Miracle-dz/UniFAR-FTUs huggingface dataset:
Properties of genetically-encoded indicators used for cytosolic and organellar Ca 2+ measurements

For the last 15 years, there has been an explosion in the development of genetically-encoded biosensors that report enzyme activity, chemical transformation, or concentration of ions and molecules in living cells. Now, there are well over 120 biosensors of different cellular targets. As a general design principle, these sensors convert a molecular event, such as the binding of a molecule to a sensing domain or a signal-induced change in protein conformation, into a change in the sensors’ fluorescence properties. In contrast to small-molecule sensors, genetically-encoded sensors are generated as cells, tissues, or organisms translate sensor-encoding nucleic acid sequences, which have been introduced by transgenic technologies. One of the best developed classes of biosensors is that of genetically-encoded Ca 2+ indicators (GECIs). Here, we briefly summarize the properties of ratiometric GECIs that permit them to be used to quantify Ca 2+ in specific cellular locations, such as the cytosol, nucleus, endoplasmic reticulum, and mitochondria. We also provide two protocols that describe in detail how to carry out such quantitative measurements in cultured mammalian cells.
Miniaturized filtering SIW power divider with arbitrary power-dividing ratio loaded by open complementary split-ring resonators

A miniaturized substrate-integrated waveguide (SIW) power divider with embedded filter response and arbitrary power-dividing ratio loaded by open complementary split-ring resonators (OCSRRs) is presented. In the proposed power divider, the miniaturization and filtering response are realized by a pair of OCSRRs, which are etched on the metal cover of the SIW structure. The design procedure indicates that the power division ratio can be adjusted by changing the locations of the output ports. In this study, three miniaturized filtering SIW power dividers with different power division ratios (1:1, 1:4, and 1:8) are implemented to evaluate the performance of the proposed structure on the size reduction. These power dividers (1:1, 1:4, and 1:8) have the overall sizes of 0. 31λg × 0. 14λg, 0. 25λg × 0. 17λg, and 0. 25λg × 0. 18λg, respectively. The measured results also agree well with the simulated results.
POLKADOTS Are Foci of Functional Interactions in T-Cell Receptor–mediated Signaling to NF- (cid:1) B □ D □ V

Stimulation of the T-cell receptor (TCR) results in the activation of several transcription factors, including NF- (cid:1) B, that are crucial for T-cell proliferation and gain of effector functions. On TCR engagement, several proteins within the TCR- directed NF- (cid:1) B signaling pathway undergo dynamic spatial redistribution, but the signiﬁcance of these redistribution events is largely unknown. We have previously described TCR-induced cytoplasmic structures called POLKADOTS (punctate and oligomeric killing or activating domains transducing signals) that are enriched in the NF- (cid:1) B signaling intermediate, Bcl10. We now show that these structures are formed only under conditions that promote efﬁcient NF- (cid:1) B activation. Furthermore, POLKADOTS formation is dependent on functional domains of speciﬁc NF- (cid:1) B signal transducers. Through use of a photoactivatable GFP, we demonstrate that POLKADOTS contain both a highly stable and a rapidly equilibrating protein component. FRET analyses show that POLKADOTS are sites of enriched interactions between Bcl10 and partner signaling proteins. These observations strongly suggest that POLKADOTS are focal sites of dynamic information exchange between cytosolic intermediates in the process of TCR activation of NF- (cid:1) B. bleaching. Confocal images were taken at on Zeiss Pascal LSM Zeiss AIM multitrack NY). Images were obtained with a (cid:2) Plan-Neoﬂuar 1.3 NA objective or a (cid:2) Plan-Apochromat 1.4 NA objective. CFP was imaged using the 405-nm line of a diode with a excitation ﬁlter, a 515-nm dichroic and a 470–500-nm emis- sion ﬁlter. YFP was imaged using the 514-nm line of an argon ion laser with a 458/514 nm excitation ﬁlter, a 515-nm dichroic and a 530–600 nm emission ﬁlter. Alexa-555 was imaged using the 543-nm line of a (Lasos) with a 405/488/543-nm excitation ﬁlter, a 515-nm dichroic and a 470–500-nm emission ﬁlter. CellTrace Bodipy methyl ester was imaged using the 543 line of a with a excitation ﬁlter, a 515-nm dichroic and a 590-nm long pass emission ﬁlter. For live cell cells were imaged in red–free 10% fetal bovine and 25 pH 7.2. were plated chamber IL) coated with poly- d -lysine, and imaging was performed with stage and objective heaters maintained at a constant temperature of
Short Communication In Vivo Expression of Major Histocompatibility Complex Molecules on Oligodendrocytes and Neurons during Viral Infection

