Miracle-dz/UniFAR-FTUs huggingface dataset:
Extensive Diversity of Ionizing-Radiation-Resistant Bacteria Recovered from Sonoran Desert Soil and Description of Nine New Species of the Genus Deinococcus Obtained from a Single Soil Sample

ABSTRACT The ionizing-radiation-resistant fractions of two soil bacterial communities were investigated by exposing an arid soil from the Sonoran Desert and a nonarid soil from a Louisiana forest to various doses of ionizing radiation using a 60Co source. The numbers of surviving bacteria decreased as the dose of gamma radiation to which the soils were exposed increased. Bacterial isolates surviving doses of 30 kGy were recovered from the Sonoran Desert soil, while no isolates were recovered from the nonarid forest soil after exposure to doses greater than 13 kGy. The phylogenetic diversities of the surviving culturable bacteria were compared for the two soils using 16S rRNA gene sequence analysis. In addition to a bacterial population that was more resistant to higher doses of ionizing radiation, the diversity of the isolates was greater in the arid soil. The taxonomic diversity of the isolates recovered was found to decrease as the level of ionizing-radiation exposure increased. Bacterial isolates of the genera Deinococcus, Geodermatophilus, and Hymenobacter were still recovered from the arid soil after exposure to doses of 17 to 30 kGy. The recovery of large numbers of extremely ionizing-radiation-resistant bacteria from an arid soil and not from a nonarid soil provides further ecological support for the hypothesis that the ionizing-radiation resistance phenotype is a consequence of the evolution of other DNA repair systems that protect cells against commonly encountered environmental stressors, such as desiccation. The diverse group of bacterial strains isolated from the arid soil sample included 60 Deinococcus strains, the characterization of which revealed nine novel species of this genus.
Internal Variability of the Winter Stratosphere. Part II: Time-Dependent Forcing

This paper considers the effect of time-dependent lower boundary wave forcing on the internal variability found to appear spontaneously in a stratosphere-only model when the forcing is perfectly steady. While the time-dependent forcing is found to modulate the internal variability, leading in some cases to frequency locking of the upper-stratospheric response to the forcing, the temporal and spatial structure of the variability remains similar to the case when the forcing is time independent. Experiments with a time-periodic modulation of the forcing amplitude indicate that the wave flux through the lower boundary is only partially related to the instantaneous forcing, but is more significantly influenced by the condition of the polar vortex itself. In cases of purely random wave forcing with zero time mean, the stratospheric response is similar to that obtained with steady forcing of magnitude equal to the root-mean-square of the time-varying forcing.
Occupational exposure to aluminum and its biomonitoring in perspective

Exposure to aluminum at work is widespread, and people are exposed to several species of aluminum, which differ markedly as to the kinetics and toxicity. Especially welding of aluminum is widely applied and continuously expanding. Inhalation of fine particles of sparsely soluble aluminum results in the retention of deposited particles in the lungs. From the lungs, aluminum is released to the blood and distributed to bones and the brain, and excreted to urine. Soluble aluminum compounds are not accumulated in the lungs. Neurotoxicity is the critical effect of exposure to sparsely soluble aluminum compounds. Studies on workers exposed to aluminum welding fumes have revealed disturbances of cognitive processes, memory and concentration, and changes in mood and EEG. Early pulmonary effects have been observed among aluminum powder-production workers using high-resolution computed tomography. The primary objective of aluminum biomonitoring (BM) is to help prevent the formation of aluminum burden in the lungs and thereby to prevent harmful accumulation of aluminum in target organs. BM of aluminum can be effectively used for this purpose in the production/use of aluminum powders, aluminum welding, as well as plasma cutting, grinding, polishing and thermal spraying of aluminum. BM of aluminum may also be similarly useful in the smelting of aluminum and probably in the production of corundum. BM can help identify exposed individuals and roughly quantitate transient exposure but cannot predict health effects in the production/use of soluble aluminum salts. For urinary aluminum (U-Al) we propose an action limit of 3 µmol/L, corrected to a relative density of 1.021, in a sample collected preshift after two days without occupational exposure, and without use of aluminum-containing drugs. This value corresponds roughly to 2.3 µmol/g creatinine. Compliance with this limit is expected to protect the worker against the critical effect of aluminum in exposure to sparsely soluble aluminum dusts, the cognitive function of the central nervous system. For serum aluminum (S-Al), we do not propose an action limit because S-Al is less sensitive as an indicator of aluminum load.
Thirty-five year mortality following receipt of SV40- contaminated polio vaccine during the neonatal period

