Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of GOME tropospheric NO 2 columns with NO 2 profiles deduced from ground-based in situ measurements

Nitrogen dioxide (NO 2 ) vertical tropospheric column densities (VTCs) retrieved from the Global Ozone Monitoring Experiment (GOME) are compared to coincident ground-based tropospheric NO 2 columns. The ground-based columns are deduced from in situ measurements at different altitudes in the Alps for 1997 to June 2003, yielding a unique long-term comparison of GOME NO 2 VTC data retrieved by a collaboration of KNMI (Royal Netherlands Meteorological Institute) and BIRA/IASB (Belgian Institute for Space Aeronomy) with independently derived tropospheric NO 2 profiles. A first comparison relates the GOME retrieved tropospheric columns to the tropospheric columns obtained by integrating the ground-based NO 2 measurements. For a second comparison, the tropospheric profiles constructed from the ground-based measurements are first multiplied with the averaging kernel (AK) of the GOME retrieval. The second approach makes the comparison independent from the a priori NO 2 profile used in the GOME retrieval. This allows splitting the total difference between the column data sets into two contributions: one that is due to differences between the a priori and the ground-based NO 2 profile shapes, and another that can be attributed to uncertainties in both the remaining retrieval parameters (such as, e.g., surface albedo or aerosol concentration) and the ground-based in situ NO 2 profiles. For anticyclonic clear sky conditions the comparison indicates a good agreement between the columns (n=157, R=0.70/0.74 for the first/second comparison approach, respectively). The mean relative difference (with respect to the ground-based columns) is −7% with a standard deviation of 40% and GOME on average slightly underestimating the ground-based columns. Both data sets show a similar seasonal behaviour with a distinct maximum of spring NO 2 VTCs. Further analysis indicates small GOME columns being systematically smaller than the ground-based ones. The influence of different shapes in the a priori and the ground-based NO 2 profile is analysed by considering AK information. It is moderate and indicates similar shapes of the profiles for clear sky conditions. Only for large GOME columns, differences between the profile shapes explain the larger part of the relative difference. In contrast, the other error sources give rise to the larger relative differences found towards smaller columns. Further, for the clear sky cases, errors from different sources are found to compensate each other partially. The comparison for cloudy cases indicates a poorer agreement between the columns (n=60, R=0.61). The mean relative difference between the columns is 60% with a standard deviation of 118% and GOME on average overestimating the ground-based columns. The clear improvement after inclusion of AK information (n=60, R=0.87) suggests larger errors in the a priori NO 2 profiles under cloudy conditions and demonstrates the importance of using accurate profile information for (partially) clouded scenes.
Deep Sequencing of HIV-1 RNA and DNA in Newly Diagnosed Patients with Baseline Drug Resistance Showed No Indications for Hidden Resistance and Is Biased by Strong Interference of Hypermutation

ABSTRACT Deep sequencing of plasma RNA or proviral DNA may be an interesting alternative to population sequencing for the detection of baseline transmitted HIV-1 drug resistance. Using a Roche 454 GS Junior HIV-1 prototype kit, we performed deep sequencing of the HIV-1 protease and reverse transcriptase genes on paired plasma and buffy coat samples from newly diagnosed HIV-1-positive individuals. Selection was based on the outcome of population sequencing and included 12 patients with either a revertant amino acid at codon 215 of the reverse transcriptase or a singleton resistance mutation, 4 patients with multiple resistance mutations, and 4 patients with wild-type virus. Deep sequencing of RNA and DNA detected 6 and 43 mutations, respectively, that were not identified by population sequencing. A subsequently performed hypermutation analysis, however, revealed hypermutation in 61.19% of 3,188 DNA reads with a resistance mutation. The removal of hypermutated reads dropped the number of additional mutations in DNA from 43 to 17. No hypermutation evidence was found in the RNA reads. Five of the 6 additional RNA mutations and all additional DNA mutations, after full exclusion of hypermutation bias, were observed in the 3 individuals with multiple resistance mutations detected by population sequencing. Despite focused selection of patients with T215 revertants or singleton mutations, deep sequencing failed to identify the resistant T215Y/F or M184V or any other resistance mutation, indicating that in most of these cases there is no hidden resistance and that the virus detected at diagnosis by population sequencing is the original infecting variant.
Other- versus self-focus and risky health behavior: the case of HIV/AIDS

