Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq

Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure–function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA–RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA–RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell.
Secrecy-Oriented Resource Sharing for Cellular Device-to-Device Underlay

This paper investigates the problem of resource and power allocation in device-to-device (D2D) underlays given a specific secrecy rate constraint. The objective is to optimize the pairing of D2D links with cellular user equipment (CUE) uplink channel resources, and to allocate their respective powers to combat against eavesdroppers for secrecy rate improvement. The proposed method first determines a set of candidate D2D links with the required signal-to-interference-plus- noise ratio level for each CUE to narrow the number of combinatorial sharing options. Afterwards, an optimization problem is formulated for maximizing the overall secrecy rate under user power constraints and minimum required secrecy rates. Finally, numerical results demonstrate the resulting performance.
On scalability of remote attestation

Among the problems of binary remote attestation, scalability has often been mentioned in literature because a verifier must know all possible measurements considered acceptable. In this paper, we show that scalability is a manageable issue when attesting a Linux distribution. The main issues remain identifying, with low time impact, the scripts executed, the configuration of components and other files types.
An Extended Jacobian Inverse Kinematics Algorithm for Doubly Nonholonomic Mobile Manipulators

Based on the concept of endogenous configuration space we derive an extended Jacobian inverse kinematics algorithm for doubly nonholonomic mobile manipulators, i.e. mobile manipulators built of a nonholonomic manipulator and a nonholonomic mobile platform. A key step in the derivation consists in de fining a local diffeomorphism between the endogenous configuration space and the suitably augmented (extended) taskspace of the mobile manipulator. This has been achieved by decomposing the Fourier series representation of control functions driving the mobile manipulator into a finite dimensional part isomorphic to the taskspace, and a complementary in finite dimensional part augmenting the taskspace. By definition, our algorithm has the property of repeatability. Theoretical considerations are illustrated with computer simulations accomplished for a 3 d.o. f. planar nonholonomic manipulator mounted on a kinematic car-type platform.
Assessment of the quality of data on age at first sexual intercourse age at first marriage and age at first birth in the Demographic and Health Surveys.

An analysis of the quality of the data on age at 1st union age at 1st birth and age at 1st sexual intercourse collected in Demographic and Health Surveys (DHS) from 22 developing countries revealed considerable variation in the accuracy and completeness of the information collected. Accurate data on these parameters is especially important since they determine the total number of years of exposure to the risk of pregnancy and identify when the period of exposure began. Completeness of reporting on data of 1st union was greatest in Latin America and weakest in West Africa but at least 75% of women in all 22 surveys provided either an age or date for this event. There was evidence of significant heaping on calendar years and durations since 1st marriage ending in 0 or 5. Also evident was an appreciable amount of forward displacement of the date of 1st union in the oldest age groups in most surveys. Finally the DHS surveys documented a far higher percentage of women married at ages 15-24 years than other surveys--a discrepancy that is considered to reflect a higher level of coverage in the DHS. Data on age at 1st exhibited similar characteristics. There was evidence in over half the surveys of forward displacement of the date of 1st birth or omission of early births among older women especially those in sub-Saharan Africa. Only 1-2% of respondents refused to provide data on age at 1st sexual intercourse. In the African countries 12-67% of women experienced intercourse 1 or more years prior to 1st union indicating that reliance on date of 1st union is insufficient to capture all sexual exposure. It is recommended that data collection procedures be modified slightly to reduce the extent that interviewers calculate the age at 1st intercourse based on the data of 1st marriage.
Screening of Neisseria gonorrhoeae for tolerant response to beta-lactam antibiotics

Minimal inhibitory concentrations (MICs) and minimal bactericidal concentrations (MBCs) of penicillin, ampicillin, cefoxitin, and cefuroxime were determined for 103 beta-lactamase-negative Neisseria gonorrhoeae clinical isolates belonging to five different auxotypes. MBC determinations were base on killing 99.9% of the inoculum after 24 h of incubation. The MBC/MIC ratio was less than or equal to 8 for ampicillin, cefoxitin, and cefuroxime in all 103 strains. Two isolates which were very susceptible to penicillin (MIC, less than or equal to 0.015 micrograms/ml) had MBCs which were considerably greater than the MICs (MBC/MIC ratios, 32 and 64) for penicillin. A beta-lactamase-negative resistant subpopulation having the same auxotype as the total population was isolated from each of these two strains. Killing curve studies were in agreement with the existence of susceptible and resistant subpopulations, which may explain the high MBC/MIC ratios.
Bacteriochlorophyllide c C-82 and C-121 Methyltransferases Are Essential for Adaptation to Low Light in Chlorobaculum tepidum