Early poliovirus vaccines, both inactivated and live attenuated, were inadvertently contaminated with simian virus 40 (SV40), a monkey virus known to be oncogenic for newborn hamsters. Although large epidemiologic studies have not identified an elevated cancer risk in persons who received SV40-contaminated vaccines, fragments of SV40 DNA have recently been identified in certain human tumours. We report the follow-up of a cohort of 1073 persons, unique because they received SV40-contaminated poliovirus vaccines as newborns in 1961–63. A previous report of the status of these subjects as of 1977–79 identified 15 deaths, none due to cancer. The present study utilized the National Death Index to identify deaths in the cohort for the years 1979–96. Expected deaths were calculated from Cleveland area sex-, age-, race- and year-specific mortality rates. Increased mortality from all causes was not found. 4 deaths from cancer were found compared to 3.16 expected (P= 0.77). However, 2 deaths from testicular cancer occurred, compared to 0.05 expected (P= 0.002), which may be a chance finding due to multiple comparisons. There were 2 deaths due to leukaemia, a non-significant finding, and no deaths due to tumours of the types putatively associated with SV40. Although these results are, for the most part, consistent with other negative epidemiologic investigations of risks from SV40-contaminated vaccines, further study of testicular cancer may be warranted, and it will be important to continue monitoring this cohort which is now reaching middle-age. © 2001 Cancer Research Campaign www.bjcancer. com
The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation

Initiation of reverse transcription of a retroviral RNA genome is strictly regulated. The tRNA primer binds to the primer binding site (PBS), and subsequent priming is triggered by the primer activation signal (PAS) that also pairs with the tRNA. We observed that in vitro reverse transcription initiation of the HIV-1 leader RNA varies in efficiency among 3′-end truncated transcripts, despite the presence of both PBS and PAS motifs. As the HIV-1 leader RNA can adopt two different foldings, we investigated if the conformational state of the transcripts did influence the efficiency of reverse transcription initiation. However, mutant transcripts that exclusively fold one or the other structure were similarly active, thereby excluding the possibility of regulation of reverse transcription initiation by the structure riboswitch. We next set out to determine the availability of the PAS element. This sequence motif enhances the efficiency of reverse transcription initiation, but its activity is regulated because the PAS motif is initially base paired within the wild-type template. We measured that the initiation efficiency on different templates correlates directly with accessibility of the PAS motif. Furthermore, changes in PAS are critical to facilitate a primer-switch to a new tRNA species, demonstrating the importance of this enhancer element.
Impact of struck-out text on writer identification

The presence of struck-out text in handwritten manuscripts may affect the accuracy of automated writer identification. This paper presents a study on such effects of struck-out text. Here we consider offline English and Bengali handwritten document images. At first, the struck-out texts are detected using a hybrid classifier of a CNN (Convolutional Neural Network) and an SVM (Support Vector Machine). Then the writer identification process is activated on normal and struck-out text separately, to ascertain the impact of struck-out texts. For writer identification, we use two methods: (a) a hand-crafted feature-based SVM classifier, and (b) CNN-extracted auto-derived features with a recurrent neural model. For the experimental analysis, we have generated a database from 100 English and 100 Bengali writers. The performance of our system is very encouraging.
The in vivo mechanism of action of CD20 monoclonal antibodies depends on local tumor burden

