Miracle-dz/UniFAR-FTUs huggingface dataset:
Conditional Expression of RNA Polymerase II in Mammalian Cells

The carboxyl-terminal domain (CTD) of the large subunit of mammalian RNA polymerase II contains 52 repeats of a heptapeptide that is the target of a variety of kinases. The hyperphosphorylated CTD recruits important factors for mRNA capping, splicing, and 3′-processing. The role of the CTD for the transcription process in vivo, however, is not yet clear. We have conditionally expressed an α-amanitin-resistant large subunit with an almost entirely deleted CTD (LS*Δ5) in B-cells. These cells have a defect in global transcription of cellular genes in the presence of α-amanitin. Moreover, pol II harboring LS*Δ5 failed to transcribe up to the promoter-proximal pause sites in thehsp70A and c-fos gene promoters. The results indicate that the CTD is already required for steps that occur before promoter-proximal pausing and maturation of mRNA.
Type D Personality as a Prognostic Factor in Heart Disease: Assessment and Mediating Mechanisms

Type D personality, a synergy between negative affectivity and social inhibition, has established itself as a serious risk factor for morbidity and mortality in patients suffering from cardiovascular disease. In this review, we summarize studies on the validity of the assessment methods of Type D, emphasizing its role as an independent vulnerability factor in the progression of cardiovascular disease. We further present evidence on the physiological characteristics that accompany the 2 psychological traits negative affectivity and social inhibition and may mediate the relation between personality and prognosis in heart disease. Further research needs to determine the mechanisms by which Type D affects the course and outcome of cardiovascular disease as well as how Type D patients may benefit from psychosocial intervention.
Antibodies to bird serum proteins in confectionery workers exposed to egg spray

In an extended study of a group of confectionery workers sensitized by exposure to egg spray, it was found that their blood serum contained antibodies to avian serum proteins. Comparison of the ratio of IgG antibodies determined by ELISA to egg yolk ‘livetins’ and pigeon serum in these patients and in pigeon breeders showed that the phenomenon is entirely due to immunological cross‐reactivity among avian blood serum proteins. These avian serum proteins in hens' eggs, not ovalbumin, were identified as the major sensitizing antigens.
Conformational stability and thermodynamic characterization of the lipoic acid bearing domain of human mitochondrial branched chain α‐ketoacid dehydrogenase

The lipoic acid bearing domain (hbLBD) of human mitochondrial branched chain α‐ketoacid dehydrogenase (BCKD) plays important role of substrate channeling in oxidative decarboxylation of the branched chain α‐ketoacids. Recently hbLBD has been found to follow two‐step folding mechanism without detectable presence of stable or kinetic intermediates. The present study describes the conformational stability underlying the folding of this small β‐barrel domain. Thermal denaturation in presence of urea and isothermal urea denaturation titrations are used to evaluate various thermodynamic parameters defining the equilibrium unfolding. The linear extrapolation model successfully describes the two‐step; native state ↔denatured state unfolding transition of hbLBD. The average temperature of maximum stability of hbLBD is estimated as 295.6 ± 0.9 K. Cold denaturation of hbLBD is also predicted and discussed.
Pyrosequencing™ technology and the need for versatile solutions in molecular clinical research

An increasing amount of genetic information is rapidly becoming available to the practitioners of medicine and pharmacology. This knowledge promises to revolutionize the determination of diagnoses and prognoses for genetically-based disorders as well as infectious diseases and to enable tailoring of treatment to suit the individual patient. As genomics becomes ripe for clinical implementation, versatile technologies that can handle all the relevant types of analyses will be requested by many clinicians. The recently established Pyrosequencing™ technology for rapid determination of short DNA sequences has gained widespread acceptance and is being used in a broad range of applications. It can provide a solution for many emerging issues in molecular clinical research and applications, owing to its reliability and high flexibility together with its user-friendly attributes.
Autoantibodies against β1-adrenergic receptor: response to induction therapy with bortezomib-containing regimens for multiple myeloma patients

