Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloud Properties Observed From the Surface and by Satellite at the Northern Edge of the Southern Ocean

A Raman depolarization lidar was deployed at Cape Grim, Australia (40.7°S, 144.7°E), at the northern edge of the Southern Ocean from July 2013 to February 2014 from which we determine cloud boundaries, cloud phase, ice virga, and cloud effective top heights. We compare surface‐based lidar with results from the raDAR/liDAR (DARDAR) data set within 1,000 km of Cape Grim. DARDAR combines information from the CloudSat and Cloud‐Aerosol Lidar with Orthogonal Polarization (CALIOP) instruments. We extract single‐layer clouds that are sufficiently thin for signal to be present on the farside of the cloud and which have a liquid cloud top phase. These conditions maximize the likelihood that both surface‐based lidar and DARDAR are observing the full vertical extent of the same clouds. Differences in low‐level cloud occurrence frequencies for these single‐layer clouds reveal that DARDAR underestimates cloud at 0.2–1.0 km altitude by a factor of 3 compared with the surface‐based lidar. When multiple cloud decks are present, the underestimate in this altitude region is around 2.5 times. Heterogeneous glaciation observed by the Cape Grim lidar in midlevel stratiform supercooled water clouds is similar to that reported by previous surface‐based observations adjacent to the Southern Ocean, with half of these clouds precipitating ice at cloud top temperatures of −20°C. This transition occurs around −15°C in the DARDAR data set, and this difference is likely due to the reduced sensitivity of surface‐based lidar in detecting precipitating ice compared with what a surface‐based radar could observe.
A rare coincidence: facioscapulohumeral muscular dystrophy and breast cancer.

AIM Facioscapulohumeral muscular dystrophy (FSHD) is an autosomally inherited neuromuscular disorder and may be associated with increased cancer risk. PATIENT A 69-year old female admitted to hospital with complaint of left axillary mass who had diagnosis of FSHD in her adulthood period. RESULTS Bilateral breast cancer diagnosis was made and the patient underwent bilateral mastectomy. Following the operation, adjuvant chemotherapy and radiotherapy performed and hormonal therapy started. CONCLUSION The patients with congenital muscular dystrophy might have an increased risk of malignancy. We consider that some genetic alterations in FSHD might have contributed to the development of bilateral breast cancer in our patient.
Anatomically Informed Basis Functions for EEG Source Localization: Combining Functional and Anatomical Constraints

Distributed linear solutions have frequently been used to solve the source localization problem in EEG. Here we introduce an approach based on the weighted minimum norm (WMN) method that imposes constraints using anatomical and physiological information derived from other imaging modalities. The anatomical constraints are used to reduce the solution space a priori by modeling the spatial source distribution with a set of basis functions. These spatial basis functions are chosen in a principled way using information theory. The reduced problem is then solved with a classical WMN method. Further (functional) constraints can be introduced in the weighting of the solution using fMRI brain responses to augment spatial priors. We used simulated data to explore the behavior of the approach over a range of the model's hyperparameters. To assess the construct validity of our method we compared it with two established approaches to the source localization problem, a simple weighted minimum norm and a maximum smoothness (Loreta-like) solution. This involved simulations, using single and multiple sources that were analyzed under different levels of confidence in the priors.
A discriminative model for identifying spatial cis-regulatory modules

Transcriptional regulation is mediated by the coordinated binding of transcription factors to the upstream region of genes. In higher eukaryotes, the binding sites of cooperating transcription factors are organized into short sequence units, called cis-regulatory modules. In this paper we propose a method for identifying modules of transcription factor binding sites in a set of co-regulated genes, using only the raw sequence data as input. Our method is based on a novel probabilistic model that describes the mechanism of cis-regulation, including the binding sites of cooperating transcription factors, the organization of these binding sites into short sequence modules, and the regulation of a gene by its modules. We show that our method is successful in discovering planted modules in simulated data and known modules in yeast. More importantly, we applied our method to a large collection of human gene sets, and found 83 significant cis-regulatory modules, which included 36 known motifs and many novel ones. Thus, our results provide one of the first comprehensive compendiums of putative cis-regulatory modules in human.
Changing of hepatitis C virus genotype patterns in France at the beginning of the third millenium: The GEMHEP GenoCII Study