Abstract We examined the relationships of other-focus and self-focus with risky health behaviors among HIV+ individuals. Participants who were recruited by an AIDS advocacy organization completed anonymous questionnaires that included measures of other-focus (i.e. empathic concern and perspective-taking) and self-focus (i.e. personal distress and exaggerated internal control); direct measures of concern about the consequences of HIV/AIDS for the self, close others, and society; and a measure of willingness to engage in HIV/AIDS risk behaviors. As predicted, other-focus measures were generally associated with less, and self-focus measures with greater, willingness to engage in risky behavior. However, concern about the consequences of HIV/AIDS for close others was similar to self-focus and was associated with greater willingness to engage in risky behavior. These results are consistent with the notion that prevention efforts focusing on the consequences of HIV/AIDS – and perhaps other communicable diseases – might be more effective if they highlighted the consequences of the disease for society.
Microwave and millimeter-wave rectifying circuit arrays and ultra-wideband antennas for wireless power transmission and communications

Microwave and Millimeter-wave Rectifying Circuit Arrays and Ultra-wideband Antennas for Wireless Power Transmission and Communications. (May 2007) Yu-Jiun Ren, B.S., National Chung-Hsing University; M.S., National Chiao-Tung University Chair of Advisory Committee: Dr. Kai Chang In the future, space solar power transmission and wireless power transmission will play an important role in gathering clean and infinite energy from space. The rectenna, i.e., a rectifying circuit combined with an antenna, is one of the most important components in the wireless power transmission system. To obtain high power and high output voltage, the use of a large rectenna array is necessary. Many novel rectennas and rectenna arrays for microwave and millimeter-wave wireless power transmission have been developed. Unlike the traditional rectifying circuit using a single diode, dual diodes are used to double the DC output voltage with the same circuit layout dimensions. The rectenna components are then combined to form rectenna arrays using different interconnections. The rectennas and the arrays are analyzed by using a linear circuit model. Furthermore, to precisely align the mainbeams of the transmitter and the receiver, a retrodirective array is developed to maintain high efficiency. The retrodirective array is able to track the incident wave and resend the signal to where it came from without any prior known information of the source location.
Accuracy and utility of an epigenetic biomarker for smoking in populations with varying rates of false self‐report

Better biomarkers to detect smoking are needed given the tremendous public health burden caused by smoking. Current biomarkers to detect smoking have significant limitations, notably a short half‐life for detection and lack of sensitivity for light smokers. These limitations may be particularly problematic in populations with less accurate self‐reporting. Prior epigenome‐wide association studies indicate that methylation status at cg05575921, a CpG residue located in the aryl hydrocarbon receptor repressor (AHRR) gene, may be a robust indicator of smoking status in individuals with as little as half of a pack‐year of smoking. In this study, we show that a novel droplet digital PCR assay for measuring methylation at cg05575921 can reliably detect smoking status, as confirmed by serum cotinine, in populations with different demographic characteristics, smoking histories, and rates of false‐negative self‐report of smoking behavior. Using logistic regression models, we show that obtaining maximum accuracy in predicting smoking status depends on appropriately weighting self‐report and cg05575921 methylation according to the characteristics of the sample being tested. Furthermore, models using only cg05575921 methylation to predict smoking perform nearly as well as those also including self‐report across populations. In conclusion, cg05575921 has significant potential as a clinical biomarker to detect smoking in populations with varying rates of accuracy in self‐report of smoking behavior.
Differential prevalence of antibodies against adeno-associated virus in healthy children and patients with mucopolysaccharidosis III: perspective for AAV-mediated gene therapy.