Abstract This study aims to investigate the predictive value of pre-chemotherapy β1R-AABs by evaluating the response of newly diagnosed symptomatic multiple myeloma (MM) patients to their treatment with a bortezomib-containing regimen. Forty-five de novo MM patients and 50 normal controls (NCs) were prospectively enrolled in this study. Serum titers of β1R-AABs were detected by ELISA. These 45 MM patients were divided into two groups (positive and negative groups) according to their β1R-AABs. Follow-up examinations were performed on these patients during chemotherapy induction. The final analysis covered all 45 MM patients, including 19 patients who were positive for MM and 26 patients who were negative for MM. Multivariate analysis revealed that pre-chemotherapy β1R-AABs are possibly independent predictors for less than very good partial response (VGPR) after the bortezomib-containing regimen treatment (odds ratio: 5.967, 95% confidence interval: 1.513–23.531; p = .011). This study demonstrates for the first time that the presence of β1R-AABs is associated with MM. Pre-chemotherapy β1R-AABs are independent predictors for less than VGPR in de novo MM patients after the bortezomib-containing regimen was administrated. Bortezomib might not significantly give rise to cardiac impairment in MM patients.
Factor VIII Inhibitor Antibodies with C2 Domain Specificity Are Less inhibitory to Factor VIII Complexed with von Willebrand Factor

Summary In order to clarify the potential role of von Willebrand factor (vWf) in attenuating the inactivation of factor VIII (fVIII) by those antibodies with C2 domain specificity, we investigated a panel of 14 human antibodies to fVIII. Immunoblotting analysis localized light chain (C2 domain) epitopes for four cases, heavy chain (A2 domain) epitopes in five cases, while the remaining five cases were both light and heavy chains. The inhibitor titer was considerably higher for Kogenate, a recombinant fVIII concentrate, than for Haemate P, a fVIII/vWf complex concentrate, in all inhibitor plasmas that had C2 domain specificity. In five inhibitor plasmas with A2 domain specificity and in five with both A2 and C2 domain specificities, Kogenate gave titers similar to or lower than those with Haemate P. The inhibitory effect of IgG of each inhibitor plasma was then compared with recombinant fVIII and its complex with vWf. When compared to the other 10 inhibitor IgGs, IgG concentration, which inhibited 50% of fVIII activity (IC50), was remarkably higher for the fVIII/vWf complex than for fVIII in all the inhibitor IgGs that had C2 domain reactivity. Competition of inhibitor IgG and vWf for fVIII binding was observed in an ELISA system. In 10 inhibitors that had C2 domain reactivity, the dose dependent inhibition of fVIII-vWf complex formation was observed, while, in the group of inhibitors with A2 domain specificity, there was no inhibition of the complex formation except one case. We conclude that a subset of fVIII inhibitors, those that bind to C2 domain determinants, are less inhibitory to fVIII when it is complexed with vWf that binds to overlapping region in the C2 domain.
A self‐report Insight Scale for psychosis: reliability, validity and sensitivity to change

Lack of insight is a frequent concomitant of psychosis and has traditionally been viewed as a binary, all or none phenomenon. Recent conceptualization has formulated insight as a continuum representing the juxtaposition of 3 factors – awareness of illness, need for treatment and attribution of symptoms. Measurement of insight has been exclusively based on interview; this method does not easily lend itself to frequent repeated measurement and requires interrater reliability to be established. A self‐report Insight Scale is presented, and evidence in support of its reliability, validity and sensitivity is provided that includes a sample of 30 patients monitored during recovery from an acute psychosis. The scale is a quick and acceptable measure that may find application in investigations of acute care, cognitive therapy of psychotic symptoms and as a method of augmenting clinical judgements of insight.
Interactions between Infections, Malnutrition and Ironnutritional Status in Pakistani Infants A Longitudinal Study

