Miracle-dz/UniFAR-FTUs huggingface dataset:
Gamma interferon and lymphotoxin, released by activated T cells, synergize to inhibit granulocyte/monocyte colony formation

We have shown that lymphocytes stimulated by PHA produce colony-forming unit of granulocyte/monocyte (CFU-GM)-stimulating and -inhibiting activities, IFN-gamma, and lymphotoxin (LT). IFN-gamma is necessary for inhibition of CFU-GM by PHA-conditioned medium (CM), as shown by experiments in which removal of IFN-gamma from PHA-CM abrogated inhibition. However, experiments in which rIFN-gamma was added to IFN- gamma-depleted PHA-CM revealed the presence, in PHA-CM, of other factors that act in synergy with IFN-gamma to inhibit CFU-GM. Fractionation of PHA-CM on a Sephadex G-100 column was used to separate IFN-gamma and LT. Colony-inhibiting activity was eluted in fractions that contained both IFN-gamma and LT activities, identifying LT as a factor present in PHA-CM that synergizes with IFN-gamma to inhibit CFU- GM. Treatment of PHA-CM with mAb against either IFN-gamma or LT completely abrogated the colony-inhibiting activity, demonstrating a requirement for both lymphokines in PHA-CM-induced inhibition of CFU- GM. Experiments using rIFN-gamma and preparations of purified LT confirmed that neither lymphokine alone, when added to bone marrow cells at the concentrations present in PHA-CM, strongly inhibited day 7 or day 14 CFU-GM, but that the two lymphokines, added together, behaved synergistically to inhibit CFU-GM by up to 70%. The inhibition observed using purified preparations of lymphokines shows that synergy between IFN-gamma and LT is sufficient to explain PHA-CM-induced inhibition of CFU-GM. Our findings suggest that activated T cells regulate hematopoiesis through the release of inhibitory as well as stimulatory factors, and that the simultaneous production of IFN-gamma and LT may represent a mechanism of suppression of hematopoiesis in the cases of bone marrow failure associated with the presence of activated T cells.
Differential Regulation of Horizontally Acquired and Core Genome Genes by the Bacterial Modulator H-NS

Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in response to external stimuli such as osmolarity and temperature. Here we provide evidence that H-NS discriminates and differentially modulates core and HGT DNA. As an example of this, plasmid R27-encoded H-NS protein has evolved to selectively silence HGT genes and does not interfere with core genome regulation. In turn, differential regulation of both gene lineages by resident chromosomal H-NS requires a helper protein: the Hha protein. Tight silencing of HGT DNA is accomplished by H-NS-Hha complexes. In contrast, core genes are modulated by H-NS homoligomers. Remarkably, the presence of Hha-like proteins is restricted to the Enterobacteriaceae. In addition, conjugative plasmids encoding H-NS variants have hitherto been isolated only from members of the family. Thus, the H-NS system in enteric bacteria presents unique evolutionary features. The capacity to selectively discriminate between core and HGT DNA may help to maintain horizontally transmitted DNA in silent form and may give these bacteria a competitive advantage in adapting to new environments, including host colonization.
The sea level fingerprint of recent ice mass fluxes

The sea level contribution from glacial sources has been accelerating during the first decade of the 21st Century (Meier et al., 2007; Velicogna, 2009). This contribution is not distributed uniformly across the world's oceans due to both oceanographic and gravitational effects. We compute the sea level signature for ice mass fluxes due to changes in the gravity field, Earth's rotation and related effects for the nine year period 2000–2008. Mass loss from Greenland results in a relative sea level (RSL) reduction for much of North Western Europe and Eastern Canada. RSL rise from this source is concentrated around South America. Losses in West Antarctica marginally compensate for this and produce maxima along the coastlines of North America, Australia and Oceania. The combined far-field pattern of wastage from all ice melt sources, is dominated by losses from the ice sheets and results in maxima at latitudes between 20° N and 40° S across the Pacific and Indian Oceans, affecting particularly vulnerable land masses in Oceania. The spatial pattern of RSL variations from ice mass losses used in this study is time-invariant and cumulative. Thus, sea level rise, based on the gravitational effects from the ice losses considered here, will be amplified for this sensitive region.
Role of HLA, KIR, MICA, and Cytokines Genes in Leprosy

