Miracle-dz/UniFAR-FTUs huggingface dataset:
Rho2 Palmitoylation Is Required for Plasma Membrane Localization and Proper Signaling to the Fission Yeast Cell Integrity Mitogen-Activated Protein Kinase Pathway

ABSTRACT The fission yeast small GTPase Rho2 regulates morphogenesis and is an upstream activator of the cell integrity pathway, whose key element, mitogen-activated protein kinase (MAPK) Pmk1, becomes activated by multiple environmental stimuli and controls several cellular functions. Here we demonstrate that farnesylated Rho2 becomes palmitoylated in vivo at cysteine-196 within its carboxyl end and that this modification allows its specific targeting to the plasma membrane. Unlike that of other palmitoylated and prenylated GTPases, the Rho2 control of morphogenesis and Pmk1 activity is strictly dependent upon plasma membrane localization and is not found in other cellular membranes. Indeed, artificial plasma membrane targeting bypassed the Rho2 need for palmitoylation in order to signal. Detailed functional analysis of Rho2 chimeras fused to the carboxyl end from the essential GTPase Rho1 showed that GTPase palmitoylation is partially dependent on the prenylation context and confirmed that Rho2 signaling is independent of Rho GTP dissociation inhibitor (GDI) function. We further demonstrate that Rho2 is an in vivo substrate for DHHC family acyltransferase Erf2 palmitoyltransferase. Remarkably, Rho3, another Erf2 target, negatively regulates Pmk1 activity in a Rho2-independent fashion, thus revealing the existence of cross talk whereby both GTPases antagonistically modulate the activity of this MAPK cascade.
Implementing outcome based education for microcontrollers

The programmable controllers and processors play important role in a wide range of embedded applications. Teaching such subjects in a meaningful way is always a challenging task as the students feel that writing code in assembly and Embedded C is difficult. The programmable controllers and processors are taught to Electrical cluster students which usually include Electronics and Communication Engineering, Telecommunication Engineering, Electronics and Instrumentation Engineering and Electrical and Electronics Engineering. The traditional method of teaching these subjects was faculty centric where the teacher teaches the theoretical concepts using blackboard or power point presentation. To enable the students to learn the practical applications, there is a need for a new approach of teaching the subject where in the student's performance is evaluated based on various factors such as communication skills, analytical skills, professional ethics etc. In this direction, the paper focuses on the methods based on Outcome Based Education (OBE), adopted by the author to make the students understand the subject better.
Evaluation of the automated coagulation analyzer CS-5100 and its utility in high throughput laboratories

Abstract Background: Automated analyzers are an important component of modern laboratories. As a representative of the newest generation of coagulation analyzers, the CS-5100 features several technical refinements including a pre-analytical assessment unit as well as multi-wavelength optical detection units. Therefore, the CS-5100 is supposed to rapidly and accurately perform a broad panel of coagulation tests. In the current study, the CS-5100 was evaluated regarding its precision and practicability in a clinical laboratory setting. Methods: The CS-5100 was evaluated regarding its intra- and inter-assay precision using commercially available control samples. Results of patient samples, including hemolytic, icteric and lipemic specimens, measured on the CS-5100 were compared to reference analyzers, which are used in our accredited laboratory. Results: The coefficients of variation, assessed in the intra- and inter-assay precision analyses were below 5% representatively for most parameters. Results, obtained by the CS-5100 showed predominantly a high comparability to used reference analyzers, with correlation coefficients ranging from 0.857 to 0.990. Only minor ranged systemic or proportional differences were found in Passing-Bablok regression between the CS-5100 and reference analyzers regarding most of the tested parameters. Lipemic samples had a tendency to deteriorate correlation coefficients, but an overall effect of the sample’s triglyceride level could be ruled out. In a routine setting, the analyzer reached a sample throughput rate of 160 tests per hour. Conclusions: The CS-5100 is able to rapidly and precisely measure patient samples. No considerable influence on test comparability was found for elevated levels of free hemoglobin, bilirubin or triglycerides.
Clinical utility of CA 72-4 serum marker in the staging and immediate post-surgical management of gastric cancer patients.

