Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutations on the FG surface loop of human papillomavirus type 16 major capsid protein affect recognition by both type‐specific neutralizing antibodies and cross‐reactive antibodies

The aim of this study was to further characterize the conformational neutralizing epitopes present on the surface‐exposed FG loop of human papillomavirus (HPV) type 16 L1 major capsid protein. We have generated previously two chimeric L1 proteins by insertion of a foreign peptide encoding an epitope of the hepatitis B core (HBc) antigen within the FG loop. In addition, three other chimeric L1 proteins were obtained by replacing three different FG loop sequences by the HBc motif and three others by point mutations. All these chimeric L1 proteins retained the ability to self‐assemble into virus‐like particles (VLPs), with the exception of the mutant with substitution of the L1 sequence 274–279 by the HBc motif. The eight chimeric VLPs were then analyzed for differential reactivity with a set of six HPV‐16 and HPV‐31 monoclonal antibodies that bound to conformational and linear epitopes. The binding patterns of these monoclonal antibodies confirmed that the FG loop contained or contributed to neutralizing conformational epitopes. The results obtained suggested that the H31.F7 antibody, an anti‐HPV‐31 cross‐reacting and neutralizing antibody, recognized a conformational epitope situated before the 266–271 sequence. In addition, H16.E70 neutralizing antibody reactivity was reduced with L1 VLPs with an Asn to Ala point mutation at position 270, suggesting that Asn is a part of the epitope recognized by this antibody. This study contributes to the understanding of the antigenic structure of HPV‐16 and ‐31 L1 proteins by confirming that the FG loop contributes to neutralizing epitopes and suggesting the existence of both type‐specific and cross‐reactive conformational epitopes within the FG loop. J. Med. Virol. 77:558–565, 2005. © 2005 Wiley‐Liss, inc.
Analysis of segmental renal gene expression by laser capture microdissection.

UNLABELLED Analysis of segmental renal gene expression by laser capture microdissection. BACKGROUND The study of normal renal physiology has been greatly aided by microdissection techniques that have delineated the exceptional functional and cellular heterogeneity both along the nephron and between different nephron populations. These techniques are not widely used to study renal injury as microdissection is difficult because of tissue necrosis or fibrosis. We developed a procedure to detect specific gene expression in specific locations of the kidney in histologic sections. METHODS The anatomic specificity of laser capture microdissection (LCM) was employed with the sensitivity of reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS LCM/RT-PCR detected mRNA for podoplanin in 2% of a single glomerulus, rat basic amino acid transporter in 6% of a single cross-section of proximal straight tubule, and renin in eight proximal convoluted tubule cross-sections. LCM/RT-PCR could isolate pure populations of proximal convoluted tubules, proximal straight tubules, and thick ascending limbs from renal histologic sections, although pure collecting ducts could not be isolated. LCM/RT-PCR localized ischemia-reperfusion-induced induction of KC/interleukin-8 primarily to the medullary thick ascending limb, and detected transforming growth factor-beta (TGF-beta) mRNA in glomeruli of a patient with membranous glomerulonephropathy. CONCLUSIONS When used with an appropriate laser spot size, LCM/RT-PCR can measure gene expression in glomeruli or specific parts of the nephron and can study alterations in steady-state mRNA levels in animal models of renal disease. The applications, limitations, and refinements of this approach are discussed.
Quantitation of thrombin‐antithrombin III complexes in human blood

Abstract. Human thrombin‐antithrombin III complex was generated in defibrinated plasma by activation of the intrinsic coagulation system and isolated using affinity chromatography on insolubilized heparin and gel filtration. The resulting material probably contained factor Xa‐antithrombin III and factor IXa‐antithrombin III as well, although no specific identification of these complexes was made. An antiserum was raised, in rabbits, against this complex and rendered specific for neoantigens by absorption with fresh human plasma in the presence of inhibitors (heparin and p‐nitrophenyl‐p'‐guanidinoben‐zoate). Further purification of the ‘specific’ antibodies was achieved by immunoabsorption on the insolubilized complex. Polystyrene particles were coated with the resultant antisera and used in an agglutination test for the determination of thrombin‐antithrombin III complexes in the plasma of healthy subjects and various patients.
Zero-order suppression for two-photon holographic excitation.

