Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioterrorism and Biocrimes: The Illicit Use of Biological Agents Since 1900 (February 2001 Revision)

Abstract : During the past five years, the threat of bioterrorism has become a subject of widespread concern. Journalists, academics, and policy analysts have considered the subject, and in most cases found much to alarm them. Most significantly, it has captured the attention of policy makers at all levels of government in the United States. Unfortunately, bioterrorism remains a poorly understood subject. Many policymakers and policy analysts present apocalyptic visions of the threat, contending that it is only a matter of time before some terrorist uses biological agents to cause mass casualties. In contrast, other analysts argue that the empirical record provides no basis for concern, and thus largely dismiss the potential threat. Neither approach is helpful. Imagining catastrophic threats inevitably leads to a requirement for impossibly large response capabilities. In contrast, denying the potential danger altogether leads to the kind of tunnel vision that led U.S. intelligence officials to totally ignore the emergence of Aum Shinrikyo in Japan, despite its overtly hostile attitude towards the United States. This study takes an intermediate course. It provides empirical evidence to support the views of those who argue that biological agents are difficult to use. It also provides abundant evidence that some people have desired to inflict mass casualties on innocent populations through employment of biological agents. Fortunately, these accounts also suggest that such people lacked the capability to follow through with their plans. The research also casts considerable doubt on our ability to predict which biological agents a perpetrator might employ. While some analysts assume that terrorists will use those agents that proved of most interest to state weapons programs, bioterrorists and biocriminals have acquired and used agents of little or no value as weapons of war.
Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks

In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm) isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra) analysis plots standardized (z-score) tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2). This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV) serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993–1994 and a single case from 2011 as well as links between two isolates from over 30 years ago. The identification of these potential links shows that JSpecies Tetra analysis can be a useful tool in rapidly assessing genetic relatedness of Lm isolates during outbreak investigations and for comparing historical isolates. Our analyses led to the identification of a highly related clonal group involved in two separate outbreaks, stone fruit and caramel apple, and suggests the possibility of a new genotype that may be better adapted for certain foods and/or environment.
Ambiguity in the Small and in the Large

This paper considers local and global multiple-prior representations of ambiguity for preferences that are (i) monotonic, (ii) Bernoullian, i.e. admit an affine utility representation when restricted to constant acts, and (iii) locally Lipschitz continuous. We do not require either Certainty Independence or Uncertainty Aversion. We show that the set of priors identified by Ghirardato, Maccheroni, and Marinacci (2004)’s ‘unambiguous preference’ relation can be characterized as a union of Clarke differentials. We then introduce a behavioral notion of ‘locally better deviation’ at an act, and show that it characterizes the Clarke differential of the preference representation at that act. These results suggest that the priors identified by these preference statements are directly related to (local) optimizing behavior.
The Response to Catechol Amine Infusion During Salicylate‐Induced Hypermetabolism in Man

The increase in oxygen consumption produced in man by salieylate administration is not associated with a rise in pulse rate or an increase in responsiveness to infusions of epinephrine or norepinephrine. It is suggested that the effects of thyroid hormone on the cardiovascular system are more dependent on the concentration of circulating thyroid hormone per se than on the concomitant increase in tissue oxygen consumption.
Late onset of the Holocene rainfall maximum in northeastern China inferred from a pollen record from the sediments of Tianchi Crater Lake

Abstract The timing of the Holocene summer monsoon maximum (HSMM) in northeastern China has been much debated and more quantitative precipitation records are needed to resolve the issue. In the present study, Holocene precipitation and temperature changes were quantitatively reconstructed from a pollen record from the sediments of Tianchi Crater Lake in northeastern China using a plant functional type-modern analogue technique (PFT-MAT). The reconstructed precipitation record indicates a gradual increase during the early to mid-Holocene and a HSMM at ~5500–3100 cal yr BP, while the temperature record exhibits a divergent pattern with a marked rise in the early Holocene and a decline thereafter. The trend of reconstructed precipitation is consistent with that from other pollen records in northeastern China, confirming the relatively late occurrence of the HSMM in the region. However, differences in the onset of the HSMM within northeastern China are also evident. No single factor appears to be responsible for the late occurrence of the HSMM in northeastern China, pointing to a potentially complex forcing mechanism of regional rainfall in the East Asian monsoon region. We suggest that further studies are needed to understand the spatiotemporal pattern of the HSMM in the region.
Application of bethesda system for cervical cytology in unhealthy cervix.