Demyelination in multiple sclerosis and in animal models is associated with infiltrating CD8 (cid:1) and CD4 (cid:1) T cells. Although oligodendrocytes and axons are damaged in these diseases, the roles T cells play in the demyelination process are not completely understood. Antigen-specific CD8 (cid:1) T cell lysis of target cells is dependent on interactions between the T cell receptor and major histocompatibility complex (MHC) class I-peptide complexes on the target cell. In the normal central nervous system, expression of MHC molecules is very low but often increases during inflammation. We set out to precisely define which central nervous system cells express MHC molecules in vivo during infection with a strain of murine hepatitis virus that causes a chronic, inflammatory demyeli-nating disease. Using double immunofluorescence labeling, we show that during acute infection with murine hepatitis virus, MHC class I is expressed in vivo by oligodendrocytes, neurons, microglia, and endo-thelia, and MHC class II is expressed only by microglia. These data indicate that oligodendrocytes and neurons have the potential to present antigen to T cells and thus be damaged by direct antigen-specific interactions with CD8 (cid:1) T lymphocytes. (Am J Pathol 2001, 159:1219–1224) Cell associated with a local inflammatory response within system occurs many neurological multiple sclerosis progressive multifocal express inter-act cells,
Mitochondrial ND-I Mutation in Leber Hereditary Optic Neuropathy

and novel "\'835-bp fragments from normal and abnormal PrP alleles are shown, as are the two larger heteroduplex fragments. The "-'835-bp fragments represent homoduplex PCR amplification products from the PrP alleles containing "-20-30 bp interstitial deletions, while the two larger heteroduplex fragments represent hybrid DNA molecules formed by the annealing of corresponding coding and anticoding segments derived from the normal (860-bp) and partially deleted ("-'835-bp) PrP alleles. The migration of the heteroduplex molecules is slowed by confirmational changes imposed by the presence of unpaired bases from the normal allele, which correspond to the deleted bases in the abnormal allele. No samples analyzed were homozygous for the deletion. Further, prior to DNA sequence analysis, we used DASH to rapidly determine whether the deleted alleles in controls were identical to that of the proband; equal amounts of PrP PCR products from each heterozygous control were mixed with those of the proband, were denatured at 950C for 10 min, were reannealed at room temperature for 30 min, and were subjected to gel electrophoresis (fig. 2). The formation of only two heteroduplex bands (fig. 2, lanes 1-4 and 6) suggests that the DNA of both individuals may have the same deletion. In contrast, the formation of four heteroduplex bands (fig. 2, lane 5) formed by the four possible combinations of coding and anticoding strands indicates that there are allelic differences between the deletions occurring in the PCR products of the heterozygous proband and those in the control. In summary, our findings of PrP interstitial gene deletions suggest that the 24-bp deletion, identified in our FCJD patient as well as in the recently cloned PrP gene and, most likely, in the uncharacterized "-'20-bp deletion reported in a Moroccan family with no his-
Linearization of vector fields on the orbit space of the action of a compact Lie group

In this paper we present results which relate the linearization of a G-equivariant vector field at an equilibrium to the linearization of the vector field obtained by projection on the orbit space of the group action. This allows us to propose a notion of hyperbolicity for an equilibrium of the projected vector field which is compatible with the orbit space structure. It provides an alternative to the notion of normal hyperbolicity for relative equilibria (flow invariant group orbits) developed by Field [9, 10].
Long-Term Oral Treatment with Non-Hypoglycemic Dose of Glibenclamide Reduces Diabetic Retinopathy Damage in the Goto-KakizakiRat Model