Background CD20 monoclonal antibodies are widely used in clinical practice. Antibody-dependent cellular cytotoxicity, complement-dependent cytotoxicity and direct cell death have been suggested to be important effector functions for CD20 antibodies. However, their specific contributions to the in vivo mechanism of action of CD20 immunotherapy have not been well defined. Design and Methods Here we studied the in vivo mechanism of action of type I (rituximab and ofatumumab) and type II (HuMab-11B8) CD20 antibodies in a peritoneal, syngeneic, mouse model with EL4-CD20 cells using low and high tumor burden. Results Interestingly, we observed striking differences in the in vivo mechanism of action of CD20 antibodies dependent on tumor load. In conditions of low tumor burden, complement was sufficient for tumor killing both for type I and type II CD20 antibodies. In contrast, in conditions of high tumor burden, activating FcγR (specifically FcγRIII), active complement and complement receptor 3 were all essential for tumor killing. Our data suggest that complement-enhanced antibody-dependent cellular cytotoxicity may critically affect tumor killing by CD20 antibodies in vivo. The type II CD20 antibody 11B8, which is a poor inducer of complement activation, was ineffective against high tumor burden. Conclusions Tumor burden affects the in vivo mechanism of action of CD20 antibodies. Low tumor load can be eliminated by complement alone, whereas elimination of high tumor load requires multiple effector mechanisms.
Embedding meshes on the star graph

Algorithms for mapping n-dimensional meshes on a star graph of degree n with expansion 1 and dilation 3 are developed. It is shown that an n-degree star graph can efficiently simulate an n-dimensional mesh. The analysis indicates that the algorithms developed for uniform meshes may not be efficiently simulated on the star graph. <<ETX>>
Alloreactive natural killer cells promote haploidentical hematopoietic stem cell transplantation by expansion of recipient‐derived CD4+CD25+ regulatory T cells

Alloreactive NK cells (Allo‐NKs) have been shown to exert advantageous effects on the outcomes of haploidentical hematopoietic stem cell transplantation (Haplo‐HSCT) for cancer treatment. However, the mechanisms of action of Allo‐NKs remain unclear. We established a novel Haplo‐HSCT conditioning regimen composed of Allo‐NKs and a low dose of immunosuppressive drugs (Allo‐NKs + Chemo) to investigate alternative mechanisms besides direct cytotoxicity. The inhibitory effects of different cell subsets on the donor–recipient mixed lymphocyte reactions (MLRs) were evaluated after Haplo‐HSCT. The quantities and functions of CD4+CD25+ regulatory T cells (Tregs) and dendritic cells (DCs) in the spleen and the thymus were examined. Our results showed that the Allo‐NKs + Chemo regimen induced systemic tolerance, and that CD4+CD25+ Tregs played a significant role in inducing and maintaining systemic tolerance after Haplo‐HSCT. Alloreactive NK cells promoted the expansion of recipient‐derived CD4+CD25+CD127− Tregs in the thymus and the spleen which could be amplified in vitro by the immature donor‐derived DC subset isolated from the thymus of Allo‐NKs + Chemo‐treated mice. Our findings suggested that Allo‐NKs are capable of inducing systemic tolerance after Haplo‐HSCT by assembling donor‐derived immature DCs to expand recipient‐derived Treg cells in the thymus.
LPA 2 receptor mediates mitogenic signals in human colon cancer cells

Yun, C. Chris, Hong Sun, Dongsheng Wang, Raluca Rusovici, Amanda Castleberry, Randy A. Hall, and Hyunsuk Shim. LPA2 receptor mediates mitogenic signals in human colon cancer cells. Am J Physiol Cell Physiol 289: C2–C11, 2005. First published February 23, 2005; doi:10.1152/ajpcell.00610. 2004. —Lysophosphatidic acid (LPA) is a mediator of multiple cellular responses. LPA mediates its effects predominantly through the G protein-coupled receptors LPA1, LPA2, and LPA3. In the present work, we studied LPA2-mediated signaling using human colon cancer cell lines, which predominantly express LPA2. LPA2 activated Akt and Erk1/2 in response to LPA. LPA mediated Akt activation was inhibited by pertussis toxin (PTX), whereas Erk1/2 activation was completely inhibited by a blocker of phospholipase C , U-73122. LPA also induced interleukin-8 (IL-8) synthesis in the colon cancer cells by primarily activating LPA2 receptor. We also found that LPA2 interacts with Na /H exchanger regulatory factor 2 (NHERF2). Activation of Akt and Erk1/2 was significantly attenuated by silencing of NHERF2 expression by RNA interference, suggesting a pivotal role of NHERF2 in LPA2-mediated signaling. We found that expression of LPA2 was elevated, whereas expression of LPA1 downregulated in several types of cancers, including ovarian and colon cancer. We conclude that LPA2 is the major LPA receptor in colon cancer cells and cellular signals by LPA2 are largely mediated through its ability to interact with NHERF2.
Time-Resolved Chirp Properties of SOAs Measured With an Optical Bandpass Filter