Many genes including HLA, KIR, and MICA genes, as well as polymorphisms in cytokines have been investigated for their role in infectious disease. HLA alleles may influence not only susceptibility or resistance to leprosy, but also the course of the disease. Some combinations of HLA and KIR may result in negative as well as positive interactions between NK cells and infected host cells with M. leprae, resulting in activation or inhibition of NK cells and, consequently, in death of bacillus. In addition, studies have demonstrated the influence of MICA genes in the pathogenesis of leprosy. Specifically, they may play a role in the interaction between NK cells and infected cells. Finally, pro- and anti-inflammatory cytokines have been influencing the clinical course of leprosy. Data from a wide variety of sources support the existence of genetic factors influencing the leprosy pathogenesis. These sources include twin studies, segregation analyses, family-based linkage and association studies, candidate gene association studies, and, most recently, genome-wide association studies (GWAS). The purpose of this brief review was to highlight the importance of some immune response genes and their correlation with the clinical forms of leprosy, as well as their implications for disease resistance and susceptibility.
Dismantling Megamos Crypto: Wirelessly Lockpicking a Vehicle Immobilizer

The Megamos Crypto transponder is used in one of the most widely deployed electronic vehicle immobilizers. It is used among others in most Audi, Fiat, Honda, Volkswagen and Volvo cars. Such an immobilizer is an antitheft device which prevents the engine of the vehicle from starting when the corresponding transponder is not present. This transponder is a passive RFID tag which is embedded in the key of the vehicle. In this paper we have reverse-engineered all proprietary security mechanisms of the transponder, including the cipher and the authentication protocol which we publish here in full detail. This article reveals several weaknesses in the design of the cipher, the authentication protocol and also in their implementation. We exploit these weaknesses in three practical attacks that recover the 96bit transponder secret key. These three attacks only require wireless communication with the system. Our first attack exploits weaknesses in the cipher design and in the authentication protocol. We show that having access to only two eavesdropped authentication traces is enough to recover the 96-bit secret key with a computational complexity of 256 cipher ticks (equivalent to 2 encryptions). Our second attack exploits a weakness in the key-update mechanism of the transponder. This attack recovers the secret key after 3× 2 authentication attempts with the transponder and negligible computational complexity. We have executed this attack in practice on several vehicles. We were able to recover the key and start the engine with a transponder emulating device. Executing this attack from beginning to end takes only 30 minutes. Our third attack exploits the fact that some car manufacturers set weak cryptographic keys in their vehicles. We propose a time-memory trade-off which recovers such a weak key after a few minutes of computation on a standard laptop.
CYGD: the Comprehensive Yeast Genome Database

The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf. de/genre/proj/yeast/.
CLK‐1 controls respiration, behavior and aging in the nematode Caenorhabditis elegans

Mutations in the clk‐1 gene of the nematode Caenorhabditis elegans result in an average slowing of a variety of developmental and physiological processes, including the cell cycle, embryogenesis, post‐embryonic growth, rhythmic behaviors and aging. In yeast, a CLK‐1 homologue is absolutely required for ubiquinone biosynthesis and thus respiration. Here we show that CLK‐1 is fully active when fused to green fluorescent protein and is found in the mitochondria of all somatic cells. The activity of mutant mitochondria, however, is only very slightly impaired, as measured in vivo by a dye‐uptake assay, and in vitro by the activity of succinate cytochrome c reductase. Overexpression of CLK‐1 activity in wild‐type worms can increase mitochondrial activity, accelerate behavioral rates during aging and shorten life span, indicating that clk‐1 regulates and controls these processes. These observations also provide strong genetic evidence that mitochondria are causally involved in aging. Furthermore, the reduced respiration of the long‐lived clk‐1 mutants suggests that longevity is promoted by the age‐dependent decrease in mitochondrial function that is observed in most species.
The Impact of Taxes on Migration in New England

Evidence from surveys of migrating households, the existing economic literature, and new analysis using data from the Internal Revenue Service all suggest that taxes do not play any notable role in causing people to leave a state. The most important factors in influencing household migration are employment and family-related reasons. If anything, higher state income taxes decrease the number of people leaving a state. Taxes do appear to influence the choice of which state to live in once a person has decided to move, but the impact is modest. If states use the revenues from higher taxes to create jobs, reduce unemployment, and reduce property crime, the small negative impacts from taxes can be easily overcome. >> Download the full study>> Download the four-page research briefs: > New England > Connecticut > Maine > Massachusetts > New Hampshire > Rhode Island > Vermont>> Download the regional press release
Script knowledge modulates retrieval-induced forgetting for eyewitness events