Summary. This cross‐sectional study aimed to investigate, during a short period between 2000 and 2001, in a large population of patients with chronic hepatitis C, the epidemiological characteristics of hepatitis C virus (HCV) genotypes in France. Data from 26 referral centres, corresponding to 1769 patients with chronic hepatitis C were collected consecutively during a 6‐month period. HCV genotyping in the 5′‐non‐coding region (NCR) was performed in each center using the line probe assay (LiPA, in 63% of cases), sequencing (25%) or primer‐specific polymerase chain reaction (PCR) (12%). HCV genotypes 1a, 1b, 2, 3, 4, 5, non‐subtyped 1 and mixed infection were found in 18, 27, 9, 21, 9, 3, 11 and 1% of our population, respectively. HCV genotype distribution was associated with gender, age, source and duration of infection, alanine aminotransferase (ALT) levels, cirrhosis, alcohol consumption, hepatitis B virus (HBV) and human immunodeficiency virus (HIV) coinfection. In multivariate analysis, only the source of infection was the independent factor significantly associated with genotype (P = 0.0001). In conclusion, this study shows a changing pattern of HCV genotypes in France, with i.v. drug abuse as the major risk factor, an increase of genotype 4, and to a lesser extent 1a and 5, and a decrease of genotypes 1b and 2. The modification of the HCV genotype pattern in France in the next 10 years may require new therapeutic strategies, and further survey studies.
Kaposi's sarcoma herpesvirus-encoded latency-associated nuclear antigen stabilizes intracellular activated Notch by targeting the Sel10 protein

Deregulation of the evolutionarily conserved Notch signaling is highly correlated with oncogenesis. Intracellular activated Notch (ICN) is a protooncogene linked to the transcription activation of a number of cellular genes involved in cell cycle regulation, differentiation, and proliferation. Stability of ICN is tightly regulated by the Sel10-mediated ubiquitin–proteasome pathway. Sel10 can function as a negative regulator of Notch and exhibits activities of a tumor-suppressor protein. This article shows that the Kaposi's sarcoma-associated herpesvirus (KSHV) latency-associated nuclear antigen (LANA) directly interacts with Sel10 and forms a complex in KSHV-infected cells. This results in suppression of ICN ubiquitination and degradation. The carboxyl terminus of LANA interacts with the F-box and WD40 domains of Sel10 and competes with ICN for binding to Sel10. This elevated level of ICN is also critical for maintaining the enhanced proliferation of KSHV-infected tumor cells. These findings describe a mechanism by which the KSHV-encoded LANA protein regulates ubiquitination of ICN mediated by the F-box component of the E3 ligase Sel10, leading to proliferation of the virus-infected cells.
Quantum Cryptography

The Internet can be thought of as a channel of information being sent from you to everyone else connected to the Internet. If you wanted to transmit your sensitive information (such as bank account numbers or military secrets) over the Internet, then you have to ensure that only the persons you intend to read your information have access to your sensitive data. Otherwise, everyone would be able to read your information, e.g., access to your bank account details and transfer money out of your account. Therefore, one needs to encrypt any data sent over the Internet. Encryption, in this context, ensures that only the intended sender and receiver can understand any message being sent over an Internet channel.
An explanatory evo-devo model for the developmental hourglass

The "developmental hourglass'' describes a pattern of increasing morphological divergence towards earlier and later embryonic development, separated by a period of significant conservation across distant species (the "phylotypic stage''). Recent studies have found evidence in support of the hourglass effect at the genomic level. For instance, the phylotypic stage expresses the oldest and most conserved transcriptomes. However, the regulatory mechanism that causes the hourglass pattern remains an open question. Here, we use an evolutionary model of regulatory gene interactions during development to identify the conditions under which the hourglass effect can emerge in a general setting. The model focuses on the hierarchical gene regulatory network that controls the developmental process, and on the evolution of a population under random perturbations in the structure of that network. The model predicts, under fairly general assumptions, the emergence of an hourglass pattern in the structure of a temporal representation of the underlying gene regulatory network. The evolutionary age of the corresponding genes also follows an hourglass pattern, with the oldest genes concentrated at the hourglass waist. The key behind the hourglass effect is that developmental regulators should have an increasingly specific function as development progresses. Analysis of developmental gene expression profiles from Drosophila melanogaster and Arabidopsis thaliana provide consistent results with our theoretical predictions.
Generalized hashing and applications to digital fingerprinting