CA 72-4 is a high molecular weight, pancarcinoma human tumor mucin which may play an important role in the identification (i.e., staging) and clinical management of patients with gastric carcinoma. In the present study of 242 patients with primary or recurrent gastric cancer, a higher percentage of these patients had measurable serum CA 72-4 levels when compared with either CA 19.9 or CEA. Moreover, the presence of positive serum CA 72-4 levels correlated with the presence of lymph node involvement and with the identification of patients with a poor prognosis due to the presence of an advanced stage of gastric cancer. Post-operative monitoring of serum CA 72-4 revealed that the disappearance of CA 72-4 often indicated curative surgery which correlated with a longer disease-free interval. Additional clinical studies are needed to better evaluate the role of CA 72-4 as a serum marker for human gastric carcinoma. Concomitant studies should also focus on what role CA 72-4 may play in the initiation and/or progression of the gastric carcinoma phenotype.
Concatenating Sequence-Based Requirements in Model-Based Testing with State Machines

: Model-based testing is a promising technique for quality assurance. In this paper, we present an approach to tackle two challenges in model-based testing: the traceability to functional requirements and the automatic derivation of test cases that represent typical behavior. Our approach is based on the assumption that functional requirements describe typical sequences of behavior. The requirements sequences can be mapped to sequences in a system behavior model and can be used for automatic test generation. In this paper, we choose UML sequence diagrams to describe requirements behavior and UML state machines to describe the complete system behavior. We present the approach, new coverage criteria, the prototype implementation ConSe-quence , and ﬁrst experiences using an ATM case study.
Permanent hexose transport upregulation in a respiration-deficient human fibroblast cell strain.

The regulation of hexose transport was studied in a human diploid fibroblast respiration-deficient cell strain (WG750). Transport of 2-deoxy-D-glucose (2-DG) was greater than sixfold higher compared with an in vivo age-matched normal cell strain (MCH55). In addition, 3-O-methylglucose transport and 14CO2 production were elevated in the mutant cell strain. Kinetic analysis revealed that the increased sugar transport in mutant cells was due to an average 5.7-fold increase in the 2-DG maximal transport rate, with no observed differences in the transport Michaelis constant for both normal and mutant cells. Also, the inhibitor constants for D-glucose inhibition of 2-DG transport were nearly identical for both cell types. Glucose deprivation led to a similar time-dependent increase in hexose transport in both cell strains. Serum refeeding of glucose-fed serum-deprived cultures led to a progressive increase in 2-DG transport in normal cells, whereas mutant cells displayed a time-delayed increase in 2-DG transport. Exposure to 67 and 670 nM insulin stimulated 2-DG transport on average 1.99 +/- 0.25- and 2.33 +/- 0.26-fold, respectively, over basal transport in the normal cells, whereas the mutant cells were significantly less sensitive to the stimulatory effects of the hormone. Insulin binding and amino acid transport (i.e., alpha-aminoisobutyric acid uptake) in the normal and mutant cells were not different. Data obtained using Western blot analysis showed that WG750 (mutant) cells expressed an increase (approximately 4-fold) in total cellular HepG2 (erythroid-brain) transporter protein compared with normal cells, thus reflecting the changes seen in hexose transport. (ABSTRACT TRUNCATED AT 250 WORDS)
Alzheimer's disease: the impact of the family on spouses, offspring, and inlaws.

This article reports the findings from a study designed to identify qualities of the multigeneration family system that affected the relationship between the demands of Alzheimer's disease on the family and the health and well-being of (a) spouses, (b) offspring, and (c) offspring's spouses or "inlaws. " Members of 97 families of patients with Alzheimer's disease, recruited from four University-affiliated Alzheimer's Centers, completed detailed questionnaires and participated in a 45-minute telephone interview to assess care-strain, personal stress, appraisals of three major domains of family life (World View, Structure/Organization, and Emotion Management), and three health and well-being indices (Anxiety/Depression, Somatic Symptoms, and Well-Being). Multivariate multiple regression equations, run separately for each of the three groups of family respondents and each of the three family domains, indicated: (1) no significant associations between the severity of the elder's disease and family member health and well-being; (2) female family members reported poorer health and well-being than male family members; and (3) caregiver strain was negatively associated with family member health and well-being. Further, appraised family qualities were associated with the health and well-being of the three groups of respondents differently: directly for offspring, interactively with severity of patient disorder for inlaws, and not at all for spouses. The data suggested that some family qualities served a protective function, whereas others exacerbated the negative effects of caregiving by affecting personal health and well-being. The findings are interpreted in terms of the different roles and expectations for care-giving placed on spouses, offspring, and inlaws. It is suggested that programs of intervention for patients with Alzheimer's and other chronic diseases should focus on the multigeneration family as the context for care, rather than only on the primary caregiver.
Gas-chromatographic Method for Volatile Congeners in Alcoholic Beverages Analysis