The interactions between infections, malnutrition and poor iron nutritional status in infants at weaning ages are poorly defined. Therefore, four groups of infants from an area with a high incidence of malnutrition (Lahore, Pakistan) were enrolled in a prospective, randomized nutritional intervention study. Between 122 and 365 days of age, the infants from one community received either a milk cereal without iron fortification (n= 29), a milk cereal fortified with ferrous fumarate (7.5 mg/100 g; n= 30), or a milk cereal fortified with ferric‐pyrophosphate (7.5 mg/100 g; n= 27). Forty‐four infants from a neighbouring community did not receive a nutritional supplement and served as the control group. Calculated mean daily energy‐ and protein intake with the cereals was between 259–287 kcal, and 9.6–10.6 g at 12 months of age, respectively. Mean daily iron intake with the fortified cereals was between 4.1–5.1 mg at corresponding age. Nutritional supplementation resulted in significantly lower incidence of malnutrition and heigher weight gain. Incidence of acute diarrhoea was significantly (p<0.05) lower in the supplemented groups. The infants fed the iron‐fortified milk cereals had significantly higher hemoglobin (mean 10.4 vs. 9.8 gdl‐1) and serum ferritin (mean 13.3 vs. 8.5 ngml‐1) values than the infants fed the non‐fortified milk cereals. However, no differences in the incidence of infections were found between the supplemented groups. It is concluded that poor nutritional intake between 122 and 365 days of age substantially contributed to the high incidence of diarrhoea and malnutrition in Pakistani infants.
Risk Ranking for Foodborne Microbial Hazards in New Zealand: Burden of Disease Estimates

Priority setting for food safety management at a national level requires risks to be ranked according to defined criteria. In this study, two approaches (disability‐adjusted life years (DALYs) and cost of illness (COI)) were used to generate estimates of the burden of disease for certain potentially foodborne diseases (campylobacteriosis, salmonellosis, listeriosis (invasive, perinatal, and nonperinatal), infection with Shiga toxin‐producing Escherichia coli (STEC), yersiniosis, and norovirus infection) and their sequelae in New Zealand. A modified Delphi approach was used to estimate the food‐attributable proportion for these diseases. The two approaches gave a similar ranking for the selected diseases, with campylobacteriosis and its sequelae accounting for the greatest proportion of the overall burden of disease by far.
Correlation of Soil Nutrient Characteristics and Reed Canarygrass (Phalaris Arundinacea: Poaceae) Abundance in Northern Illinois (USA)

ABSTRACT Phalaris arundinacea L. (reed canarygrass) is an aggressive graminoid species that invades wetlands in much of the northern United States. In areas previously used for agriculture and other recently disturbed habitats, P. arundinacea out-competes the native flora and creates monocultures, which reduce biodiversity and alter ecosystem functioning. Much research has focused on the growth response of P. arundinacea to varying abiotic and biotic conditions in the lab or under controlled field conditions, but few studies have examined if these results are congruent with what is observed in natural settings. We examined the relationship between P. arundinacea abundance and soil nutrient characteristics at Glacial Park, USA, a conservation area in northeastern Illinois. We found significant positive relationships between P. arundinacea abundance and total inorganic nitrogen, calcium and cation exchange capacity in the soil. These results are consistent with controlled experiments showing increased P. arundinacea growth in nitrogen-rich soil, and also suggest that calcium may influence P. arundinacea abundance in restored areas in the Midwest.
Disassembly of F-Actin Cytoskeleton after Interaction of Bacillus cereus with Fully Differentiated Human Intestinal Caco-2 Cells

ABSTRACT In the present study, the role of direct procaryote-eucaryote interactions in the virulence of Bacillus cereus was investigated. As a model of human enterocytes, differentiated Caco-2 cells were used. Infection of fully differentiated Caco-2 cells with B. cereus in the exponential phase of growth, in order to minimize the concentration of spores or sporulating microorganisms, shows that a strain-dependent cytopathic effect develops. Interestingly, addition of 3-h-old cultures of some strains resulted in complete detachment of the cultured cells after a 3-h infection whereas no such effect was found after a 3-h infection with 16-h-old cultures. Infection of enterocyte-like cells with B. cereus leads to disruption of the F-actin network and necrosis. Even though the effect of secreted factors cannot be ruled out, direct eucaryote-procaryote interaction seems to be necessary. In addition, we observed that some B. cereus strains were able to be internalized in Caco-2 cells. Our findings add a new insight into the mechanisms of virulence of B. cereus in the context of intestinal infection.
DETECTION OF TARGET SUBSTANCES USING AFFINITY-BASED MEMS / NEMS SENSORS : A PROBLEM OF SELECTIVITY