Let C be a code of length n over an alphabet of q letters. An n-word y is called a descendant of a set of t codewords x/sup 1/, . , x/sup t/ if yi /spl isin/ {x/sub i//sup 1/, . , x/sub i//sup t/} for all i=1, . , n. A code is said to have the t-identifying parent property if for any n-word that is a descendant of at most t parents it is possible to identify at least one of them. We study a generalization of hashing, (t, u)-hashing, which ensures identification, and provide tight estimates of the rates.
Improving Small File Performance in Object-based Storage (CMU-PDL-06-104)

This paper proposes architectural refinements, server-driven metadata prefetching and namespace flattening, for improving the efficiency of small file workloads in object-based storage systems. Server-driven metadata prefetching consists of having the metadata server provide information and capabilities for multiple objects, rather than just one, in response to each lookup. Doing so allows clients to access the contents of many small files for each metadata server interaction, reducing access latency and metadata server load. Namespace flattening encodes the directory hierarchy into object IDs such that namespace locality translates to object ID similarity. Doing so exposes namespace relationships among objects (e.g., as hints to storage devices), improves locality in metadata indices, and enables use of ranges for exploiting them. Trace-driven simulations and experiments with a prototype implementation show significant performance benefits for small file workloads. Acknowledgements: We thank the members and companies of the PDL Consortium (including APC, EMC, Equallogic, Hewlett-Packard, Hitachi, IBM, Intel, Microsoft, Network Appliance, Oracle, Panasas, Seagate, Sun, and Symantec) for their interest, insights, feedback, and support. We also thank Intel, IBM, Network Appliances, Seagate, and Sun for hardware donations that enabled this work. This material is based on research sponsored in part by the National Science Foundation, via grant #CNS-0326453, by the Air Force Research Laboratory, under agreement number F49620–01–1–0433, and by the Army Research Office, under agreement number DAAD19–02–1–0389. James Hendricks is supported in part by an NDSEG Fellowship, which is sponsored by the Department of Defense.
TRIM5α requires Ube2W to anchor Lys63-linked ubiquitin chains and restrict reverse transcription

TRIM5α is an antiviral, cytoplasmic, E3 ubiquitin (Ub) ligase that assembles on incoming retroviral capsids and induces their premature dissociation. It inhibits reverse transcription of the viral genome and can also synthesize unanchored polyubiquitin (polyUb) chains to stimulate innate immune responses. Here, we show that TRIM5α employs the E2 Ub‐conjugating enzyme Ube2W to anchor the Lys63‐linked polyUb chains in a process of TRIM5α auto‐ubiquitination. Chain anchoring is initiated, in cells and in vitro, through Ube2W‐catalyzed monoubiquitination of TRIM5α. This modification serves as a substrate for the elongation of anchored Lys63‐linked polyUb chains, catalyzed by the heterodimeric E2 enzyme Ube2N/Ube2V2. Ube2W targets multiple TRIM5α internal lysines with Ub especially lysines 45 and 50, rather than modifying the N‐terminal amino group, which is instead αN‐acetylated in cells. E2 depletion or Ub mutation inhibits TRIM5α ubiquitination in cells and restores restricted viral reverse transcription, but not infection. Our data indicate that the stepwise formation of anchored Lys63‐linked polyUb is a critical early step in the TRIM5α restriction mechanism and identify the E2 Ub‐conjugating cofactors involved.
Biocontrol of Bacillus subtilis against Infection of Arabidopsis Roots by Pseudomonas syringae Is Facilitated by Biofilm Formation and Surfactin Production1