Alcoholic fermentation of fruits and cereals is the primary source of alcoholic beverages production. The main component in these drinks is ethanol; but there are also many secondary products like glycerin or acetaldehyde, and mixtures of other higher-order alcohols called “fusel”, also known as congeners. They are important for the characterization of alcoholic beverages and also for forensic medicine purposes, when drivers assertions concerning alcoholic beverages consumption have to be verified in order to prosecute them for driving under influence. We developed a gas-chromatographic method of qualitative and quantitative analysis of alcohol congeners in our toxicology laboratory. The method was validated in terms of linearity, precision, accuracy and detection limits. Our findings are consistent with other from the literature relative to this type of analytical determinations.
Sequencing of Cytomegalovirus UL97 Gene for Genotypic Antiviral Resistance Testing

ABSTRACT The widespread use of ganciclovir (GCV) to treat cytomegalovirus (CMV) infections in immunosuppressed patients has led to the development of drug resistance. Phenotypic assays for CMV drug resistance are presently too time-consuming to be therapeutically useful. To support the development of genotypic assays for GCV resistance, the complete sequences of the UL97 phosphotransferase genes in 28 phenotypically GCV-sensitive CMV clinical isolates were determined. The gene was found to be highly conserved, with nucleotide sequence identity among strains ranging from 98.6 to 100% and amino acid sequence identity of >99%. Primers for a genotypic assay were designed to amplify codons 400 to 707, because all known UL97 mutations conferring drug resistance occur at three sites within this region. This part of the UL97 gene was amplified from over 50 clinical isolates, and two sequencing reactions for the coding strand were successfully used to identify GCV resistance mutations. This genotypic assay can be performed in 48 h using genomic DNA extracted from cell monolayers at very low levels of virus infectivity, thus rapidly providing therapeutically useful results.
Recognition of corners of planar checkboard pattern image

The recognition of the internal corners of a planar checkerboard calibration pattern image is very important to camera calibration. An effective approach is proposed to automatically recognize the internal corners of the planar checkerboard calibration pattern image based on the characteristics of local intensity and the grid line architecture of the planar checkerboard pattern image. The proposed procedure consists of the detection of image corners, the recognition of the corners at the intersections of black and white squares and the recognition of the corners at the intersections of two groups of grid lines. Experiments show that the proposed approach obviously reduces the time cost for camera calibration, speeds up calibration process and is especially adapted for automatic calibration based on multiple images.
First epidemiological study on occupational radar exposure in the French Navy: a 26-year cohort study

This retrospective cohort study deals with the causes of death among 57,000 military personnel who served in the French Navy surface vessels and were observed over the period 1975–2000. We successively compared the mortality rate and the specific causes of death between two groups differing in their potential exposure levels to radar. Occupational exposure was defined according to the on-board workplace (radar and control groups). The age-adjusted death ratios of the navy personnel were compared. For all causes of death, the results showed that 885 deaths in the radar group and 299 in the control group occurred (RR = 1.00 (95 % CI: 0.88–1.14)). RRs were 0.92 (95 % CI: 0.69–1.24) for neoplasms. For the duration of follow-up, the results did not show an increased health risk for military personnel exposed to higher levels of radio frequencies in the radar group, but the number of deaths was very small for some cancer sites.
Differentially-fed omnidirectional circularly polarized patch antenna for RF energy harvesting