Diabetic retinopathy (DR) remains a major cause of vision loss, due to macular edema, retinal ischemia and death of retinal neurons. We previously demonstrated that acute administration of glibenclamide into the vitreous, or given orally at a non-hypoglycemic dose, protected the structure and the function of the retina in three animal models that each mimic aspects of diabetic retinopathy in humans. In this pilot study, we investigated whether one year of chronic oral glibenclamide, in a non-hypoglycemic regimen (Amglidia®, 0.4 mg/kg, Ammtek/Nordic Pharma, 5 d/week), could alleviate the retinopathy that develops in the Goto-Kakizaki (GK) rat. In vivo, retinal function was assessed by electroretinography (ERG), retinal thickness by optical coherence tomography (OCT) and retinal perfusion by fluorescein and indocyanin green angiographies. The integrity of the retinal pigment epithelium (RPE) that constitutes the outer retinal barrier was evaluated by quantitative analysis of the RPE morphology on flat-mounted fundus ex vivo. Oral glibenclamide did not significantly reduce the Hb1Ac levels but still improved retinal function, as witnessed by the reduction in scotopic implicit times, limited diabetes-induced neuroretinal thickening and the extension of ischemic areas, and it improved the capillary coverage. These results indicate that low doses of oral glibenclamide could still be beneficial for the prevention of type 2 diabetic retinopathy. Whether the retinas ofpatients treated specifically with glibenclamideare less at risk of developing diabetic complications remains to be demonstrated.
Insider threats and Insider Intrusion Detection

this survey paper narrates insider threats and their detection types and methods. Insider threats are emerging nowadays, it is important to identify these threats as they are generating critical problems to the system. This paper pays particular attention to the categories of threats and different types of detection methods. Based on different strategies, statistical and machine learning methods for detecting these threats, are identified and summarized here.
Site-directed mutagenesis of dicarboxylic acids near the active site of Bacillus cereus 5/B/6 f-lactamase II

An amino acid residue functioning as a general base has been proposed to assist in the hydrolysis of /8-lactam antibiotics by the zinc-containing Bacillus cereus fl-lactamase II [Bicknell & Waley (1985) Biochemistry 24, 6876-6887]. Oligonucleotide-directed mutagenesis of cloned Bacillus cereus 5/B/6 fl-lactamase II was used in an 'in vivo' study to investigate the role of carboxy-group-containing amino acids near the active site of the enzyme. Substitution ofasparagine for the wild-type aspartic acid residue at position 81 resulted in fully functional enzyme. An aspartic acid residue at position 90 is essential for ,J-lactamase II to confer any detectable ampicillin and cephalosporin C resistance to Escherichia coli. Conversion of Asp90 into Asn90 or Glul* lead to the synthesis of inactive enzyme, suggesting that the spatial position of the fl-carboxy group of Asp" is critical for enzyme function.
The Heartmate Risk Score Predicts Morbidity and Mortality in Unselected LVAD Recipients and Risk Stratifies INTERMACS Class 1 Patients

Objectives— Evaluation of the Heartmate Risk Score and of its potential benefits in clinical practice. Background— The Heartmate Risk Score (HMRS) has been shown to correlate with mortality in the cohort of patients enrolled in the Heartmate II trials but its validity in unselected, “real world” populations remains unclear. Methods— We identified a cohort of 269 consecutive patients who received a Heartmate II left ventricular assist device at our institution between June 2005 and June 2013. 90-day and two year mortality rates as well as frequency of several morbid events were compared by retrospectively assigned HMRS category groups. The analysis was repeated within the subgroup of INTERMACS class 1 patients. Results— Receiver Operating Curve (ROC) analysis showed that the HMRS correlated with 90-day mortality with an AUC of 0.70. Stratification in low, mid and high HMRS groups identified patients with increasing hazard of 90-day mortality, increasing long term mortality, increasing rate of GI bleeding events and increasing median number of days spent in the hospital in the first year post implant. Within INTERMACS class 1 patients, those in the highest HMRS group were found to have a relative risk of 90-day mortality 5.7 times higher than those in the lowest HMRS group (39.1% vs 6.9%, p=0.029). Conclusions— HMRS is a valid clinical tool to stratify risk of morbidity and mortality after implant of Heartmate II devices in unselected patients and can be used to predict short term mortality risk in INTERMACS class 1 patients. evaluated with a Poisson regression model having the log follow-up years as offset and scaled to account for over-dispersion. Pair-wise comparisons among HMRS categories were conducted through the model and Tukey’s method for multiple comparison tests was used to adjust p-values. Kaplan-Meier survival curves were developed by HMRS category to evaluate long-term (2 year) survival. The log-rank test was used to assess differences between curves. The results from a logistic model including only HMRS were compared to a model including HMRS, history of CAD, and vasopressors to evaluate the ability to improve upon HMRS as a predictor of 90-day mortality. The impact of these additional variables to the HMRS was evaluated by comparing the change in the c-statistic and calculating the category-free Net Reclassification Improvement (category-free NRI). (11) Data analysis was performed with SAS (Cary, North Carolina) and GraphPad Prism 6 (Software MacKiev).
Visceral Adiposity in Relation to Body Adiposity and Nutritional Status in Elderly Patients with Stable Coronary Artery Disease