Chirp properties induced by semiconductor optical amplifiers (SOAs) are investigated by a simple chirp measurement method using an optical bandpass filter. We measure the chirp properties of signals generated by an SOA-based wavelength converter at noninverted and inverted logic operations. These results demonstrate well the features of the chirp properties induced by SOA.
Metabolic Changes and Serum Ghrelin Level in Patients with Psoriasis

Background. Serum ghrelin levels may be related to metabolic and clinical changes in patients with psoriasis. Objective. This study was performed to determine the possible effects of serum ghrelin in patients with psoriasis. Methods. The study population consisted of 25 patients with plaque psoriasis. The patients were questioned with regard to age, gender, age of onset, duration of disease, height, weight, and body mass index (BMI). In addition, fasting blood sugar, triglyceride, cholesterol levels, insulin, and ghrelin levels were measured. Results. The mean serum ghrelin level was 45.41 ± 22.41 in the psoriasis group and 29.92 ± 14.65 in the healthy control group. Serum ghrelin level was significantly higher in the psoriasis group compared with the controls (P = 0.01). The mean ghrelin level in patients with a lower PASI score was significantly higher than in those with a higher PASI score (P = 0.02). Conclusion. The present study was performed to determine the effects of ghrelin in psoriasis patients. We found a negative correlation between severity of psoriasis and ghrelin level. Larger and especially experimental studies focusing on correlation of immune system-ghrelin levels and severity of psoriasis may be valuable to clarify the etiopathogenesis of the disease.
Local energy minimality of capillary surfaces in the presence of symmetry

Consider the stationary capillary problem of a drop of liquid attached to a fixed surface, so that the drop minimizes an energy functional subject to a volume constraint. There are many such capillary problems in which, due to the symmetry of the fixed surface, one cannot hope for a capillary surface which is a strict local minimum for energy. A weaker concept which is sensible to consider is that of local minimality modulo the isometries of space which map the fixed surface into itself. In other words, it is reasonable to attempt to show that, given a capillary surface, any nearby comparison surface will have energy greater than or equal to the given surface, and if the energy is equal, the comparison surface is simply a translation or rotation of the given surface. Eigenvalue conditions are derived which imply that a capillary surface is a strict local minimum modulo isometries, and are applied to the specific example of a liquid bridge between two parallel planes.
Ex vivo assessment of serum cytokines in patients with cystic echinococcosis of the liver

To investigate the usefulness of serum cytokine levels in the diagnosis of active cystic echinococcosis, we evaluated the cytokine profile of patients with hepatic cystic echinococcosis in different cyst stages, CE 1‐2 (active), CE3a‐3b (transitional) and CE4‐5 (inactive). Ex vivo assessment of Th1 (IL12, TNFα) and Th2 (IL4, IL10) cytokines in sera was carried out using ELISA. Percentages of positive samples and median levels of IL12, TNFα and IL10 did not differ significantly between groups. However, patients with CE3b cysts, a stage clinically unresponsive to treatments, had statistically significantly higher median levels of IL4 and percentage of positive samples for IL4. We conclude that the analysis of serum cytokine dosage, at least in its present form, is not useful as a marker of cyst activity. However, our results support recent findings suggesting the chronic activity of CE3b cysts and suggest that this might be partly because of a skewed Th2 response.
Importance of Operational Factors in the Reproducibility of Aspergillus Galactomannan Enzyme Immune Assay