INTRODUCTION Women presenting with unhealthy cervix needs to be evaluated with Papanicolaou (Pap) smear for epithelial abnormalities. AIM To detect epithelial cell abnormalities in unhealthy cervix using the 2001Bethesda system of reporting for cervical cytology and to confirm histopathologicaly the findings of Pap smear. MATERIALS AND METHODS In this study, 125 women with clinical diagnosis of unhealthy cervix underwent conventional cytology. Cervical biopsies were taken from abnormal areas seen on colposcopy and sent for histopathology. RESULTS Out of 125 Pap smears, 122 were satisfactory for evaluation (19 normal, 86 negative for intraepithelial lesion or malignancy and 17 with epithelial cell abnormality) and 3 were unsatisfactory (one hemorrhagic and two severe inflammation). Out of 17 (13.60%) cases with epithelial cell abnormality, ASC-US was seen in 6 (4.80%), LSIL in 7 (5.60%), HSIL in 1 (0.80%), squamous cell carcinoma in 1 (0.80%), AGC endocervical in 1 (0.80%) and adenocarcinoma in 1 (0.80%) patients. Cervical biopsy was taken in 67 women. Diagnostic accuracy of Pap smear for preinvasive and invasive disease was 81.15% with overall sensitivity and specificity 78.57% and 88.67% respectively and predictive value of 64.71%. CONCLUSION Women with clinical diagnosis of unhealthy cervix should be evaluated by cytology to detect any premalignant or malignant lesions. The Bethesda system for cervical cytology reporting should be used universally as it will give a standardized interpretation.
Hardware transactional memory for GPU architectures

Graphics processor units (GPUs) are designed to efficiently exploit thread level parallelism (TLP), multiplexing execution of 1000s of concurrent threads on a relatively smaller set of single-instruction, multiple-thread (SIMT) cores to hide various long latency operations. While threads within a CUDA block/OpenCL workgroup can communicate efficiently through an intra-core scratchpad memory, threads in different blocks can only communicate via global memory accesses. Programmers wishing to exploit such communication have to consider data-races that may occur when multiple threads modify the same memory location. Recent GPUs provide a form of inter-block communication through atomic operations for single 32-bit/64-bit words. Although fine-grained locks can be constructed from these atomic operations, synchronization using locks is prone to deadlock. In this paper, we propose to solve these problems by extending GPUs to support transactional memory (TM). Major challenges include supporting 1000s of concurrent transactions and committing non-conflicting transactions in parallel. We propose KILO TM, a novel hardware TM design for GPUs that scales to 1000s of concurrent transactions. Without cache coherency hardware to depend on, it uses word-level, value-based conflict detection to avoid broadcast communication and reduce on-chip storage overhead. It employs speculative validation using a novel bloomfilter organization to increase transaction commit parallelism. For a set of TM-enhanced GPU applications, KILO TM captures 59% of the performance of fine-grained locking, and is on average 128×faster than executing all transactions serially, for an estimated hardware area overhead of 0.5% of a commercial GPU.
A neural model for binocular vergence control without explicit calculation of disparity

A computational model for the control of horizontal vergence, based on a population of disparity tuned complex cells, is presented. The model directly extracts the disparity-vergence response by combining the outputs of the disparity detectors without explicit calculation of the disparity map. The resulting vergence control yields to stable fixation and has small response time to a wide range of disparities. Experimental simulations with synthetic stimuli in depth validated the approach.
Evolution of Precipitation Structure During the November DYNAMO MJO Event: Cloud‐Resolving Model Intercomparison and Cross Validation Using Radar Observations

Evolution of precipitation structures are simulated and compared with radar observations for the November Madden‐Julian Oscillation (MJO) event during the DYNAmics of the MJO (DYNAMO) field campaign. Three ground‐based, ship‐borne, and spaceborne precipitation radars and three cloud‐resolving models (CRMs) driven by observed large‐scale forcing are used to study precipitation structures at different locations over the central equatorial Indian Ocean. Convective strength is represented by 0‐dBZ echo‐top heights, and convective organization by contiguous 17‐dBZ areas. The multi‐radar and multi‐model framework allows for more stringent model validations. The emphasis is on testing models' ability to simulate subtle differences observed at different radar sites when the MJO event passed through. The results show that CRMs forced by site‐specific large‐scale forcing can reproduce not only common features in cloud populations but also subtle variations observed by different radars. The comparisons also revealed common deficiencies in CRM simulations where they underestimate radar echo‐top heights for the strongest convection within large, organized precipitation features. Cross validations with multiple radars and models also enable quantitative comparisons in CRM sensitivity studies using different large‐scale forcing, microphysical schemes and parameters, resolutions, and domain sizes. In terms of radar echo‐top height temporal variations, many model sensitivity tests have better correlations than radar/model comparisons, indicating robustness in model performance on this aspect. It is further shown that well‐validated model simulations could be used to constrain uncertainties in observed echo‐top heights when the low‐resolution surveillance scanning strategy is used.
Molecular Diversity of the Antimicrobial Domain of Beta-Defensin 3 and Homologous Peptides