ABSTRACT Bacteriochlorophyll (BChl) c is the major photosynthetic pigment in the green sulfur bacterium Chlorobaculum tepidum, in which it forms protein-independent aggregates that function in light harvesting. BChls c, d, and e are found only in chlorosome-producing bacteria and are unique among chlorophylls because of methylations that occur at the C-82 and C-121 carbons. Two genes required for these methylation reactions were identified and designated bchQ (CT1777) and bchR (CT1320). BchQ and BchR are members of the radical S-adenosylmethionine (SAM) protein superfamily; each has sequence motifs to ligate a [4Fe-4S] cluster, and we propose that they catalyze the methyl group transfers. bchQ, bchR, and bchQ bchR mutants of C. tepidum were constructed and characterized. The bchQ mutant produced BChl c that was not methylated at C-82, the bchR mutant produced BChl c that was not methylated at C-121, and the double mutant produced [8-ethyl, 12-methyl]-BChl c that lacked methylation at both the C-82 and C-121 positions. Compared to the wild type, the Qy absorption bands for BChl c in the mutant cells were narrower and blue shifted to various extents. All three mutants grew slower and had a lower cellular BChl c content than the wild type, an effect that was especially pronounced at low light intensities. These observations show that the C-82 and C-121 methylations of BChl c play important roles in the adaptation of C. tepidum to low light intensity. The data additionally suggest that these methylations also directly or indirectly affect the regulation of the BChl c biosynthetic pathway.
Recompiling Utility Functions in a Changing World

Our previous work considers a method for building a numeric utility function out of qualitative ceteris paribus preferences, or preferences other things held equal. Dynamic domains embody changes in preferences. This can come in many forms. The preferences themselves may change, the variables over which preferences are expressed may change, or the forms of utility independence that hold in the domain may change. We consider the consequences for each type of change to our system, and conclude that inherent ambiguities in our representation allow for simpler handling of change than might otherwise be the case. Decision Support and Preference While classical decision theory can appear too limited or too rigorous to support decision-making in dynamic domains and under changing conditions, many decision-theoretic formalisms have great conceptual benefit. Researchers in artificial intelligence have made several formulations of qualitative decision theory (Wellman & Doyle 1991; Tan & Pearl 1994; Boutilier et al. 1999), applicable in domains where accurate probabilities and time consuming preference elicitation techniques are either unavailable or undesirable. Such qualitative preference formulations allow decision makers to make natural statements, representing user’s intuitions about the decision space and easing the preference elicitation task. Including qualitative preferences in decision support systems allows personalization. Decision support systems that aim to help more than one decision maker need a way to represent the differences between different users. The most direct method is to represent their preferences. By preferences we mean the desires, tastes, and priorities that a person has, and that furthermore differ from person to person, causing two different people faced with the same decision to make different choices. Ceteris Paribus Preferences in Dynamic
Invariant Chain Controls H2-M Proteolysis in Mouse Splenocytes and Dendritic Cells

The association of invariant (Ii) chain with major histocompatibility complex (MHC) class II dimers is required for proper antigen presentation to T cells by antigen-presenting cells. Mice lacking Ii chain have severe abnormalities in class II transport, T cell selection, and B cell maturation. We demonstrate here that H2-M, which is required for efficient class II antigenic peptide loading, is unexpectedly downregulated in splenocytes and mature dendritic cells (DCs) from Ii−/− mice. Downregulation reflects an increased rate of degradation in Ii−/− cells. Degradation apparently occurs within lysosomes, as it is prevented by cysteine protease inhibitors such as E64, but not by the proteasome inhibitor lactacystin. Thus, Ii chain may act as a lysosomal protease inhibitor in B cells and DCs, with its deletion contributing indirectly to the loss of H2-M.
Overlapping Domain Decomposition : Convergence 2 Proofs 3