Relatively little is known about the exact mechanisms used by Bacillus subtilis in its behavior as a biocontrol agent on plants. Here, we report the development of a sensitive plant infection model demonstrating that the bacterial pathogen Pseudomonas syringae pv tomato DC3000 is capable of infecting Arabidopsis roots both in vitro and in soil. Using this infection model, we demonstrated the biocontrol ability of a wild-type B. subtilis strain 6051 against P. syringae. Arabidopsis root surfaces treated with B. subtilis were analyzed with confocal scanning laser microscopy to reveal a three-dimensional B. subtilis biofilm. It is known that formation of biofilms by B. subtilis is a complex process that includes secretion of surfactin, a lipopeptide antimicrobial agent. To determine the role of surfactin in biocontrol by B. subtilis, we tested a mutant strain, M1, with a deletion in a surfactin synthase gene and, thus, deficient in surfactin production. B. subtilis M1 was ineffective as a biocontrol agent against P. syringae infectivity in Arabidopsis and also failed to form robust biofilms on either roots or inert surfaces. The antibacterial activity of surfactin against P. syringae was determined in both broth and agar cultures and also by live-dead staining methods. Although the minimum inhibitory concentrations determined were relatively high (25 μg mL-1), the levels of the lipopeptide in roots colonized by B. subtilis are likely to be sufficient to kill P. syringae. Our results collectively indicate that upon root colonization, B. subtilis 6051 forms a stable, extensive biofilm and secretes surfactin, which act together to protect plants against attack by pathogenic bacteria.
THE MINIMAL POLYNOMIAL AND SOME APPLICATIONS

The easiest matrices to compute with are the diagonal ones. The sum and product of diagonal matrices can be computed componentwise along the main diagonal, and taking powers of a diagonal matrix is simple too. All the complications of matrix operations are gone when working only with diagonal matrices. If a matrix A is not diagonal but can be conjugated to a diagonal matrix, say D := PAP−1 is diagonal, then A = P−1DP so Ak = P−1DkP for all integers k, which reduces us to computations with a diagonal matrix. In many applications of linear algebra (e.g., dynamical systems, differential equations, Markov chains, recursive sequences) powers of a matrix are crucial to understanding the situation, so the relevance of knowing when we can conjugate a nondiagonal matrix into a diagonal matrix is clear. We want look at the coordinate-free formulation of the idea of a diagonal matrix, which will be called a diagonalizable operator. There is a special polynomial, the minimal polynomial (generally not equal to the characteristic polynomial), which will tell us exactly when a linear operator is diagonalizable. The minimal polynomial will also give us information about nilpotent operators (those having a power equal to O). All linear operators under discussion are understood to be acting on nonzero finitedimensional vector spaces over a given field F .
Agronomic Performance of Single Crosses of Maize in Kiambu and Embu Counties of Kenya

Aims: This study was conducted to determine the agronomic performance of respective maize single crosses in different environments in varying soil and climatic zones in Kenya. Methodology: The trials were conducted at experimental stations of Kenya Agricultural and Livestock Research Organization (KALRO), Muguga South and KALRO Embu in Kiambu and Embu counties of Kenya respectively. The germplasm used in this study were 36 single crosses among 18 inbred lines of maize. The experiment was laid out in a 6 x 6 lattice randomized complete block design (RCBD) with two replications. Agronomic performance was measured by collecting and analyzing data on plant height, ear height, disease scores of maize streak virus and gray leaf spot and grain yield. Data was subjected to analysis of variance (ANOVA) using Genstat 12 program for individual single crosses. Mean separation was done using Tukey’s comparison method at 5% significance level. Results: The best performing crosses in Muguga were also the best in Embu on grain yield production with exception of cross MUL 516 x MUL508 which had a mean grain yield of 11.9 t/ha in Muguga but produced 2.7 t/ha in Embu which was attributed to other factors other than genetic makeup. Variation in yield showed a diverse genetic background of genotypes studied under these conditions. The grain yield ranged between 1.01 t/ha (MUL533 x MUL513) to 11.9 t/ha (MUL 516 x MUL 508) both in Muguga). The best performing cross for grain yield in Muguga was MUL 516 x MUL 508) while in Embu the best performing cross for grain yield was MUL541 x POPA. Data on disease scores where natural infestation was visually scored showed that majority of the crosses had a score of one confirming their near immunity status. Conclusions: For grain yield improvement crosses MUL508 x MUL688, POPA x MUL14, MUL513 x MUL114 and MUL513 x CN244 can further be evaluated and eventually released to farmers as they indicated promising relationship with yield potential compared to other crosses. Further research on agronomic performance of the crosses can be done not only in the research sites but also in other regions of Kenya.
Comparison of Ear Notch Immunohistochemistry, Ear Notch Antigen-Capture ELISA, and Buffy Coat Virus Isolation for Detection of Calves Persistently Infected with Bovine Viral Diarrhea Virus