To determine the influence of knowledge schemata on inhibitory processes we analysed how the typicality of the actions of an event modulated retrieval-induced forgetting (RIF). Participants were presented with a realistic videotape of a bank robbery. Based on a normative study, high- and low-typicality actions of the event were determined. After watching the video, participants practised retrieving either half of the high- or half of the low-typicality actions, and their performance was compared against a no-practice control group. Tests given immediately after the event and after a 1-week retention interval demonstrated significant RIF for low-typicality actions exclusively when low-typicality actions were practised, but a comparable forgetting effect did not emerge for highly schematic actions. These findings confirm that highly integrated script knowledge protects high-typicality actions of an event from inhibitory processes, and demonstrate that RIF's effects last far longer than has been previously found.
Assessing the potential for developing internal diatom‐based transfer functions for Lake Baikal

We explore possible quantitative relationships between diatom species and environmental data for Lake Baikal using multivariate techniques. Our approach differs from published studies in other regions (on training sets and transfer functions) because (1) although only one lake is examined, we use the internal lake gradients rather than gradients among lakes and (2) the majority of the dominant diatom taxa are endemic. Canonical correspondence analysis on 93 surface sediment diatom assemblages reveals that major taxa show distinct relationships with measured environmental variables. Five significant variables were identified: snow thickness on ice (which accumulates on the frozen lake surface between January and April/May), water depth, suspended matter, annual solar radiation, and mean July temperature of surface waters. The strongest relationship is with snow thickness, which influences light levels in the water below the ice. A diatom‐based inference model has been developed to predict snow thickness on the ice using weighted averaging (WA) and WA with tolerance down‐weighting (WAtol) models. Results suggest that Lake Baikal diatom assemblages in surface sediments can be used to develop a robust model for estimating snow thickness across frozen Lake Baikal (r2jack = 0.607, RMSEP = 0.138 log cm). This model has potential applications for recent paleoclimate studies in this region of continental Eurasia.
Intensive care unit occupancy and patient outcomes*

Principle:Although intensive care units (ICUs) with higher overall patient volume may achieve better outcomes than lower volume ICUs, there are few data on the effects of increasing patient loads on patients within the ICU. Objectives:To examine the association of ICU occupancy with the patient outcomes within the same ICU. Methods:We examined 200,499 patients in 108 ICUs using the Acute Physiology and Chronic Health Evaluation IV database in 2002–2005. Daily census on the day of admission was determined for each patient and defined in relation to the mean census. We used conditional logistic regression to compare inpatient outcomes of patients admitted on high census days to those admitted in the same ICU on low census days. We controlled for severity of illness at the patient level using data on clinical, demographic, and physiologic variables on admission to the ICU. Measurements and Main Results:Patients admitted on high census days had the same odds of inpatient mortality or transfer to another hospital as patients admitted on average or on low census days. These findings were robust to multiple alternative definitions of day of admission census and were confirmed in several subgroup analyses. Conclusions:The ICUs in this data are able to function as high reliability organizations. They are able to scale up their operations to meet the needs of a wide range of operating conditions while maintaining consistent patient mortality outcomes.
Video Copy Detection motivated by Image Classification using Sparse Coding

In the presence of a vast amount of digital video data, the protection of intellectual property of the creator is of utmost importance. Video copy detection, which is used to find copyright infringements, is also useful in video information retrieval. We propose a novel technique for video copy detection using an image classification framework and sparse coding. The underlying image classification framework is based on non-negative sparse coding, low-rank and sparse matrix decomposition techniques along with Spatial Pyramid Matching (LR-Sc+SPM). SIFT features from each image are encoded using non-negative sparse coding. Using Spatial Pyramid Matching + Max pooling, we capture the spatial relations between the sparse codes. Low-rank and sparse matrix decomposition is then used to exploit correlations and dissimilarities between images of the same class. Extending this to video copy detection, we create a framework where scene change detection is performed using edge maps. The resulting scenes are divided into classes and, using the same image classification framework, a multi-class linear SVM is trained. We evaluate our proposed algorithm against two state-of-the-art techniques for video copy detection with accuracy and computational time being the metrics.
Transposition of the human Hsmar1 transposon: rate-limiting steps and the importance of the flanking TA dinucleotide in second strand cleavage

