Mutations . 74 Isolation of umuD and umuC mutations. 75 Identification of the umuD and umuC gene products . 75 umuD and umuC Analogs on Naturally Occurring Plasmids . 75 pKM101 . 75 Relationship of pKM101-mediated processes to cellular gene functions . 76 mucA and mucB genes of pKM101 are analogs of umuD and umuC . 76 Distribution of umuDC functions in other bacteria . 76 A Second Requirement for the RecA Protein in Mutagenesis . 77 Effect of the recA430 mutation on mutagenesis . 77 Evidence suggesting that UV mutagenesis does not require the induction of genes other than those repressed by LexA . 77 Other evidence.77 Targeting of UV and Chemical Mutagenesis . 78 Most UV and chemical mutagenesis is targeted . 78 Hotspots . 78 Concept of HFOs and LFOs . 79 (i) HFOs . 79 (ii) LFOs . 79 Consequences of SOS Processing of DNA Not Damaged by Exogenous Agents . 79 Relationship of SOS processing to the spontaneous mutation frequency . 79 Mutagenesis of undamaged bacteriophage in SOS-induced cells which depends on SOS processing 80
Natural Language Queries in CBR Systems

Case Based Reasoning (CBR) systems reason by similarity between current unsolved problems and past solved problems. In such systems interaction between users and the reasoning module is very important to identify the specific aspects of the query problem. In this paper we describe a textual interface module included into JCOLIBRI, a Java framework to design CBR systems. To be able to "understand" the query, the module processes the text using information extraction, analysis and reasoning techniques, based on external resources like domain ontologies and other linguistic resources such as Wordnet.
YouTube pranking across cultures

Online pranking videos are common online and popular among middle-school students, teens and young adults. When we examined 200 YouTube examples of the Scary Maze Game prank, we explored the relationship between perpetrator, victim and witness, finding that while American children under age 12 were commonly featured as victims in Scary Maze Game prank videos, only rarely were German children represented as victims. U.S. videos also lingered on the pain of prank victims, even looping the emotional response of the victim to create an instant replay effect and using post-production techniques, including editing, music and title credits. As an expression of the schadenfreude that people experience when both enacting and viewing bad pranks, online pranking is a dimension of the dark side of participatory culture.
0 Spatial Effects in Dyadic Data

Political units often spatially depend in their political choices on other units. This is no less so in dyadic settings where, as in much of international relations research, the focus of the analysis is the pair or dyad of two political units. Yet, with few exceptions social scientists have analyzed contagion only in monadic datasets, consisting of individual political units. This article explicates and categorizes all possible forms of modeling spatial lags in both undirected and directed dyadic data. This enables scholars to formulate and test novel mechanisms of contagion, thus paving the way for a whole new generation of analyzing spatial dependence between dyads of political units. We illustrate the modeling flexibility gained from an understanding of the full set of specification options for spatial effects in dyadic data by an application to the diffusion of bilateral investment treaties between developed and developing countries, building and extending on a study published in this journal (Elkins et al. 2006). We find that in addition to the target country contagion modeled in the original article, there is also evidence for positive target-to-dyad and source-to-dyad contagion, whereas source country contagion seems to negatively affect the likelihood of signing a bilateral investment treaty.
Organization of Spontaneous Behaviors of Sleeping Neonates

The time intervals between spontaneous behaviors of 209 infants were tallied. The frequency distributions of time intervals between spontaneous behaviors showed that behaviors were usually spaced closely in time. However, none of the spontaneous behaviors occurred with a set interval between successive behaviors. All spontaneous behaviors conformed to a single pattern of temporal organization, regardless of the particular behaviors displayed, the infant's sex, or sleep state. The pattern approximated a systematic alternation of periods of increasing and decreasing time intervals between successive behaviors. These data conflict with Wolff's theory of neural discharge but support Wolff's hypothesis about substitution.
Genetic management of chondrodystrophy in California condors

Five out of 169 fertile California condor (Gymnogyps californianus) eggs laid in captivity have exhibited chondrodystrophy, a lethal form of dwarfism. Pedigree records indicate that this chondrodystrophy, like similar conditions in chickens, turkeys and quail, is probably inherited as an autosomal, recessive allele. We estimate that the frequency of this putative allele is about 9%. This high frequency is probably due to a founder effect. We consider three management options for the allele: ignoring it, eliminating it by selection and minimizing its phenotypic manifestation by avoiding matings between possible carriers. We recommend minimizing its phenotypic expression because an unacceptably large proportion of condors (up to 78 out of 146) would be prevented from breeding under a selection strategy designed to eliminate the allele. We predict that many captive populations will prove similar to the California condor population in that it will prove inadvisable or impractical to select against one or more deleterious alleles detected in the population.
Longitudinal analysis of phonemic clustering and switching during word-list generation in Huntington's disease.