During the last two decades many domain decomposition algorithms have been con8 structed and lot of techniques have been developed to prove the convergence of the 9 algorithms at the continuous level. Among the techniques used to prove the conver10 gence of classical Schwarz algorithms, the first technique is the maximum principle 11 used by Schwarz. Adopting this technique M. Gander and H. Zhao proved a conver12 gence result for n-dimensional linear heat equation in [4]. The second technique is 13 that of the orthogonal projections, used by P. L. Lions in [7], and his convergence 14 results are for linear Laplace equation and linear Stokes equation. In the same pa15 per, P. L. Lions also proved that the Schwarz sequences for linear elliptic equations 16 are related to classical minimization methods over product spaces and this technique 17 was then used by L. Badea in [1] for nonlinear monotone elliptic problems. Another 18 technique is the Fourier and Laplace transforms used in the papers [3, 5] for some 19 1-dimensional evolution equations, with constant coefficients. In [10, 11], S. H. Lui 20 used the idea of upper-lower solutions methods to study the convergence problem for 21 some PDEs, with initial guess to be an upper or lower solution of the equations and 22 monotone iterations. For nonoverlapping optimized Schwarz methods, P. L. Lions 23 in [8] proposed to use an energy estimate argument to study the convergence of the 24 algorithm. The energy estimate technique was then developed in [2] for Helmholtz 25 equation and it has then become a very powerful tool to study nonoverlapping prob26 lems. J.-H. Kimn in [6] proved the convergence of an overlapping optimized Schwarz 27 method for Poisson’s equation with Robin boundary data and S. Loisel and D. B. 28 Szyld in [9] extended the technique of J.-H. Kimn to linear symmetric elliptic equa29 tion. Another technique is to use semiclassical analysis, which works for overlapping 30 optimized Schwarz methods with rectangle subdomains, linear advection diffusion 31 equations on the half plane (see [12]). This paper is devoted to the study of the con32 vergence of Schwarz methods at the continuous level. We give a sketch of the proof 33 of the convergence of optimized Schwarz methods for semilinear parabolic equa34 tions, with multiple subdomains. Complete convergence proofs for both classical 35
Acute fulminant myocarditis in scrub typhus

Abstract Scrub typhus is a zoonotic disease caused by Orientia tsutsugamushi in which humans are accidental hosts. It is a febrile illness which is confined to rural Asia and the Western Pacific islands. Severe complications are very rare. We report four cases of acute fulminant myocarditis in children with scrub typhus. This complication led to severe cardiogenic shock and death in two of them. We believe this is the first report of fulminant myocarditis complicating scrub typhus in children.
Interannual variability of sea surface height difference between western Pacific Ocean and eastern Indian Ocean and its effect to geostrophic current in Lombok Strait

Interannual variability of sea surface height (SSH) in western Pacific Ocean and eastern Indian Ocean occurs as a result of the ENSO phenomena. This variability affects SSH difference between both of those oceans. In normal condition, SSH in western Pacific Ocean is higher than in eastern Indian Ocean which causes a current that passes through Indonesia which known as the Indonesian Throughflow (ITF). This study used SSH and geostrophic currents data from 1993 to 2015 which obtained from AVISO satellite altimetry data to determine the variability of SSH difference in ENSO condition which represented by the sea surface temperature (SST) anomaly of Niño 3.4 data from NOAA and its relation to the geostrophic currents in Lombok Strait which is one of the ITF crossing path. The result of the correlation calculation of ENSO condition to SSH difference between western Pacific Ocean and eastern Indian Ocean shows the negative value. It means that SSH difference at both oceans have opposite condition that when El Nino happened SSH in western Pacific Ocean is lower than the eastern Indian Ocean and when La Niña happened SSH in the western Pacific Ocean is higher than the eastern Indian Ocean. The SSH difference does not affect the direction of geostrophic currents but affects its speed.
Support Vector Machines with Binary Tree Architecture for Multi-Class Classification

For multi-class classification with Support Vector Machines (SVMs) a binary decision tree architecture is proposed for computational efficiency. The proposed SVM- based binary tree takes advantage of both the efficient computation of the tree architecture and the high classification accuracy of SVMs. A modified Self-Organizing Map (SOM), K- SOM (Kernel-based SOM), is introduced to convert the multi-class problems into binary trees, in which the binary decisions are made by SVMs. For consistency between the SOM and SVM the K-SOM utilizes distance measures at the kernel space, not at the input space. Also, by allowing overlaps in the binary decision tree, it overcomes the performance degradation of the tree structure, and shows classification accuracy comparable to those of the popular multi-class SVM approaches with "one-to-one" and "one-to-the others". Keywords—Support Vector Machine, multi-class classification, Self-Organizing Map, binary decision tree
B‐50/GAP43 Expression Correlates with Process Outgrowth in the Embryonic Mouse Nervous System