Human β-defensin 3 has received great interest for possible pharmaceutical applications. To characterize the biology of this antimicrobial peptide, the mouse β-defensin 14 has been selected as a prototypical model. This report provides definite evidence of true orthology between these defensins and reveals molecular diversity of a mammalian specific domain responsible for their antimicrobial activity. Specifically, this analysis demonstrates that eleven amino acid residues of the antimicrobial domain have been mutated by positive selection to confer protein niche specialization. These data support the notion that natural selection acts as evolutionary force driving the proliferation and diversification of defensins and introduce a novel strategy for the design of more effective antibiotics.
Origin and Diversification of Land Plant CC-Type Glutaredoxins

Glutaredoxins (GRXs) are ubiquitous glutathione-dependent oxidoreductase enzymes implicated in redox homeostasis, particularly oxidative stress response. Three major classes of GRX genes exist, the CPYC, CGFS classes are present in all pro- and eukaryote species, whereas the CC-type class GRXs are specific to land plants. In the basal land plant Physcomitrella patens, only two CC-type GRXs are present, compared with 21 in Arabidopsis. In contrast, sizes of the CPYC and CGFS classes remained rather similar throughout plant evolution, raising the interesting question as to when the CC-type GRXs first originated and how and why they expanded during land plant evolution. Recent evidence suggests that CC-type GRXs may have been recruited during evolution into diverse plant-specific functions of flower development (ROXY1, ROXY2) and pathogenesis response (ROXY19/GRX480). In the present study, GRX genes from the genomes of a range of green algae and evolutionarily diverse land plant species were identified; Ostreococcus, Micromonas, Volvox, Selaginella, Vitis, Sorghum, and Brachypodium. Previously identified sequences from Chlamydomonas, Physcomitrella, Oryza, Arabidopsis, and Populus were integrated to generate a more comprehensive understanding of the forces behind the evolution of various GRX classes. The analysis indicates that the CC-type GRXs probably arose by diversification from the CPYC class, at a time coinciding with colonization of land by plants. This strong differential expansion of the CC-type class occurred exclusively in the angiosperms, mainly through paleopolyploidy duplication events shortly after the monocot–eudicot split, and more recently through multiple tandem duplications that occurred independently in five investigated angiosperm lineages. The presented data suggest that following duplications, subfunctionalization, and subsequent neofunctionalization likely facilitated the sequestration of land plant-specific CC-type GRXs into novel functions such as development and pathogenesis response.
Image-Specific Prior Adaptation for Denoising

Image priors are essential to many image restoration applications, including denoising, deblurring, and inpainting. Existing methods use either priors from the given image (internal) or priors from a separate collection of images (external). We find through statistical analysis that unifying the internal and external patch priors may yield a better patch prior. We propose a novel prior learning algorithm that combines the strength of both internal and external priors. In particular, we first learn a generic Gaussian mixture model from a collection of training images and then adapt the model to the given image by simultaneously adding additional components and refining the component parameters. We apply this image-specific prior to image denoising. The experimental results show that our approach yields better or competitive denoising results in terms of both the peak signal-to-noise ratio and structural similarity.
Cascaded displays

We demonstrate that layered spatial light modulators (SLMs), subject to fixed lateral displacements and refreshed at staggered intervals, can synthesize images with greater spatiotemporal resolution than that afforded by any single SLM used in their construction. Dubbed cascaded displays, such architectures enable superresolution flat panel displays (e.g., using thin stacks of liquid crystal displays (LCDs)) and digital projectors (e.g., relaying the image of one SLM onto another). We introduce a comprehensive optimization framework, leveraging non-negative matrix and tensor factorization, that decomposes target images and videos into multi-layered, time-multiplexed attenuation patterns---offering a flexible trade-off between apparent image brightness, spatial resolution, and refresh rate. Through this analysis, we develop a real-time dual-layer factorization method that quadruples spatial resolution and doubles refresh rate. Compared to prior superresolution displays, cascaded displays place fewer restrictions on the hardware, offering thin designs without moving parts or the necessity of temporal multiplexing. Furthermore, cascaded displays are the first use of multi-layer displays to increase apparent temporal resolution. We validate these concepts using two custom-built prototypes: a dual-layer LCD and a dual-modulation liquid crystal on silicon (LCoS) projector, with the former emphasizing head-mounted display (HMD) applications.
Saccade impairments in patients with fronto-temporal dementia