Introduction: The accumulation of visceral abdominal tissue (VAT) seems to be a hallmark feature of abdominal obesity and substantially contributes to metabolic abnormalities. There are numerous factors that make the body-mass index (BMI) a suboptimal measure of adiposity. The visceral adiposity index (VAI) may be considered a simple surrogate marker of visceral adipose tissue dysfunction. However, the evidence comparing general to visceral adiposity in CAD is scarce. Therefore, we have set out to investigate visceral adiposity in relation to general adiposity in patients with stable CAD. Material and methods: A total of 204 patients with stable CAD hospitalized in the Department of Medicine and the Department of Geriatrics entered the study. Based on the VAI-defined adipose tissue dysfunction (ATD) types, the study population (N = 204) was divided into four groups: (1) no ATD (N = 66), (2) mild ATD (N = 50), (3) moderate ATD (N = 48), and (4) severe ATD (N = 40). Nutritional status was assessed using the Controlling Nutritional Status (CONUT) score. Results: Patients with moderate and severe ATD were the youngest (median 67 years), yet their metabolic age was the oldest (median 80 and 84 years, respectively). CONUT scores were similar across all four study groups. The VAI had only a modest positive correlation with BMI (r = 0.59 p < 0.01) and body adiposity index (BAI) (r = 0.40 p < 0.01). There was no correlation between VAI and CONUT scores. There was high variability in the distribution of BMI-defined weight categories across all four types of ATD. A total of 75% of patients with normal nutritional status had some form of ATD, and one-third of patients with moderate or severe malnutrition did not have any ATD (p = 0.008). In contrast, 55–60% of patients with mild, moderate, or severe ATD had normal nutritional status (p = 0.008). ROC analysis demonstrated that BMI and BAI have poor predictive value in determining no ATD. Both BMI (AUC 0.78 p < 0.0001) and BAI (AUC 0.66 p = 0.003) had strong predictive value for determining severe ATD (the difference between AUC 0.12 being p = 0.0002). However, BMI predicted mild ATD and severe ATD better than BAI. Conclusions: ATD and malnutrition were common in patients with CAD. Notably, this study has shown a high rate of misclassification of visceral ATD via BMI and BAI. In addition, we demonstrated that the majority of patients with normal nutritional status had some form of ATD and as much as one-third of patients with moderate or severe malnutrition did not have any ATD. These findings have important clinical ramifications for everyday practice regarding the line between health and disease in the context of malnutrition in terms of body composition and visceral ATD, which are significant for developing an accurate definition of the standards for the intensity of clinical interventions.
Practice of Epidemiology CP * Trends: An Online Tool for Comparing Cohort and Period Trends Across Cancer Sites

Cohort or period components of trends can provide a rationale for new research or point to clues on the effective-ness of control strategies. Graphical display of trends guides models that quantify the experience of a population. In this paper, a method for smoothing rates by single year of age and year is developed and displayed to show the contributions of period and cohort to trends. The magnitude of the contribution of period and/or cohort in a model for trends may be assessed by the percentage of deviance explained and the relative contributions of cohort (C) and period (P) individually, known as the C-P score. The method is illustrated using Surveillance, Epidemiology, and End Results data (1975 – 2014) on lung and bronchial cancer mortality in females and prostate and colorectal cancer incidence in males. Smoothed age-period and age-cohort rates provide a useful ﬁ rst step in studies of etiology and the impact of disease control without imposing a restrictive model. We found that, in this data set, cohort predominates for female lung and bronchial cancer and period predominates for male prostate cancer. However, the effects change with age for male colorectal cancer incidence, indicating an age shift in relevant exposures. These methods are applied on an interactive website for both incidence and mortality at over 20 cancer sites in the United States.
Chapter 12 Plague vaccines: status and future