Wavefront shaping with liquid-crystal spatial light modulators (LC-SLMs) is frequently hindered by a remaining fraction of undiffracted light, the so-called "zero-order. " This contribution is all the more detrimental in configurations for which the LC-SLM is Fourier conjugated to a sample by a lens, because in these cases this undiffracted light produces a diffraction-limited spot at the image focal plane. In this Letter we propose to minimize two-photon (2P) excitation of the sample, resulting from this unmodulated light, by introducing optical aberrations to the excitation beam. Aberrations are subsequently compensated by the LC-SLM, but only for the modulated part of the beam, and not for the zero-order component. In order to experimentally demonstrate the method, we use astigmatism as the optical aberration, by simply adding one or two cylindrical lenses in the optical path of the beam. A 10⁴ decrease in zero-order-induced 2P fluorescence intensity is demonstrated. Combining this approach with temporal focusing is shown to decrease zero-order fluorescence by a factor of 4·10⁶.
Characterization of the Hemorrhagic Reaction Caused by Vibrio vulnificus Metalloprotease, a Member of the Thermolysin Family

ABSTRACT Vibrio vulnificus is an opportunistic human pathogen causing wound infections and septicemia, characterized by hemorrhagic and edematous damage to the skin. This human pathogen secretes a metalloprotease (V. vulnificus protease [VVP]) as an important virulence determinant. When several bacterial metalloproteases including VVP were injected intradermally into dorsal skin, VVP showed the greatest hemorrhagic activity. The level of the in vivo hemorrhagic activity of the bacterial metalloproteases was significantly correlated with that of the in vitro proteolytic activity for the reconstituted basement membrane gel. Of two major basement membrane components (laminin and type IV collagen), only type IV collagen was easily digested by VVP. Additionally, the immunoglobulin G antibody against type IV collagen, but not against laminin, showed sufficient protection against the hemorrhagic reaction caused by VVP. Capillary vessels are known to be stabilized by binding of the basal surface of vascular endothelial cells to the basement membrane. Therefore, specific degradation of type IV collagen may cause destruction of the basement membrane, breakdown of capillary vessels, and leakage of blood components including erythrocytes.
Mapping forest canopy height using TanDEM-X DSM and airborne LiDAR DTM

This study assesses the potential of single-pass TanDEM-X interferometric SAR (InSAR) data to map forest canopy height, when a corresponding accurate digital terrain model (DTM) is available. In the proposed method, the forest canopy height model (CHM) is extracted by subtracting an airborne lidar DTM from the TanDEM-X digital surface model (DSM). We showed that the TanDEM-X coherence is influenced by local incidence angles and tree basal area. These factors should be taken into account when estimating forest canopy height using TanDEM-X combined to lidar data.
Changes in liver-specific compared to common gene transcription during primary culture of mouse hepatocytes

Liver-specific mRNA sequences were examined in primary cultures of mouse hepatocytes. After cell disaggregation by collagenase treatment and for at least 24 h in culture, little change in liver-specific mRNA concentrations was noted. Gradually over a period of 140 h, liver-specific mRNAs declined. In contrast, transcriptional assays in which liver cell nuclei were used to produce 32P-labeled nuclear RNA showed that liver-specific gene transcription was greatly diminished within 24 h, while polymerase II transcription of "common" genes and transcription of tRNA and rRNA did not decline. Thus, a prompt differential transcriptional effect seems to underlie the gradual loss of tissue specificity of the primary cultures.
An Extension of Panjer's Recursion

Abstract Sundt and Jewell have shown that a nondegenerate claim number distribution Q = {qn}nϵN0 satisfies the recursion for all n≥0 if and only if Q is a binomial, Poisson or negativebinomial distribution. This recursion is of interest since it yields a recursion for the aggregate claims distribution in the collective model of risk theory when the claim size distribution is integer-valued as well. A similar characterization of claim number distributions satisfying the above recursion for all n ≥ 1 has been obtained by Willmot. In the present paper we extend these results and the subsequent recursion for the aggregate claims distribution to the case where the recursion holds for all n ≥ k with arbitrary k. Our results are of interest in catastrophe excess-of-loss reinsurance.
Frozen Breast Milk at -20°C and -80°C: A Longitudinal Study of Glutathione Peroxidase Activity and Malondialdehyde Concentration