Recombinant AAV vectors are promising gene therapy tools. However, pre-existing antibodies (Abs) to many useful AAV serotypes pose a critical challenge for the translation of gene therapies. As part of AAV gene therapy program for treating MPS III patients, we investigated the seroprevalence profiles of AAV1-9 and rh74 in MPS IIIA/IIIB patients and in healthy children. Using ELISA for αAAV-IgG, we observed significantly higher sero-prevalence for AAV1 and AAVrh74 in 2-7y-old MPS III patients than in healthy controls. Seroprevalence for the majority of tested AAV serotypes appear to peak before age 8y in MPS III subjects, with the exception of increases in αAAV8 and αAAV9 Abs in 8-19y-old MPS IIIA patients. In contrast, we observed significant increases in seroprevalence for virtually all tested AAV serotypes in 8-15y-old healthy children compared to 2-7y-olds. Co-prevalence and Ab level correlation results followed the previously established divergence-based clade positions of AAV1-9. Interestingly, the individuals positive for αAAVrh74-Abs showed the lowest co-prevalence with Abs for AAV1-9 (22-40%), however, all or nearly all (77-100%) of subjects that were seropositive for any of serotypes 1-9, were also positive for αAAVrh74-IgG. Notably, the majority (78%) of αAAV seropositive individuals were also Ab-positive for 1-5 of the tested AAV serotypes, mostly with low levels of αAAV-Abs (1:50-100), while a minority (22%) were seropositive for ≥6 AAV serotypes, mostly with high levels of αAAV-IgG for multiple serotypes. In general, the highest IgG levels were reactive to AAV2, AAV3, and AAVrh74. The data illustrate the complex seroprevalence profiles of AAV1-9 and rh74 in MPS patients and healthy children, indicating the potential association of AAV seroprevalence with age and disease conditions. The broad co-prevalence of Abs for different AAV serotypes reinforces the challenge of pre-existing αAAV-Abs for translating AAV gene therapy to clinical applications, regardless of the vector serotype.
Natural Single-Nucleotide Variations in the HIV-1 Genomic SA1prox Region Can Alter Viral Replication Ability by Regulating Vif Expression Levels

ABSTRACT We previously found that natural single-nucleotide variations located within a proximal region of splicing acceptor 1 (SA1prox) in the HIV-1 genome could alter the viral replication potential and mRNA expression pattern, especially the vif mRNA level. Here, we studied the virological and molecular basis of nucleotide sequence variations in SA1prox for alterations of viral replication ability. Consistent with our previous findings, variant clones indeed expressed Vif at different levels and grew distinctively in cells with various APOBEC3G expression levels. Similar effects were observed for natural variations found in HIV-2 SA1prox, suggesting the importance of the SA1prox sequence. To define nucleotides critical for the regulation of HIV-1 Vif expression, effects of natural SA1prox variations newly found in the HIV Sequence Compendium database on vif mRNA/Vif protein levels were examined. Seven out of nine variations were found to produce Vif at lower, higher, or more excessive levels than wild-type NL4-3. Combination experiments of variations giving distinct Vif levels suggested that the variations mutually affected vif transcript production. While low and high producers of Vif grew in an APOBEC3G-dependent manner, excessive expressers always showed an impeded growth phenotype due to defects in single-cycle infectivity and/or virion production levels. The phenotype of excessive expressers was not due primarily to inadequate expression of Tat or Rev, although SA1prox variations altered the overall HIV-1 mRNA expression pattern. Collectively, our results demonstrate that HIV SA1prox regulates Vif expression levels and suggest a relationship between SA1prox and viral adaptation/evolution given that variations occurred naturally. IMPORTANCE While human cells possess restriction factors to inhibit HIV-1 replication, HIV-1 encodes antagonists to overcome these barriers. Conflicts between host restriction factors and viral counterparts are critical driving forces behind mutual evolution. The interplay of cellular APOBEC3G and viral Vif proteins is a typical example. Here, we demonstrate that naturally occurring single-nucleotide variations in the proximal region of splicing acceptor 1 (SA1prox) of the HIV-1 genome frequently alter Vif expression levels, thereby modulating viral replication potential in cells with various ABOBEC3G levels. The results of the present study reveal a previously unidentified and important way for HIV-1 to compete with APOBEC3G restriction by regulating its Vif expression levels. We propose that SA1prox plays a regulatory role in Vif counteraction against APOBEC3G in order to contribute to HIV-1 replication and evolution, and this may be applicable to other primate lentiviruses.
Tick attachment cement – reviewing the mysteries of a biological skin plug system