Three major plague pandemics caused by the Gram-negative bacterium Yersinia pestis have killed nearly 200 million people in human history. Due to its extreme virulence and the ease of its transmission, Y. pestis has been used purposefully for biowarfare in the past. Currently, plague epidemics is still breaking out sporadically most of parts of the world, including the United States. Approximately 2,000 cases of plague are reported each year to the World Health Organization. However, the potential use of the bacteria in modern times as an agent of bioterrorism and emergence of a Y. pestis strain resistant to eight antibiotics brings out severe public health concerns. Therefore, prophylactic vaccination against this disease holds the brightest prospect for its long-term prevention. Here, we summarize the progress of current vaccines development for counteracting plague.
CAUSAL INFERENCE, PATH ANALYSIS AND RECURSIVE STRUCTURAL EQUATIONS MODELS

Rubin's model for causal inference in experiments and observational studies is enlarged to analyze the problem of “causes causing causes” and is compared to path analysis and recursive structural equations models. A special quasi-experimental design, the encouragement design, is used to give concreteness to the discussion by focusing on the simplest problem that involves both direct and indirect causation. Rubin's model is shown to extend easily to this situation and to specify conditions under which the parameters of path analysis and recursive structural equations models have causal interpretations.
Superfluidité dans un gaz de fermions ultrafroids

Ce memoire de these est divise en deux parties. La premiere est consacree a l'etude de la superfluidite dans un gaz de fermions ultra-froids. En utilisant un gaz degenere de lithium 6 au voisinage d'une resonance de Feshbach nous avons obtenu un superfluide fermionique et etudie son evolution en fonction de l'energie de liaison des paires. Afin de caracteriser la transition BEC-BCS entre un condensat de Bose-Einstein de molecules et un etat BCS de paires de Cooper faiblement liees, nous avons etudie l'expansion du nuage en absence ou en presence d'interactions. Nous avons ainsi extrait la distribution en impulsion du systeme et sonde son caractere hydrodynamique. La seconde partie concerne la conception et la realisation d'un montage experimental de seconde generation. Par rapport a l'ancien dispositif, ses principaux atouts sont un gain d'un ordre de grandeur sur le nombre d'atomes pieges, un bon acces optique, une grande stabilite et reproductibilite ainsi qu'un taux de repetition cinq fois superieur. La nouvelle experience a deja permis d'atteindre le seuil de degenerescence quantique du lithium 7 avec des performances tres satisfaisantes et donne acces a la simulation de hamiltoniens de matiere condensee avec des fermions ultra-froids.
High-resolution structure of a self-assembly-competent form of a hydrophobic peptide captured in a soluble β -sheet scaffold

β -Rich self-assembly is a major structural class of polypeptides, but still little is known about their atomic structures and biophysical properties. Major impediments for structural and biophysical studies of peptide self-assemblies include their insolubility and heterogeneous composition. We have developed a model system, termed “peptide self-assembly mimic (PSAM)”, based on the single-layer β -sheet of Borrelia outer surface protein A (OspA). PSAM allows for the capture of a defined number of self-assembly-like peptide repeats within a water-soluble protein, making structural and energetics studies possible. In this work, we extend our PSAM approach to a highly hydrophobic peptide sequence. We show that a penta Ile peptide (Ile 5 ), which is insoluble and forms β -rich self-assemblies in aqueous solution, can be captured within the PSAM scaffold in a form capable of self-assembly. The 1.1-Å crystal structure revealed that the Ile 5 stretch forms a highly regular β -strand within this flat β -sheet. Self-assembly models built with multiple copies of the crystal structure of the Ile 5 peptide segment showed no steric conflicts, indicating that this conformation represents an assembly-competent form. The PSAM retained high conformational stability, suggesting that the flat β -strand of the Ile 5 stretch primed for self-assembly is a low-energy conformation of the Ile 5 stretch and rationalizing its high propensity for self-assembly. The ability of the PSAM to “solubilize” an otherwise insoluble peptide stretch suggests the potential of the PSAM approach to the characterization of self-assembling peptides.