Background The Platelia Aspergillus Ag assay (Bio-Rad) is designed for detecting Aspergillus galactomannan (GM) and is widely used for diagnosing invasive aspergillosis but is hampered by variable occurrences of unreproducible positive results. Frequency and origin of these unreproducible results have not been formally studied. Methods Different technicians simultaneously performed four tests on 550 consecutive sera from adult patients (Test#1-Test#2 for extraction#1 and Test#3-Test#4 for extraction#2). The samples were classified as confirmed negative [all tests with GM optical density index (GM-ODI) <0.5], confirmed positive (all tests with GM-ODI ≥0.5), extraction unreproducible positive (Test#1 and Test#2 ODIs ≥0.5, and Test#3 and Test#4 GM-ODIs <0.5, or conversely), and ELISA unreproducible positive (only one test with GM-ODI ≥0.5). The samples with positive and negative GM-ODIs within the assay coefficient of variation values were classified as non-conclusive. Four similar additional tests were performed after ≤72h storage at 4°C and a new GM test after 8 months at -20°C. Results Five-hundred-twenty sera (94.5%) were confirmed negative, 15 (2.7%) confirmed positive, 4 (0.7%) extraction unreproducible positive, 6 (1.1%) ELISA unreproducible positive, and 5 (0.9%) non-conclusive. Upon retesting, the unreproducible positive results turned negative except for one which turned non-conclusive. The confirmed positive and non-conclusive had similar GM-ODIs (p>0.4) upon retesting after storage ≤72h at 4°C (n = 20) or eight months at -20°C (n = 17). Conclusions Operational unreproducible positives represent 33% of the GM-positive results and a second sample evaluation appears mandatory to avoid useless investigations or treatments. When operational artifacts are excluded, GM remains stable at standard storage conditions.
Deadlock Immunity: Enabling Systems to Defend Against Deadlocks

Deadlock immunity is a property by which programs, once afflicted by a given deadlock, develop resistance against future occurrences of that and similar deadlocks. We describe a technique that enables programs to automatically gain such immunity without assistance from programmers or users. We implemented the technique for both Java and POSIX threads and evaluated it with several real systems, including MySQL, JBoss, SQLite, Apache ActiveMQ, Limewire, and Java JDK. The results demonstrate effectiveness against real deadlock bugs, while incurring modest performance overhead and scaling to 1024 threads. We therefore conclude that deadlock immunity offers programmers and users an attractive tool for coping with elusive deadlocks.
Multiple Signals Regulate GALTranscription in Yeast

ABSTRACT Gal4p activates transcription of the Saccharomyces GALgenes in response to galactose and is phosphorylated during interaction with the RNA polymerase II (Pol II) holoenzyme. One phosphorylation at S699 is necessary for full GAL induction and is mediated by Srb10p/CDK8 of the RNA Pol II holoenzyme mediator subcomplex. Gal4p S699 phosphorylation is necessary for sensitive response to inducer, and its requirement for GAL induction can be abrogated by high concentrations of galactose in strains expressing wild-typeGAL2 and GAL3. Gal4p S699 phosphorylation occurs independently of Gal3p and is responsible for the long-term adaptation response observed in gal3 yeast.SRB10 and GAL3 are shown to represent parallel mechanisms for GAL gene induction. These results demonstrate that Gal4p activity is controlled by two independent signals: one that acts through Gal3p-galactose and a second that is mediated by the holoenzyme-associated cyclin-dependent kinase Srb10p. Since Srb10p is regulated independently of galactose, our results suggest a function for CDK8 in coordinating responses to specific inducers with the environment through the phosphorylation of gene-specific activators.
Gulliver project: performers and visitors

This paper discusses two projects in our research environment. The Gulliverproject, an ambitious project conceived by some artists connected to our research efforts, and the Aveiro-project, as well ambitious, but with goals that can be achieved beause of technological developments, rather than be dependent on artistic and ‘political’ (read: financial) sources. Both projects are on virtual and augmented reality. The main goal is to design inhabited environments, where ‘inhabited’ refers to autonomous agents and agents that represent humans, realtime or off-line, visiting the virtual environment and interacting with other agents. The Gulliver environment has been designed by two artists: Matjaž Stuk and Alena Hudcovicova. The Aveiro project is a research effort of a group of researchers trying to design models of intelligence and interaction underlying the behavior of (groups of) agents inhabiting virtual worlds. In this paper we survey the current state of both projects and we discuss current and future attempts to have music performances by virtual and real performers in these environments.