The majority of ticks in the family Ixodidae secrete a substance anchoring their mouthparts to the host skin. This substance is termed cement. It has adhesive properties and seals the lesion during feeding. The particular chemical composition and the curing process of the cement are unclear. This review summarizes the literature, starting with a historical overview, briefly introducing the different hypotheses on the origin of the adhesive and how the tick salivary glands have been identified as its source. Details on the sequence of cement deposition, the curing process and detachment are provided. Other possible functions of the cement, such as protection from the host immune system and antimicrobial properties, are presented. Histochemical and ultrastructural data of the intracellular granules in the salivary gland cells, as well as the secreted cement, suggest that proteins constitute the main material, with biochemical data revealing glycine to be the dominant amino acid. Applied methods and their restrictions are discussed. Tick cement is compared with adhesives of other animals such as barnacles, mussels and sea urchins. Finally, we address the potential of tick cement for the field of biomaterial research and in particular for medical applications in future.
Automated Pick-Place of Silicon Nanowires

Pick-place of single nanowires inside scanning electron microscopes (SEM) is useful for prototyping functional devices and characterizing nanowires's properties. Nanowire pick-place has been typically performed via teleoperation, which is time-consuming and highly skill-dependent. This paper presents an automated approach to the pick-place of single nanowires. Through SEM visual detection and vision-based motion control, the system automatically transferred individual silicon nanowires from their growth substrate to a microelectromechanical systems (MEMS) device that characterized the nanowires's electromechanical properties. The performance of the nanorobotic pick-up and placement procedures was experimentally quantified.
The Effects of Gender Composition in Academic Departments on Faculty Turnover

Using data collected from a sample of 50 academic departments over the years 1977–88, the authors test several hypotheses about the effects of departmental gender composition on faculty turnover. They find that as the proportion of women in a department grew, turnover among women also increased, confirming the prediction that increases in the relative size of a minority will result in increased intergroup competition and conflict. The evidence also suggests, however, that when the proportion of female faculty reached a threshold of about 35–40%, turnover among women began to decline. The proportion of women had a negligible or negative impact on turnover among male faculty. The authors discuss the implications of this research for the implementation of affirmative action policies.
The Ms6 Mycolyl-Arabinogalactan Esterase LysB is Essential for an Efficient Mycobacteriophage-Induced Lysis

All dsDNA phages encode two proteins involved in host lysis, an endolysin and a holin that target the peptidoglycan and cytoplasmic membrane, respectively. Bacteriophages that infect Gram-negative bacteria encode additional proteins, the spanins, involved in disruption of the outer membrane. Recently, a gene located in the lytic cassette was identified in the genomes of mycobacteriophages, which encodes a protein (LysB) with mycolyl-arabinogalactan esterase activity. Taking in consideration the complex mycobacterial cell envelope that mycobacteriophages encounter during their life cycle, it is valuable to evaluate the role of these proteins in lysis. In the present work, we constructed an Ms6 mutant defective on lysB and showed that Ms6 LysB has an important role in lysis. In the absence of LysB, lysis still occurs but the newly synthesized phage particles are deficiently released to the environment. Using cryo-electron microscopy and tomography to register the changes in the lysis phenotype, we show that at 150 min post-adsorption, mycobacteria cells are incompletely lysed and phage particles are retained inside the cell, while cells infected with Ms6wt are completely lysed. Our results confirm that Ms6 LysB is necessary for an efficient lysis of Mycobacterium smegmatis, acting, similarly to spanins, in the third step of the lysis process.
Escherichia coli Probiotic Strain ED1a in Pigs Has a Limited Impact on the Gut Carriage of Extended-Spectrum-β-Lactamase-Producing E. coli