When breast milk extraction and storage is required before ingestion, it is important to establish the conditions that ensure the least losses in milk quality, like the antioxidant capacity. The present study evaluates glutathione peroxidase activity and malondialdehyde concentration of breast milk when stored frozen, comparing the effects of 2 temperatures (—20°C and —80°C) and different storage times (15, 30, and 60 days). The results indicate that freezing induces losses in the antioxidant properties of breast milk and that such losses increase with the duration of storage and differ in intensity according to the temperature. It is concluded that to maximally preserve the antioxidant properties of breast milk, it is advisable to store the latter at —80°C for a period of less than 30 days, rather than for shorter time periods at the usual temperature of —20°C. J Hum Lact. 26(1):35-41.
Empirical evaluation of receiver‐based TCP delay control in CDMA2000 networks

Wide‐area broadband wireless technologies such as CDMA2000 often suffer from variable transfer rate and long latency. In particular, TCP window‐based rate control causes excessive buffering at the base station because of the lower transfer rate of the wireless link than that of the wired backhaul link. This performance characteristic of TCP further increases the end‐to‐end delay, and additional resources are required at the base station. This paper presents a practical mechanism to control the end‐to‐end TCP delay for CDMA2000 networks (or other similar wireless technologies). The key idea is to reduce and stabilize RTT (round‐trip time) by dynamically controlling the TCP advertised window size, based on a runtime measurement of the wireless channel condition at the mobile station. The proposed system has been implemented by modifying the Linux protocol stack. The experiment results, conducted on a commercial CDMA2000 1x network, show that the proposed scheme greatly reduces the TCP delay in non‐congested networks, while not sacrificing the TCP throughput in congested networks. Copyright © 2006 John Wiley & Sons, Ltd.
Attention Deficit Hyperactivity Disorder, Other Mental Health Problems, Substance Use, and Driving: Examination of a Population-Based, Representative Canadian Sample

Purpose: The purpose of this study is to examine the relationships among self-reported screening measures of attention deficit hyperactivity disorder (ADHD), other psychiatric problems, and driving-related outcomes in a provincially representative sample of adults 18 years and older living in the province of Ontario, Canada. Methods: The study examined the results of the Centre for Addictions and Mental Health (CAMH) Ontario Monitor, an ongoing repeated cross-sectional telephone survey of Ontario adults over a 2-year period. Measures included ADHD measures (Adult ADHD Self-Report Scale-V1.1 [ASRS-V1.1], previous ADHD diagnosis, ADHD medication use); psychiatric distress measures (General Health Questionnaire [GHQ12], use of pain, anxiety, and depression medication); antisocial behavior measure (The Antisocial Personality Disorder Scale from the Mini-International Neuropsychiatric Interview [APD]); substance use and abuse measures (alcohol, cannabis, and cocaine), Alcohol Use Disorders Identification Test (AUDIT), Alcohol, Smoking and Substance Involvement Screening Test (ASSIST), driving-related outcomes (driving after drinking, driving after cannabis use, street racing, collisions in past year), and sociodemographics (gender, age, vehicle-kilometers traveled). Results: A total of 4,014 Ontario residents were sampled, of which 3,485 reported having a valid driver's license. Overall, 3.22% screened positive for ADHD symptoms on the ASRS-V1.1 screening tool. A greater percentage of those who screened positive were younger, reported previous ADHD diagnosis and medication use, distress, antisocial behavior, anti-anxiety and antidepressant medication use, substance use, and social problems compared to those who screened negative. However, there were no statistically significant differences between those who screened positive or negative for ADHD symptoms on self-reported driving after having 2 or more drinks in the previous hour; within an hour of using cannabis, marijuana, or hash; or in a street race or collision involvement as a driver in the past year. When a sequential regression was conducted to predict self-reported collisions, younger age and higher weekly kilometers driven showed higher odds of collision involvement, and the odds ratio for cannabis use ever approached statistical significance. Discussion: This study is the first population-based study of a representative sample of adults 18 years and older living in Ontario, Canada. These results showed no relationship between the ADHD screen and collision when age, sex, and kilometers driven are controlled for. However, these analyses are based on self-report screeners and not psychiatric diagnoses and a limited sample of ADHD respondents. Thus, these results should be interpreted with caution.
Myeloid-Derived Suppressor Cells Play Crucial Roles in the Regulation of Mouse Collagen-Induced Arthritis