Two characteristics of word-list generation performance are forming clusters (i.e., contiguous words from the same subcategory) and switching among them. Patients with frontal lobe pathology show reduced switching on letter-cued word generation tasks, and clustering has been associated with temporal lobe functioning. Letter-cued word generation was examined in 72 patients with Huntington's disease (HD) and 41 healthy participants of equivalent age and education. As predicted, the patients showed reduced switching but normal clustering. In addition, switching but not clustering correlated inversely with disease severity, as measured by both movement and mental status scales. Furthermore, 5-year longitudinal analysis revealed a monotonic decrease in switching over time, whereas clustering performance remained stable. Control participants performed uniformly over time on both measures. These results are consistent with a progressive reduction in cognitive flexibility attributed to disruption of frontal-subcortical circuits secondary to neostriatal pathology in HD.
Caracterización de poblaciones españolas de "Lolium rigidum" Gaud., para caracteres agro-morfológicos e isoenzimáticos

Se caracterizaron en el Centro de Investigaciones Agrarias de Mabegondo (A Coruna) entre 1996 y 1997 diez poblaciones espanolas de raygras anual (Lolium rigidum Gaud.). Se aplico un analisis de componentes principales con el fin de describir la variabilidad agro-morfologica. Las poblaciones mostraron una gran variabilidad para los caracteres agro-morfologicos e isoenzimaticos estudiados. La diversidad isoenzimatica se evaluo mediante cinco loci. Una de las poblaciones de nuestro trabajo (Pontevedra) mostro una fecha de espigado y una produccion de forraje mas tardias que el testigo empleado, al igual que una parecida abundancia de inflorescencias, lo cual parece indicar una capacidad similar de produccion de semilla y con ello de autoresiembra de la pradera. Los parametros estadisticos de genetica de poblaciones fueron mas altos que los citados en otras especies alogamas (numero medio de alelos=3,7 y heterocigosidad media esperada=0,493). La diversidad genetica se explico sobre todo por el componente intrapoblacional. La diferenciacion interpoblacional solo explico un 12% de la diversidad total. Se discute el uso de estos recursos geneticos.
Probable transfusion‐transmission of Anaplasma phagocytophilum by leukoreduced platelets

Anaplasma phagocytophilum (AP), a tick‐borne obligate intracellular bacterium, causes human granulocytic anaplasmosis (HGA) and has been implicated in seven transfusion‐transmitted (TT)‐HGA cases associated with red blood cells (RBCs). Here we report the first probable case of TT‐HGA involving leukoreduced platelets (PLTs).
The Design Theory Nexus

Managers frequently face ill-structured or "wicked" problems. Such problems are characterized by a large degree of uncertainty with respect to how the problem should be approached and how to establish and evaluate the set of alternative solutions. A design theory nexus is a set of constructs and methods that enable the construction of models that connect numerous design theories with alternative solutions. It thereby offers a unique problem-solving approach that is particularly useful for addressing ill-structured or wicked problems. For each alternative solution in a design theory nexus one or more unique criteria are established to formulate a specific design theory. We develop a general method for constructing a design theory nexus and illustrate its utility using two field studies. One develops and applies an organizational change nexus. The other develops and applies a user involvement nexus. Each is a specific instantiation of the general design theory nexus constructs. Using these illustrations, we provide examples of how to evaluate
The performance of the adaptive aggregation mechanism (AAM) in lossy wireless networks

The adaptive packet aggregation algorithm AAM has been shown to have a superior performance over the FIFO algorithm in terms of a greater average number of sub-packets assembled into an aggregate packet for a given value of average delay. Here, we will show that the AAM algorithm has a superior performance compared to the FIFO algorithm in terms of the aggregation trade-off in achieving the maximum average throughput with the minimum average delay in wireless networks as the average size of an AAM aggregate packet is larger than that of a FIFO aggregate packet. The analysis is based upon ns-3 simulation and includes operation under lossless and lossy channel conditions which includes the impact of PHY rate adaption scheme.
Neuropilin-1 interacts with integrin β1 and modulates pancreatic cancer cell growth, survival and invasion