ABSTRACT Four trials were conducted to evaluate the impact of Escherichia coli probiotic strain ED1a administration to pigs on the gut carriage or survival in manure of extended-spectrum-β-lactamase-producing E. coli. Groups of pigs were orally inoculated with strain E. coli M63 carrying the blaCTX-M-1 gene (n = 84) or used as a control (n = 26). In the first two trials, 24 of 40 E. coli M63-inoculated pigs were given E. coli ED1a orally for 6 days starting 8 days after oral inoculation. In the third trial, 10 E. coli M63-inoculated pigs were given either E. coli ED1a or probiotic E. coli Nissle 1917 for 5 days. In the fourth trial, E. coli ED1a was given to a sow and its 12 piglets, and these 12 piglets plus 12 piglets that had not received E. coli ED1a were then inoculated with E. coli M63. Fecal shedding of cefotaxime-resistant Enterobacteriaceae (CTX-RE) was studied by culture, and blaCTX-M-1 genes were quantified by PCR. The persistence of CTX-RE in manure samples from inoculated pigs or manure samples inoculated in vitro with E. coli M63 with or without probiotics was studied. The results showed that E. coli M63 and ED1a were good gut colonizers. The reduction in the level of fecal excretion of CTX-RE in E. coli ED1a-treated pigs compared to that in nontreated pigs was usually less than 1 log10 CFU and was mainly observed during the probiotic administration period. The results obtained with E. coli Nissle 1917 did not differ significantly from those obtained with E. coli ED1a. CTX-RE survival did not differ significantly in manure samples with or without probiotic treatment. In conclusion, under our experimental conditions, E. coli ED1a and E. coli Nissle 1917 could not durably prevent CTX-RE colonization of the pig gut.
Extended-Doublet Half-Mode Substrate Integrated Waveguide Bandpass Filter With Wide Stopband

A half-mode substrate integrated waveguide (HSIW) filter incorporated with co-planar waveguide (CPW) and co-planar strip (CPS) is proposed. Quarter-wavelength CPW and half-wavelength CPS resonators etched on the top metal layer are used to realized extended-doublet topology. Meanwhile, wide stopband characteristic is obtained, which is due to different higher order resonant frequencies of HSIW, CPS, and CPW. Finally, an HSIW filter is designed and measured, good agreements are achieved between measured and simulated S-parameters.
Expanding the CRISPR/Cas9 toolkit for Pichia pastoris with efficient donor integration and alternative resistance markers

Komagataella phaffii (syn. Pichia pastoris) is one of the most commonly used host systems for recombinant protein expression. Achieving targeted genetic modifications had been hindered by low frequencies of homologous recombination (HR). Recently, a CRISPR/Cas9 genome editing system has been implemented for P. pastoris enabling gene knockouts based on indels (insertion, deletions) via non‐homologous end joining (NHEJ) at near 100% efficiency. However, specifically integrating homologous donor cassettes via HR for replacement studies had proven difficult resulting at most in ∼20% correct integration using CRISPR/Cas9. Here, we demonstrate the CRISPR/Cas9 mediated integration of markerless donor cassettes at efficiencies approaching 100% using a ku70 deletion strain. The Ku70p is involved in NHEJ repair and lack of the protein appears to favor repair via HR near exclusively. While the absolute number of transformants in the Δku70 strain is reduced, virtually all surviving transformants showed correct integration. In the wildtype strain, markerless donor cassette integration was also improved up to 25‐fold by placing an autonomously replicating sequence (ARS) on the donor cassette. Alternative strategies for improving donor cassette integration using a Cas9 nickase variant or reducing off targeting associated toxicity using a high fidelity Cas9 variant were so far not successful in our hands in P. pastoris. Furthermore we provide Cas9/gRNA expression plasmids with a Geneticin resistance marker which proved to be versatile tools for marker recycling. The reported CRSIPR‐Cas9 tools can be applied for modifying existing production strains and also pave the way for markerless whole genome modification studies in P. pastoris.
Hardness and slip systems of orthorhombic hen egg-white lysozyme crystals

Abstract Hardness and slip systems by an indentation method were investigated on different habit planes of orthorhombic hen egg-white lysozyme (O-HEWL) crystals containing water. A dependence of the hardness on the water-evaporation time exhibits three stages as incubation, transition and saturated ones, as tetragonal (T)-HEWL crystals reported previously. The hardness values of (1 1 0), (0 1 0) and (0 1 1) habit planes of O-HEWL in the incubation stage or wet condition exhibits 6, 8 and 10 MPa, respectively. The hardness depends on indented planes but it is independent of the air-humidity and crystal volumes. These values correspond to the intrinsic hardness for O-HEWL crystals containing water. In the incubation stage, the slip traces are clearly observed around the indentation mark and the corresponding six kinds of slip systems are identified to be {0 1 1}<1 0 0>, {1 1 0}<1 1 0>, {0 1 1}<0 1 1>, {1 1 0}<0 0 1>, {1 0 0}<0 0 1> and {0 1 0}<0 0 1>.