Myeloid-derived suppressor cells (MDSCs) are of myeloid origin and are able to suppress T cell responses. The role of MDSCs in autoimmune diseases remains controversial, and little is known about the function of MDSCs in autoimmune arthritis. In this study, we clarify that MDSCs play crucial roles in the regulation of proinflammatory immune response in a collagen-induced arthritis (CIA) mouse model. MDSCs accumulated in the spleens of mice with CIA when arthritis severity peaked. These MDSCs inhibited the proliferation of CD4+ T cells and their differentiation into Th17 cells in vitro. Moreover, MDSCs inhibited the production of IFN-γ, IL-2, TNF-α, and IL-6 by CD4+ T cells in vitro, whereas they promoted the production of IL-10. Adoptive transfer of MDSCs reduced the severity of CIA in vivo, which was accompanied by a decrease in the number of CD4+ T cells and Th17 cells in the draining lymph nodes. However, depletion of MDSCs abrogated the spontaneous improvement of CIA. In conclusion, MDSCs in CIA suppress the progression of CIA by inhibiting the proinflammatory immune response of CD4+ T cells. These observations suggest that MDSCs play crucial roles in the regulation of autoimmune arthritis, which could be exploited in new cell-based therapies for human rheumatoid arthritis.
Fabrication and characterization of solid-state nanopore arrays for high-throughput DNA sequencing

We report the fabrication and characterization of uniformly sized nanopore arrays, integrated into an optical detection system for high-throughput DNA sequencing applications. Nanopore arrays were fabricated using focused ion beam milling, followed by TiO2 coating using atomic layer deposition. The TiO2 layer decreases the initial pore diameter down to the sub-10 nm range, compatible with the requirements for nanopore-based sequencing using optical readout. We find that the TiO2 layers produce a lower photoluminescence background as compared with the more widely used Al2O3 coatings. The functionality of the nanopore array was demonstrated by the simultaneous optical detection of DNA–quantum dot conjugates, which were electro-kinetically driven through the nanopores. Our optical scheme employs total internal reflection fluorescence microscopy to illuminate a wide area of the TiO2-coated membrane. A highly parallel system for observing DNA capture events in a uniformly sized 6 × 6 nanopore array was experimentally realized.
Bandpass sampling for software radio receivers, and the effect of oversampling on aperture jitter

To maximize reconfigurability in software radio receivers, digitization should occur as close to the antenna as possible. Bandpass sampling allows the digitization of bandpass signals at RF or intermediate frequencies without significantly increasing the sampling rate. This enables a more flexible receiver to be realized allowing for many radio functions to be defined in software. Sampling of signals at high carrier frequencies has associated problems such as the effects of aperture jitter. Jitter can limit the frequency at which digitization occurs and also degrade receiver performance. This paper investigates the effects of jitter on signal quality in bandpass sampling systems.
Overexpression of α‐synuclein in an astrocyte cell line promotes autophagy inhibition and apoptosis

α‐Synuclein is the major component of neuronal cytoplasmic aggregates called Lewy bodies, the main pathological hallmark of Parkinson disease. Although neurons are the predominant cells expressing α‐synuclein in the brain, recent studies have demonstrated that primary astrocytes in culture also express α‐synuclein and regulate α‐synuclein trafficking. Astrocytes have a neuroprotective role in several detrimental brain conditions; we therefore analyzed the effects of the overexpression of wild‐type α‐synuclein and its A30P and A53T mutants on autophagy and apoptosis. We observed that in immortalized astrocyte cell lines, overexpression of α‐synuclein proteins promotes the decrease of LC3‐II and the increase of p62 protein levels, suggesting the inhibition of autophagy. When these cells were treated with rotenone, there was a loss of mitochondrial membrane potential, especially in cells expressing mutant α‐synuclein. The level of this decrease was related to the toxicity of the mutants because they show a more intense and sustained effect. The decrease in autophagy and the mitochondrial changes in conjunction with parkin expression levels may sensitize astrocytes to apoptosis.
Outcome of Renal Transplant Recipients Admitted to an Intensive Care Unit: A 10-Year Cohort Study