Two techniques performed on skin biopsy samples (ear notches), immunohistochemistry (IHC) and antigen-capture ELISA (AgELISA), were compared for detection of bovine viral diarrhea virus (BVDV) persistent infection (PI) in 559 Angus calves between the ages of 1 and 5 months. The calves also were tested for BVDV infection using virus isolation (VI) and reverse transcription (RT)-PCR on buffy coat samples and for antibodies to BVDV types 1a and 2 by serum neutralization (SN). Sixty-seven of 559 (12.0%) calves tested positive at initial screening by IHC, AgELISA, or VI, and all 67 were kept for a minimum of 3 months and retested monthly by IHC, AgELISA, VI, RT-PCR, and SN. Of the calves positive at initial screening, 59/67 (88.1%) were determined PI and 8/67 (11.9%) were determined acutely infected. Both IHC and AgELISA detected 100% of PI calves; however, IHC and AgELISA also detected 6 and 8 acutely infected calves, respectively, at initial screening. Furthermore, IHC and AgELISA continued to detect 3 and 4 acutely infected calves, respectively, 3 months after initial screening. Three acutely infected calves had IHC staining indistinguishable from PI calves at initial screening. Both IHC and AgELISA are accurate at detecting BVDV-infected calves, but veterinarians and producers should be advised that both tests detect some calves acutely infected with BVDV in addition to PI animals. Repeat testing using VI or RT-PCR on buffy coat samples should be performed at 30 days after initial screening to conclusively discriminate between acute and PI.
Preserve ordering property of generated LSPS for minimum generation error training in HMM-based speech synthesis

Ordering property is an important property of LSP and closely connected with the naturalness of reconstructed speech. When LSP is adopted as spectrum feature in HMM-based parametric speech synthesis, the ordering property cannot be guaranteed because diagonal covariance matrix is used in conventional system and the cross-dimension correlation of LSP vector is ignored. It will cause unstable issue in synthesized speech. In this paper, we propose some methods to preserve the ordering property of generated LSPs for MGE training by introducing mis-ordering related distance measurements into model training criterion. Experimental results show that two methods can alleviate the mis-orderings significantly without degrading the MGE performance, and one of which, the minimum mis-ordering counting method, requires no acoustic observations for model optimization.
The relationship between xylem conduit diameter and cavitation caused by freezing.

The centrifuge method for measuring the resistance of xylem to cavitation by water stress was modified to also account for any additional cavitation that might occur from a freeze-thaw cycle. A strong correlation was found between cavitation by freezing and mean conduit diameter. On the one extreme, a tracheid-bearing conifer and diffuse-porous angiosperms with small-diameter vessels (mean diameter <30 μm) showed no freezing-induced cavitation under modest water stress (xylem pressure = -0.5 MPa), whereas species with larger diameter vessels (mean >40 μm) were nearly completely cavitated under the same conditions. Species with intermediate mean diameters (30-40 μm) showed partial cavitation by freezing. These results are consistent with a critical diameter of 44 μm at or above which cavitation would occur by a freeze-thaw cycle at -0.5 MPa. As expected, vulnerability to cavitation by freezing was correlated with the hydraulic conductivity per stem transverse area. The results confirm and extend previous reports that small-diameter conduits are relatively resistant to cavitation by freezing. It appears that the centrifuge method, modified to include freeze-thaw cycles, may be useful in separating the interactive effects of xylem pressure and freezing on cavitation.