Affinity-based micro/nanosensors intended for detection of various chemical or biological agents in a liquid or gaseous environment have a great potential for both civilian and military applications. Selective detection of a target substance is based on highly specific binding of its particles to the functionalized surface of the sensing element. However, samples taken from the environment often contain substances other than the target, which can also bind with a certain affinity to the same functionalizing layer or binding sites, thus affecting the sensor's response. In this paper we analyze the influence of limited selectivity of a sensor on its time response. The results show that binding of a non-target substance can cause a significant change in both the equilibrium value and the rate of the sensor's response. The presented analysis enables improvement of accuracy of determination of the target substance concentration in detection methods based on time domain measurements of the sensor's output signal. It is also useful for development of methods for simultaneous detection of multiple substances.
Formally Verifying Flow Properties in Industrial Systems

: In contrast to other IT systems, industrial systems often do not only require classical properties like data conﬁdentiality or authentication of the communication, but have special needs due to their interaction with physical world. For example, the reordering or deletion of some commands sent to a machine can cause the system to enter an unsafe state with potentially catastrophic effects. To prevent such attacks, the integrity of the message ﬂow is necessary. We provide a formal deﬁnition of Flow Integrity . We apply our framework to two well-known industrial protocols: OPC-UA and MODBUS. Using T AMARIN , a cryptographic protocol veriﬁcation tool, we conﬁrm that most of the secure modes of these protocols ensure Flow Integrity given a resilient network. However, we also identify a weakness in a supposedly secure version of MODBUS.
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

We introduce cap analysis gene expression (CAGE), which is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20 nucleotides from 5′ end mRNAs. CAGE allows high-throughout gene expression analysis and the profiling of transcriptional start points (TSP), including promoter usage analysis. By analyzing four libraries (brain, cortex, hippocampus, and cerebellum), we redefined more accurately the TSPs of 11-27% of the analyzed transcriptional units that were hit. The frequency of CAGE tags correlates well with results from other analyses, such as serial analysis of gene expression, and furthermore maps the TSPs more accurately, including in tissue-specific cases. The high-throughput nature of this technology paves the way for understanding gene networks via correlation of promoter usage and gene transcriptional factor expression.
Adaptive Modulation for OFDM-Based Multiple Description Progressive Image Transmission

This paper addresses the use of adaptive modulation in progressive image transmission with multiple description coding in conjunction with an Orthogonal Frequency Division Multiplexing (OFDM) system. Specifically, two adaptive systems are considered: variable rate with fixed power, and variable rate with variable power. An algorithm is proposed to allocate power and constellation size at each subchannel by maximizing the throughput. Simulation results confirm that cross-layer optimization with adaptive modulation enhances system performance.
Phylogenetic Relationships of Bitterling Fishes (Teleostei: Cypriniformes: Acheilognathinae), Inferred from Mitochondrial Cytochrome b Sequences

Bitterling (Teleostei: Acheilognathinae) are small cyprinid fishes with a discrete distribution in East Asia and Europe. We used a complete mitochondrial cytochrome b sequence (1141 bp) from 49 species or subspecies in three genera (Tanakia, Rhodeus, and Acheilognathus), sampled across the major part of their distribution, to elucidate their phylogeny and biogeography, focusing particularly on their origin and dispersal. Based on high support value, the monophyletic Acheilognathinae separated into two major clades, Acheilognathus and Tanakia-Rhodeus. In the latter clade, the monophyly of Rhodeus was poorly supported, though it was topologically nested in Tanakia. On the basis of molecular-clock calibration, both clades diverged in the middle Miocene, with Tanakia-Rhodeus diverging slightly earlier than Acheilognathus. The Tanakia-Rhodeus clade expanded its distribution westward from the Far East, eventually reaching Europe, while Acheilognathus dispersed in the temperate regions of East Asia. A feature common to both clades is that most extant species, including Japanese endemics, appeared by the end of the Pliocene, corresponding with the present delineation of the Japanese archipelago. Autumn-spawning species with an embryonic diapause, unique to bitterling among cyprinid fishes, formed two distinct lineages (barbatulusrhombeus and longipinnis-typus) within Acheilognathus. The estimated time of divergence of the two lineages was approximately from the late Pliocene, a period characterized by glaciations. The timing of divergence suggests that the shift of spawning from spring to autumn, coupled with embryonic diapause, convergently emerged twice in the evolution of bitterling, possibly as an adaptation to the climate of the late Pliocene.
The syringe skin hook: the history and evolution of the improvised skin hook