The hypothesis that B‐50/GAP43, a membrane‐associated phosphoprotein, is involved in process outgrowth has been tested by studying the developmental pattern of expression of B‐50/GAP43 mRNA and protein during mouse neuroembryogenesis. B‐50/GAP43 mRNA is first detectable at embryonic day 8.5 (E8.5) in the presumptive acoustico‐facialis ganglion. Subsequently, both B‐50/GAP43 mRNA and protein were co‐expressed in a series of neural structures: in the ventral neural tube (from E9.5) and dorsal root ganglia (from E10.5), in the marginal layer of the neuroepithelium surrounding the brain vesicles and in the cranial ganglia (from E9.5), in the autonomic nervous system (from E10.5), in the olfactory neuroepithelium and in the mesenteric nervous system (from E11.5), in a continuum of brain regions (from E12.5) and in the retina (from E13.5). Immunoreactive fibers were always seen arising from these regions when they expressed B‐50/GAP43 mRNA. The spatial and temporal pattern of B‐50/GAP43 expression demonstrates that this protein is absent from neuroblasts and consistently appears in neurons committed to fiber outgrowth. The expression of the protein in immature neurons is independent of their embryological origin. Our detailed study of B‐50/GAP43 expression during mouse neuroembryogenesis supports the view that this protein is involved in a process common to all neurons elaborating fibers.
Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction

Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association.
Runtime Support for Dynamic Skeletons Implementation

Algorithmic skeletons have proved to be a good solution to the problem of implementing parallel applications with specify communication structures. They define the overall structure of the computation, hiding the complex communication details. Nowadays, the different frameworks available offer a fixed set of skeletons. The programmer can implement efficient programs if the computation and communication patterns match the available skeletons. Because of that, the usage of skeleton frameworks has been limited to an important but relative small set of patterns featuring the most common parallel structures, such as map, pipeline, farm, or wavefront. In this paper, we present a programming model that can be used to implement efficient and portable parallel skeletons. We also discuss its implementation and integration into Hitmap, a tool for hierarchical tiling and mapping. This combined proposal allows to develop tailored static and dynamic skeletons while still hiding implementation and communication details. The performance of the implementation is measured against a wellknown skeleton framework. Keywords—Algorithm skeletons, Parallel programming models, Dynamic computation
Tumor-cell homing to lymph nodes and bone marrow and CXCR4 expression in esophageal cancer.

BACKGROUND The chemokine and bone marrow-homing receptor CXCR4 has been implicated in metastatic dissemination of various cancers. We investigated CXCR4 expression in esophageal cancer specimens and its association with survival, lymph node microinvolvement, and bone marrow micrometastasis. METHODS We analyzed frozen tumor specimens from 136 patients with completely resected esophageal cancer for CXCR4 expression by immunohistochemistry. Lymph node microinvolvement and bone marrow micrometastasis were assessed by immunohistochemistry with monoclonal antibodies Ber-EP4 (against epithelial cell adhesion molecule) and pancytokeratin A45-B/B3 (against several cytokeratins), respectively. Associations between CXCR4 expression and clinicopathologic features, including tumor stage, histologic grade, lymph node metastasis and microinvolvement, bone marrow micrometastasis, and survival, were investigated with Fisher's test, log-rank test, and Cox multivariable analysis. All statistical tests were two-sided. RESULTS CXCR4 protein was expressed in 75 (55%) of 136 esophageal tumors examined. CXCR4 expression was statistically significantly associated with reduced median overall and disease-specific survival, compared with CXCR4 nonexpression (P < .001; log-rank test). The median overall survival of patients with CXCR4-positive tumors was 20 months and with CXCR4-negative tumors, 76 months (difference = 56 months, 95% confidence interval [CI] = 4 to 108 months; P < .001). The median disease-specific survival of patients with CXCR4-positive tumors was 25 months and with CXCR4-negative tumors was 97 months (difference = 72 months, 95% CI = 34 to 110 months; P < .001). CXCR4 expression was statistically significantly associated with increased lymph node microinvolvement (P < .001) and with increased bone marrow micrometastasis (P < .001). In multivariable analysis, CXCR4 expression, compared with its nonexpression, was identified as the independent variable that was most strongly associated with reduced disease-specific survival (relative risk [RR] of death = 2.03, 95% CI = 1.20 to 3.41; P = .008) and overall survival (RR of death = 2.18, 95% CI = 1.33 to 3.59; P = .002). CONCLUSION CXCR4 expression was associated with poor clinical outcome in esophageal cancer patients. CXCR4 may have a role in early metastatic spread because its expression was associated with micrometastases to both the lymph nodes and bone marrow. Thus, CXCR4 should be explored further as a target for adjuvant therapy for micrometastatic disease.