Neuropilin-1 (Np-1) is a co-receptor for vascular endothelial growth factor-A (VEGF-A), and both are expressed at high levels in pancreatic ductal adenocarcinomas (PDACs). While VEGF-A has been implicated in tumor angiogenesis, the role of Np-1 in PDAC is less clearly defined. Accordingly, PANC-1 pancreatic cancer cells, which express relatively high levels of Np-1, were transfected with the Np-1 antisense cDNA. By comparison with sham transfected cells, Np-1 antisense expressing clones (Np-1AS) exhibited decreased anchorage independent growth, adhesion and invasiveness, and prolonged doubling times. Np-1AS were also more sensitive to the pro-apoptotic actions of ActD, as evidenced by PARP cleavage, caspase 9 activation, and annexin V staining. ActD decreased Bcl-xL and STAT5 levels in the antisense expressing cells, but not in sham-transfected cells, and did not alter STAT3, Bcl-2, phospho-AKT, AKT, Bad, Bax, or Bak levels. Immunoprecipitation followed by immunoblotting revealed that Np-1 associated with integrin β1, and integrin β1 blockade attenuated adhesion. However, Np-AS expressing clones exhibited enhanced tyrosine phosphorylated focal adhesion kinase. Thus, Np-1 confers a growth and survival advantage to PANC-1 cells, and interacts with integrin β1 to coordinate signaling events that promote cell adherence and invasiveness.
Polycystic ovary syndrome in adolescence and early adulthood

Polycystic ovaries and the associated syndrome are recognized as the most common cause of endocrine disturbances in adult women, but much less research has been performed to examine how polycystic ovary syndrome (PCOS) presents in girls and young women. Polycystic ovaries have been demonstrated in childhood, and there is evidence to show that even very young women may show symptoms and signs of the associated syndrome. Closer examination of younger populations (ˇ- 25 years of age), and in particular, studies of girls during the transition from puberty into early adulthood (adolescence), may provide new insights into the pathogenesis and natural history of polycystic ovaries and PCOS, and may indicate whether polycystic ovaries could potentially be considered as a marker for health screening. Consideration should be given to the management of girls and young women with polycystic ovaries and PCOS as this group may have different needs and health risks compared with older women.
MRI of pleural diseases

Purpose of review Imaging plays an important role in the diagnosis and optimal treatment of patients with pleural diseases. MRI is a noninvasive imaging modality, which is not commonly used as first-line investigation in this field, but is often called upon to solve specific dilemmas. In this review, the basic methodology of MRI and its usefulness in pleural diseases will be explored. Recent findings Recent advances in MRI technology have allowed the application of novel sequences, not only for anatomical but also for functional imaging. Improvement was mainly achieved by means of diffusion-weighted and dynamic contrast-enhanced MRI. These sequences can be used not only for detection, but also for characterization of pleural lesions. Even detection of pleural tumor recurrence and treatment response monitoring is possible. Summary The use of conventional and functional MR sequences has led to improvements in the detection and characterization of pleural diseases. This technique, whether or not in combination with SPECT and PET (so called multimodality approach), could be an added value in the near future.
Multiple Propionyl Coenzyme A-Supplying Pathways for Production of the Bioplastic Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) in Haloferax mediterranei

ABSTRACT Haloferax mediterranei is able to accumulate the bioplastic poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) with more than 10 mol% 3-hydroxyvalerate (3HV) from unrelated carbon sources. However, the pathways that produce propionyl coenzyme A (propionyl-CoA), an important precursor of 3HV monomer, have not yet been determined. Bioinformatic analysis of H. mediterranei genome indicated that this strain uses multiple pathways for propionyl-CoA biosynthesis, including the citramalate/2-oxobutyrate pathway, the aspartate/2-oxobutyrate pathway, the methylmalonyl-CoA pathway, and a novel 3-hydroxypropionate pathway. Cofeeding of pathway intermediates and inactivating pathway-specific genes supported that these four pathways were indeed involved in the biosynthesis of 3HV monomer. The novel 3-hydroxypropionate pathway that couples CO2 assimilation with PHBV biosynthesis was further confirmed by analysis of 13C positional enrichment in 3HV. Notably, 13C metabolic flux analysis showed that the citramalate/2-oxobutyrate pathway (53.0% flux) and the 3-hydroxypropionate pathway (30.6% flux) were the two main generators of propionyl-CoA from glucose. In addition, genetic perturbation on the transcriptome of the ΔphaEC mutant (deficient in PHBV accumulation) revealed that a considerable number of genes in the four propionyl-CoA synthetic pathways were significantly downregulated. We determined for the first time four propionyl-CoA-supplying pathways for PHBV production in haloarchaea, particularly including a new 3-hydroxypropionate pathway. These results would provide novel strategies for the production of PHBV with controllable 3HV molar fraction.
Effects of ecdysterone on the deposition of cockroach cuticle in vitro.