A differentially-fed omnidirectional circularly-polarized antenna is investigated for application in RF energy harvesting. The antenna is composed of a two-layer substrate and back-to-back printed square patches which have two diagonal stubs and one truncation. The patches share a common ground plane. Both patches generate circular polarization (CP) and omnidirectional CP is provided. The antenna provides an axial-ratio bandwidth of 20 MHz from 2.43 GHz to 2.45 GHz. In order to measure the proposed differentially-fed antenna, a feed network connected between the SMA port and differential port is designed. Furthermore, the combined configurations with the proposed antenna, bandpass filter and rectifier can be built and convert the electromagnetic field to DC. The measured output voltage is 255mV at 2.40GHz.
The role of the TIM8–13 complex in the import of Tim23 into mitochondria

Tim8 and Tim13 are non‐essential, conserved proteins of the mitochondrial intermembrane space, which are organized in a hetero‐oligomeric complex. They are structurally related to Tim9 and Tim10, essential components of the import machinery for mitochondrial carrier proteins. Here we show that the TIM8–13 complex interacts with translocation intermediates of Tim23, which are partially translocated across the outer membrane but not with fully imported or assembled Tim23. The TIM8–13 complex binds to the N‐terminal or intermediate domain of Tim23. It traps the incoming precursor in the intermembrane space thereby preventing retrograde translocation. The TIM8–13 complex is strictly required for import of Tim23 under conditions when a low membrane potential exists in the mitochondria. The human homologue of Tim8 is encoded by the DDP1 (deafness/dystonia peptide 1) gene, which is associated with the Mohr–Tranebjaerg syndrome (MTS), a progressive neurodegenerative disorder leading to deafness. It is demonstrated that import of human Tim23 is dependent on a high membrane potential. A mechanism to explain the pathology of MTS is discussed.
Infectious Complications in Children With Acute Myeloid Leukemia and Down Syndrome: Analysis of the Prospective Multicenter Trial AML‐BFM 2004

Children with acute myeloid leukemia (AML) and Down syndrome have high survival rates with intensity‐reduced chemotherapeutic regimens, although the optimal balance between dose intensity and treatment toxicity has not been determined. We, therefore, characterized infectious complications in children with AML and Down syndrome treated according to AML‐BFM 2004 study (ClinicalTrials.gov NCT00111345; amended 2006 for Down syndrome with reduced intensity).
Terrific Protein Traffic: The Mystery of Effector Protein Delivery by Filamentous Plant Pathogens

Many biotrophic fungal and oomycete plant pathogens deliver effector proteins directly into host cells during infection. Recent advances are revealing the extensive effector repertoires of these pathogens and are beginning to shed light on how they manipulate host cells to establish a parasitic relationship. Surprisingly, oomycete effectors seem to share a common uptake system with those from the human malaria pathogen. The current explosion of information is opening new research avenues in molecular plant pathology and is providing new opportunities to limit the impact of plant disease on food production.
Facile and straightforward synthesis of superparamagnetic reduced graphene oxide–Fe3O4 hybrid composite by a solvothermal reaction

A superparamagnetic reduced graphene oxide–Fe3O4 hybrid composite (rGO–Fe3O4) was prepared via a facile and straightforward method through the solvothermal reaction of iron (III) acetylacetonate (Fe(acac)3) and graphene oxide (GO) in ethylenediamine (EDA) and water. By this method, chemical reduction of GO as well as the formation of Fe3O4 nanoparticles (NPs) can be achieved in one step. The Fe3O4 NPs are firmly deposited on the surfaces of rGO, avoiding their reassembly to graphite. The rGO sheets prevent the agglomeration of Fe3O4 NPs and enable a uniform dispersion of these metal oxide particles. The size distribution and coverage density of Fe3O4 NPs deposited on rGO can be controlled by varying the initial mass ratio of GO and iron precursor, Fe(acac)3. With an initial mass ratio of GO and Fe(acac)3 of 5:5, the surfaces of rGO sheets are densely covered by spherical Fe3O4 NPs with an average size of 19.9 nm. The magnetic-functionalized rGO hybrid exhibits a good magnetic property and the specific saturation magnetization (Ms) is 13.2 emu g−1. The adsorption test of methylene blue from aqueous solution demonstrates the potential application of this rGO-Fe3O4 hybrid composite in removing organic dyes from polluted water.
tRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana

tRNA-derived fragments (tRFs) constitute a new class of short regulatory RNAs that are a product of nascent or mature tRNA processing. tRF sequences have been identified in all domains of life; however, most published research pertains to human, yeast and some bacterial organisms. Despite growing interest in plant tRFs and accumulating evidence of their function in plant development and stress responses, no public, web-based repository dedicated to these molecules is currently available. Here, we introduce tRex (http://combio.pl/trex)-the first comprehensive data-driven online resource specifically dedicated to tRFs in the model plant Arabidopsis thaliana. The portal is based on verified Arabidopsis tRNA annotation and includes in-house-generated and publicly available small RNA sequencing experiments from various tissues, ecotypes, genotypes and stress conditions. The provided web-based tools are designed in a user-friendly manner and allow for seamless exploration of the data that are presented in the form of dynamic tables and cumulative coverage profiles. The tRex database is connected to external genomic and citation resources, which makes it a one-stop solution for Arabidopsis tRF-related research.
Efficient Multihop Broadcasting With Network Coding in Duty-Cycled Wireless Sensor Networks (NET)

In this article, we focus on the issue of multihop broadcasting for a batch of packets in duty-cycled wireless sensor networks (WSNs). When the conventional single-hop broadcasting scheme with network coding is applied to multihop scenario, a forwarder has to occupy its surrounding wireless medium until all its one-hop forwarders decode the received packets. Thus, forwarding of neighboring forwarders is significantly delayed. We propose an efficient multihop broadcasting with network coding (EMBNC) by selecting downstream forwarders in a two-hop manner. Encoded packets are delivered from a forwarder to its downstream forwarders with the cooperation of auxiliary nodes. A forwarder terminates its forwarding once auxiliary nodes collectively receive enough packets, which efficiently decreases time to occupy wireless medium. Auxiliary nodes can also receive more encoded packets when downstream forwarders are transmitting. Simulation results show EMBNC achieves high performance in terms of broadcast delay, energy consumption, and average duty cycle.
Long-term Outcomes of Photorefractive Keratectomy in Eyes With Previous Epikeratophakia for Keratoconus

Purpose: To determine the long-term safety and effectiveness of photorefractive keratectomy (PRK) in the treatment of refractive errors after epikeratophakia (EP) for keratoconus. Methods: Ten patients (14 eyes) who had refractive errors after EP for keratoconus received PRK surgery. Uncorrected visual acuity (UCVA), best spectacle-corrected visual acuity (BSCVA), refractive error, corneal astigmatism, pachymetry, corneal topography, and complications were monitored. Results: Mean follow-up after PRK was 63.4 ± 19.8 months. Mean spherical equivalent was −5.5 ± 3.9 D before PRK, −0.9 ± 0.5 D at 1 month after PRK, and −1.5 ± 1.0 D at 3 years. Mean astigmatism was 4.2 ± 2.1 D before PRK, 1.2 ± 0.5 D at 1 month after PRK, and 1.5 ± 0.6 D at 3 years. Thirteen (93%) eyes had an UCVA <20/40, and 12 (86%) had a BSCVA of 20/40 or better before PRK. At 1 year, the UCVA was 20/40 or better in 8 (57%) eyes, and the BSCVA was 20/40 or better in all eyes. Mean central corneal thickness was 749 ± 35 μm before PRK and 621 ± 56 μm at 3 years. During the follow-up period, haze (grade no more than 1.0) was observed in 2 eyes. No immune rejection episode or recurrent keratoconus was found. Conclusions: PRK appears to be reliable and safe for the correction of residual ametropia after EP for keratoconus, and the visual acuity can remain stable after PRK for a long time.
Determination of influenza virus proteins required for genome replication

An artificial vaccinia virus vector-driven replication system for influenza virus RNA has been developed. In this system, a synthetic NS-like gene is replicated and expressed by influenza virus proteins supplied through infection with vaccinia virus recombinant vectors. The minimum subset of influenza virus proteins needed for specific replication and expression of the viral ribonucleoprotein was found to be the three polymerase proteins (PB1, PB2, and PA) and the nucleoprotein.