Background. Epidemiology and prognosis of severe complications related to renal transplantation requiring admission to intensive care unit (ICU) have not been assessed precisely. This study was undertaken to evaluate the outcome in this population and to identify the factors of prognosis. Methods. All records of adult renal transplant recipients admitted to our ICU from 1997 to 2007 were reviewed including transplant variables, clinical and biological parameters, use of mechanical ventilation, catecholamine support, or dialysis or both. Mortality was assessed and data were analyzed to identify predictive factors of outcome. Results. Twenty-seven women and 30 men, median age 54 years, were included in the study. Eighteen patients were oliguric, 35 were mechanically ventilated, 32 underwent hemodialysis, and 36 needed catecholamine. Twenty-three patients died (40.3%), a mortality significantly higher than in a matched by age and gravity scores control group of nontransplant ICU patients. By univariate analysis, survivors had a significantly lower ICU severity scores, a higher mean arterial pressure, a higher Glasgow Coma Score, a higher serum albumin, and a lower serum lactate on ICU admission. The need for catecholamine support, mechanical ventilation or dialysis or both during the ICU stay worsens the outcome significantly. Using the multivariate analysis, only the mean arterial pressure and the need for mechanical ventilation were predictive of mortality. Conclusion. The incidence of severe transplant-related complications requiring an admission to an ICU was at 16 of 1000 patients year with a mortality rate higher than the general ICU population (40% vs. 20%). These data suggest that immunosuppressive treatment of transplant patients with severe complications worsens significantly their outcome.
Transcripts for Functionally Distinct Isoforms of Chicken GATA-5 Are Differentially Expressed from Alternative First Exons*

Our analysis of cDNA and genomic clones unexpectedly revealed that the chicken gata-5 gene is differentially expressed from alternative first exons. Moreover, we show that the respective transcripts are differentially processed to yield mRNAs for two distinct isoforms of GATA-5. The major isoform, which we described previously, has two CXNCX17CNXC zinc fingers typical of a vertebrate GATA factor. The minor isoform, on the other hand, has only one such zinc finger. We show that this novel isoform localizes within the nuclei of transfected cells and can bind to a consensus GATA site. This truncated isoform of GATA-5 is compromised in its ability to transactivate a simple target gene, however, and thus is functionally distinct from the major isoform of GATA-5.
Initial diagnosis and treatment in first‐episode psychosis: can an operationalized diagnostic classification system enhance treating clinicians' diagnosis and the treatment chosen?

Aim: Diagnosis during the initial stages of first‐episode psychosis is particularly challenging but crucial in deciding on treatment. This is compounded by important differences in the two major classification systems, International Classification of Diseases, 10th revision (ICD‐10) and Diagnostic and Statistical Manual of Mental Disorders, fourth edition (DSM‐IV). We aimed to compare the concordance between an operationalized diagnosis using Operational Criteria Checklist (OPCRIT) and treating clinician‐generated diagnosis in first‐episode psychosis diagnosis and its correlation with treatment prescribed.
Effect of vitamin D Deficiency and 1,25‐dihydroxyvitamin D3 on metabolism and D‐glucose transport in rat cerebral cortex

We previously demonstrated that feeding rats Steenbock and Black's rickets‐inducing diet produces remarkable changes in the metabolic pattern of the in testinal mucosa, kidney, and liver and in some membrane transport Systems of intestinal mucosa and kidney. 1,25‐Dihydroxyvitamin D3 administration to rachitic rats did not always prove to be effective in restoring normal values.
On subvarieties with ample normal bundle

We show that a pseudoeffective R-divisor has numerical dimension 0 if it is numerically trivial on a subvariety with ample normal bundle. This implies that the cycle class of a curve with ample normal bundle is big, giving an affirmative answer to a question of Peternell. We also give other positivity properties such subvarieties.