Quantitative studies were made of the stimulation of cuticular deposition in cockroach leg regenerates in vitro by the molting hormone ecdysterone. Preliminary experiments showed that the hormone remained active and that the tissues remained sensitive in vitro for as long as 30 days. Large doses given one week apart resulted in the production of multiple cuticles, but small doses given at shorter intervals gave a single, cumulative response. Time-dosage studies showed that the concentration of the hormone and the length of exposure make roughly equal contributions to the effect of the dose.
A geometrical study on voltage collapse mechanisms of power systems

In this paper, the mechanism of voltage collapse is studied based on a nonlinear model and transversality theory, and a unified explanation of the phenomena of voltage collapse is given. The research shows that the fundamental reason for voltage collapse is due to the non-transversal intersection between solution manifolds of the injection branch equations in the voltage-current space. It is also proved that this non-transversal intersection exactly corresponds to the static state bifurcation point. These conclusions are valid no matter differential algebraic equations or power flow equations being employed.
Characterization of a serum response factor-like protein in Saccharomyces cerevisiae, Rlm1, which has transcriptional activity regulated by the Mpk1 (Slt2) mitogen-activated protein kinase pathway

The Mpk1 (Slt2) mitogen-activated protein (MAP) kinase has been implicated in several biological processes in Saccharomyces cerevisiae. The Rlm1 protein, a member of the MADS box family of transcription factors, functions downstream of Mpk1 in the pathway. To characterize the role of Rlm1 in mediating the transcriptional activation by the Mpk1 pathway, we constructed a LexA-Rlm1 deltaN chimera in which sequences, including the MADS box domain of the Rlm1 protein, were replaced by the LexA DNA binding domain and tested the ability of this chimera to activate a LexA operator-controlled reporter gene. In this assay, the Rlm1 protein was found to activate transcription in a manner regulated by the Mpk1 pathway. The Mpk1 protein kinase phosphorylated Rlm1 deltaN in vitro and the LexA-Rlm1 deltaN chimera protein was phosphorylated in vivo in a Mpk1-dependent manner. These results suggest that Mpk1 regulates the transcriptional activity of Rlm1 by directly phosphorylating it. We identified a Mpk1-like protein kinase, Mlp1, as an Rlm1-associated protein by using the yeast two-hybrid system. Overexpression of MLP1 suppresses the caffeine-sensitive phenotype of the bck1 delta mutation. The additivity of the mlp1 delta defect with the Mpk1 delta defect with regard to the caffeine sensitivity, combined with the results of genetic epistasis experiments, suggested that the activity of Rlm1 is regulated independently by Mpk1 MAP kinase and the Mlp1 MAP kinase-like kinase.
Sphingosine kinases are not required for inflammatory responses in macrophages.

Background: Sphingosine kinases (Sphk) were proposed to be essential for inflammatory responses. Results: Robust inflammatory responses were seen in macrophages that lack However, intracellular sphingolipids and autophagic vesicles were induced. Conclusions: Sphingosine kinases are not required for
On the usage and measurement of landscape connectivity

This paper examines the usage and measurement of “landscape connectivity” in 33 recent studies. Connectivity is defined as the degree to which a landscape facilitates or impedes movement of organisms among resource patches. However, connectivity is actually used in a variety of ways in the literature. This has led to confusion and lack of clarity related to (1) function vs structure, (2) patch isolation vs landscape connectivity and, (3) corridors vs connectivity. We suggest the term connectivity should be reserved for its original purpose. We highlight nine studies; these include modeling studies that actually measured connectivity in accordance with the definition, and empirical studies that measured key components of connectivity. We found that measurements of connectivity provide results that can be interpreted as recommending habitat fragmentation to enhance landscape connectivity. We discuss reasons for this misleading conclusion, and suggest a new way of quantifying connectivity, which avoids this problem. We also recommend a method for reducing sampling intensity in landscape-scale empirical studies of connectivity.