Hsmar1 is a member of the mariner family of DNA transposons. Although widespread in nature, their molecular mechanism remains obscure. Many other cut-and-paste elements use a hairpin intermediate to cleave the two strands of DNA at each transposon end. However, this intermediate is absent in mariner, suggesting that these elements use a fundamentally different mechanism for second-strand cleavage. We have taken advantage of the faithful and efficient in vitro reaction provided by Hsmar1 to characterize the products and intermediates of transposition. We report different factors that particularly affect the reaction, which are the reaction pH and the transposase concentration. Kinetic analysis revealed that first-strand nicking and integration are rapid. The rate of the reaction is limited in part by the divalent metal ion-dependent assembly of a complex between transposase and the transposon end(s) prior to the first catalytic step. Second-strand cleavage is the rate-limiting catalytic step of the reaction. We discuss our data in light of a model for the two metal ion catalytic mechanism and propose that mariner excision involves a significant conformational change between first- and second-strand cleavage at each transposon end. Furthermore, this conformational change requires specific contacts between transposase and the flanking TA dinucleotide.
Preclinical Assessment of Viral Vectored and Protein Vaccines Targeting the Duffy-Binding Protein Region II of Plasmodium Vivax

Malaria vaccine development has largely focused on Plasmodium falciparum; however, a reawakening to the importance of Plasmodium vivax has spurred efforts to develop vaccines against this difficult to treat and at times severe form of relapsing malaria, which constitutes a significant proportion of human malaria cases worldwide. The almost complete dependence of P. vivax red blood cell invasion on the interaction of the P. vivax Duffy-binding protein region II (PvDBP_RII) with the human Duffy antigen receptor for chemokines (DARC) makes this antigen an attractive vaccine candidate against blood-stage P. vivax. Here, we generated both preclinical and clinically compatible adenoviral and poxviral vectored vaccine candidates expressing the Salvador I allele of PvDBP_RII – including human adenovirus serotype 5 (HAdV5), chimpanzee adenovirus serotype 63 (ChAd63), and modified vaccinia virus Ankara (MVA) vectors. We report on the antibody and T cell immunogenicity of these vaccines in mice or rabbits, either used alone in a viral vectored prime-boost regime or in “mixed-modality” adenovirus prime – protein-in-adjuvant boost regimes (using a recombinant PvDBP_RII protein antigen formulated in Montanide®ISA720 or Abisco®100 adjuvants). Antibodies induced by these regimes were found to bind to native parasite antigen from P. vivax infected Thai patients and were capable of inhibiting the binding of PvDBP_RII to its receptor DARC using an in vitro binding inhibition assay. In recent years, recombinant ChAd63 and MVA vectors have been quickly translated into human clinical trials for numerous antigens from P. falciparum as well as a growing number of other pathogens. The vectors reported here are immunogenic in small animals, elicit antibodies against PvDBP_RII, and have recently entered clinical trials, which will provide the first assessment of the safety and immunogenicity of the PvDBP_RII antigen in humans.
Telematics and Gender Discrimination: Some Usage-Based Evidence on Whether Men’s Risk of Accidents Differs from Women’s

Pay-as-you-drive ( PAYD ), or usage-based automobile insurance (UBI), is a policy agreement tied to vehicle usage. In this paper we analyze the effect of the distance traveled on the risk of accidents among young drivers with a PAYD policy. We use regression models for survival data to estimate how long it takes them to have their first accident at fault during the coverage period. Our empirical application with real data is presented and shows that gender differences are mainly attributable to the intensity of use. Indeed, although gender has a significant effect in explaining the time to the first crash, this effect is no longer significant when the average distance traveled per day is introduced in the model. This suggests that gender differences in the risk of accidents are, to a large extent, attributable to the fact that men drive more often than women. Estimates of the time to the first accident for different driver risk types are presented. We conclude that no gender discrimination is necessary if telematics provides enough information on driving habits.
Optimal energy allocation and storage control for distributed estimation with sensor collaboration

In wireless sensor networks with energy harvesting nodes, we study the problem of energy allocation and storage control for distributed estimation with sensor collaboration, where collaboration refers to the act of sharing measurements with neighboring sensors prior to transmission to a fusion center. To jointly design energy allocation and storage control polices, we formulate a nonconvex optimization problem in which the estimation distortion is minimized subject to energy harvesting and storage constraints. We show that the resulting optimization problem contains two special types of nonconvexities: cardinality function and difference of convex functions. By exploiting the problem structure, locally optimal solutions are found via an ℓ1 relaxation and a convex-concave procedure. Numerical experiments are provided to show the effectiveness of our approach.
Convergecast scheduling problem in case of given aggregation tree: The complexity status and some special cases

We consider the problem of conflict-free data aggregation in distributed wireless radio networks, that is known as a Convergecast Scheduling Problem. This problem is strongly NP-hard in general. However the complexity status of the problem remained open in the case when the aggregation tree was given. We have proved that in this case, the problem is also NP-hard. Additionally, we proposed several new approximate suboptimal solutions in the special cases of the problem on the grid graphs.