SIR, The cosmetic results from skin surgery depend upon a number of variables, particularly those relating to surgical techniques and the handling of tissue. Skin hooks provide the least traumatic way of manipulating skin borders and are an important tool for the provision of an intact specimen for histopathological assessment. We therefore feel that skin hooks should be available in the surgical packs for all routine skin surgery. However, when standard skin hooks are not available, one can improvise. The manufacture of improvised, disposable skin hooks at the operating table is well reported. Fischl described an early improvised skin hook. He manipulated the point of a safety pin to create a hooked end (Fig. 1A). The use of safety pins is cumbersome and has been superseded by the development of readily available disposable sterile needles. Thus more recent reports have focused on the use of a syringe with a disposable needle attached. The needle is bent to create the desired hooked effect (Fig. 1B). This has the advantage of sterility and is quick and easy to manufacture. A disadvantage of this technique is that there is the possibility of the syringe skin hook separating into its constitutive elements, the syringe and the needle, when the skin is under tension. This may lead to inconvenience in surgery and may increase the risk of injury to the surgeon. The risk of injury may be further increased if larger needles are used to create the hook, as larger hooks can easily penetrate through the skin. This risk of separation can be reduced by the use of a syringe with a locking mechanism for the needle (Fig. 1C); however, syringes with the Luer locking system may not be readily available. We report further evolution of this technique by using the insulin syringe with a fixed, integrated needle, which we commonly use for the administration of local anaesthetic. The skin hook is formed by grasping the distal needle with either the suture holder or by using artery forceps and bending the tip through 180 (Fig. 2A). A skin hook is formed (Fig. 2B). The fixed needle reduces the chance of separation of the needle from the syringe when the skin is under tension (Fig. 2C). Thus, the theoretical risk of needlestick injury caused by separation of the needle from the syringe is reduced. We have found the insulin syringe fixed hook to be an invaluable tool, superior to previously described improvised hooks and very cheap to make (approximately 7 p). The improvised hook is often necessary in situations where one is limited by the number of hooks available. It also offers the surgeon more control over the hook angle. In our experience the insulin syringe fixed hook is an effective, safe device and we would like to bring it to the attention of others.
[Insulin resistance and components of metabolic syndrome, analysis by gender and stage of adolescence].

OBJECTIVE To analyze the influence of metabolic syndrome components in insulin resistance, by gender and adolescence phase. SUBJECTS AND METHODS We evaluated biochemical, clinical, lifestyle and body composition data of 800 adolescents from 10 to 19 years old, from both genders, from Viçosa, MG/Brasil, and there was the division by stage: early (10 to 13 years), intermediate (14 to 16 years) and late (17 to 19 years). RESULTS 10.3 and 3.4% had, respectively, insulin resistance and metabolic syndrome. In the initial phase there was a higher prevalence of dyslipidemia and intermediate hyperuricemia and excess body fat. Females had a higher prevalence of dyslipidemia, excess body fat and insulin resistance and higher male prevalence of low HDL, hyperuricemia and blood pressure changes. Those from the initial phase had higher levels of total cholesterol, LDL, HDL, triglycerides, fasting glucose and waist/hip ratio, stayed less time sitting and had more meals (p < 0.05) in relation to other phases. The final model, adjusted for gender, was different for each phase of adolescence. CONCLUSIONS Insulin resistance is associated with inadequate body composition, in biochemical levels and lifestyle, being the factors associated different in each phase of adolescence.