Background: Early diagnosis of fronto-temporal dementia (FTD) is often difficult because of the non-specific presentation. Saccadic eye movements, which are mainly controlled by the frontal areas, may provide a powerful tool for the analysis of fontal lobe dysfunction. The pattern of saccadic abnormalities has not previously been investigated in patients with FTD. Objective: To study saccade tasks in a group of 23 patients with FTD and compare the results with aged matched healthy controls. Methods: Triggering and inhibition of reflexive prosaccades were evaluated in a prosaccade and an antisaccade task, respectively, while the ability to withhold an antisaccade during a delay was explored in a delayed antisaccade task. Patients with progressive supranuclear palsy (PSP), in whom the pattern of eye movement deficit is well documented, were studied with the same protocol. To characterise the frontal lobe dysfunction in FTD more precisely, a battery of neuropsychological tests was carried out in these patients. Results: Patients with FTD showed impaired reflexive saccade inhibition, similar to that observed in patients with PSP, and a decreased ability to withhold an antisaccade. Conclusions: Inhibition of reflexive and voluntary saccades appears to be independently processed. A delayed antisaccade task could be useful for the early diagnosis of FTD.
Immunomodulation of Fucosyl-Lactose and Lacto-N-Fucopentaose on Mononuclear Cells from Multiple Sclerosis and Healthy Subjects

The 1,2-fucosyl-oligosaccharides, and among these the 2’-fucosyl-lactose (2’-FL) and lacto-N-fucopentaose (LNFP)-I, are quantitatively the most represented oligosaccharides of human milk. They are also seen to represent an important immune device to prevent nursing infants from severe infectious diarrhoea. Recent evidences show that the appearance of 2’-FL and LNFP-I in human colostrums is synchronised with the macrophage inhibition and that LNFP-III induces a Th2 response from the mouse peripheral immune system. Since mannosyl-fucosyl receptors are described on the macrophage surface, all these evidences allow us to investigate on the possible immune function of human 2’-FL and LNFP-I in vitro on LPS-activated mononuclear cells (MNC) from 12 patients with multiple sclerosis (MS) and 20 matched health controls (HC). We found that 2’-FL and LNFP-I significantly decrease, to a different extent, the MNC proliferation from both HC and MS patients, in a linear and dose-dependent manner. 2’-FL and LNFP-I also reduce the production of IL-12 and IFN-γ, particularly in MS patients as compared to HC (p=0.01 and p<0.001, respectively), while increasing that of IL-10. The overall immunomodulatory effect of 2’-FL and LNFP I here presented may represent a future therapeutic option for the abnormal immune response found in some monocyte-mediated diseases.
Gaussianity analysis of ambient noise in littoral tropical water

The performance predictions for sonar assume a background of Gaussian noise, however, deviation from this assumption may generate false alarms. This paper attempts to find out whether the ambient noise in tropical waters of the western coast of Indian continental is Gaussian. Gaussianity is tested using graphical, numerical and verified using formal normality tests like Kolmogorov Smirnov (KS) test and Lilliefors (LF) test. Ambient noise recorded at 30 m of depth using passive sonar is found non-Gaussian. The percentage of Gaussianity is calculated periodically eight times over the day at an interval of one hour every five minutes recording. The effect of known noise sources like wind speed, tide height and temperature, on the percentage of Gaussianity, is found linear.
Synopsis of the knowledge on the Brazilian estuarine fishes

A substantial amount of information on the Brazilian estuarine fishes has been collected, but is still largely fragmented into different sources. This study presents a summary of the available knowledge on the biodiversity of estuarine fishes in Brazil, a brief analysis of the historical development of estuarine ichthyology and identifies current research gaps in the country. A total of 796 fish species were inventoried, representing about 2.3% of current valid fish species and about 17.6% of the Brazilian fish fauna. Data evidenced the existence of large coastal stretches inadequately sampled and a lack of human resources and infrastructure in parts of the coast. Large gaps in basic knowledge about the biology and ecology of the species were also detected. Reducing these deficiencies is of utmost importance for the study, documentation and conservation of the Brazilian biodiversity.