Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of bacterial lactase genes in intestinal contents of mice with antibiotics-induced diarrhea

AIM To investigate the diversity of bacterial lactase genes in the intestinal contents of mice with antibiotics-induced diarrhea. METHODS Following 2 d of adaptive feeding, 12 specific pathogen-free Kunming mice were randomly divided into the control group and model group. The mouse model of antibiotics-induced diarrhea was established by gastric perfusion with mixed antibiotics (23.33 mL·kg-1·d-1) composed of gentamicin sulfate and cephradine capsules administered for 5 days, and the control group was treated with an equal amount of sterile water. Contents of the jejunum and ileum were then collected and metagenomic DNA was extracted, after which analysis of bacterial lactase genes using operational taxonomic units (OTUs) was carried out after amplification and sequencing. RESULTS OTUs were 871 and 963 in the model group and control group, respectively, and 690 of these were identical. There were significant differences in Chao1 and ACE indices between the two groups (P < 0.05). Principal component analysis, principal coordination analysis and nonmetric multidimensional scaling analyses showed that OTUs distribution in the control group was relatively intensive, and differences among individuals were small, while in the model group, they were widely dispersed and more diversified. Bacterial lactase genes from the intestinal contents of the control group were related to Proteobacteria, Actinobacteria, Firmicutes and unclassified bacteria. Of these, Proteobacteria was the most abundant phylum. In contrast, the bacterial population was less diverse and abundant in the model group, as the abundance of Bradyrhizobium sp. BTAi1, Agrobacterium sp. H13-3, Acidovorax sp. KKS102, Azoarcus sp. KH32C and Aeromonas caviae was lower than that in the control group. In addition, of the known species, the control group and model group had their own unique genera, respectively. CONCLUSION Antibiotics reduce the diversity of bacterial lactase genes in the intestinal contents, decrease the abundance of lactase gene, change the lactase gene strains, and transform their structures.
Differential transcription of exon 1 of the human c-fms gene in placental trophoblasts and monocytes

Structural analysis of the 5' end of the human c-fms gene revealed that a large intron of about 25 kilobases separates an upstream noncoding exon (exon 1) from the signal peptide-containing exon (exon 2). Northern (RNA) blot analysis, S1 nuclease mapping, and primer extensions showed that exon 1 is transcribed in placenta but not in cells of the monocytic lineage. This is due to the differential usage of promoters, separated by approximately 25 kilobases, in a cell-specific manner. One major c-fms transcript was observed in U-937 cells, whereas multiple initiation sites for transcription appeared to be utilized in placental cells. Nucleotide sequence comparisons showed that the 3' end of the human platelet-derived growth factor receptor gene lies approximately 350 base pairs upstream of the major initiation sites for c-fms transcription in placental trophoblasts.
Crystal structure of a heterodimer of phospholipase A2 from Naja naja sagittifera at 2.3 Å resolution reveals the presence of a new PLA2‐like protein with a novel cys 32–Cys 49 disulphide bridge with a bound sugar at the substrate‐binding site

The crystal structure of the phospholipase A2 (PLA2) heterodimer from Naja naja sagittifera reveals the presence of a new PLA2‐like protein with eight disulphide bridges. The heterodimer is formed between a commonly observed group I PLA2 having seven characteristic disulfide bonds and a novel PLA2‐like protein (Cys–PLA2) containing two extra cysteines at two highly conserved sites (positions 32 and 49) of structural and functional importantance. The crystals of the heterodimer belong to tetragonal space group P41212 with cell dimensions, a = b = 77.7 Å and c = 68.4 Å corresponding to a solvent content of 33%, which is one of the lowest values observed so far in the PLA2 crystals. The structure has been solved with molecular replacement method and refined to a final R value of 21.6% [Rfree = 25.6%]. The electron density revealed the presence of cysteines 32 and 49 that are covalently linked to give rise to an eighth disulphide bridge in the PLA2‐like monomer. A non‐protein high‐quality electron density was also observed at the substrate‐binding site in the PLA2‐like protein that has been interpreted as N‐acetylglucosamine. The overall tertiary folds of the two monomers are similar having all features of PLA2‐type folding. A zinc ion is detected at the interface of the heterodimer with fivefold coordination while another zinc ion was found on the surface of Cys–PLA2 with sixfold coordination. The conformations of the calcium‐binding loops of both monomers are significantly different from each other as well as from those in other group I PLA2s. The N‐acetylglucosamine molecule is favorably placed in the substrate‐binding site of Cys–PLA2 and forms five hydrogen bonds and several van der Waals interactions with protein atoms, thus indicating a strong affinity. It also provides clue of the possible mechanism of sugar recognition by PLA2 and PLA2‐like proteins. The formation of heterodimer seems to have been induced by zinc ion. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Five-Terminal Switched Transformer Average Modeling and AC Analysis of PFC Converters

A simple and accurate five-terminal switched transformer average model is proposed and its generalized equations are derived. The proposed model is capable of both time domain and AC analysis of DC-DC, AC-DC, and is especially suitable for single-stage power factor correction (PFC) converters. Unlike other models presented in literature, the proposed switching cell includes the transformer leakage inductance, an intermediate bus input, and still addresses both continuous and discontinuous conduction modes. The model was applied to two topologies, the bi-flyback and the flyboost parallel/series forward converters. The time domain results show great accuracy when compared with the slower and time consuming switching simulation. The AC analysis is also predicted with greater accuracy exposing the dynamics of such converters, a task that was not as easily addressed before when the unique characteristics of single-stage are considered. The frequency domain analysis was also verified with experimental results for the bi-flyback converter. The model is very relevant to isolated flyback converters including the PFC examples provided, which are not as easily or as accurately modeled by other approaches.
Leisure and Stress-Coping: Implications for Therapeutic Recreation Practice

Within the field of leisure studies there is growing evidence of the value of leisure activity and experience in the course of coping with and adjusting to the kinds of acute and chronic life stressors that clients in therapeutic recreation (TR) settings may encounter. A review of leisurecoping literature is provided, drawing on research and theory-building in the leisure studies field. Following this, implications for TR practice are outlined. This review identifies the need to give particular attention to individual differences in leisure’s influence in coping with stress, as well as to the effects of different leisure activities and experiences in developing guidelines for various aspects of TR service, including TR assessment and intervention.
Cellular Census: Explorations in Urban Data Collection

Much of our understanding of urban systems comes from traditional data collection methods such as surveys by person or phone. These approaches can provide detailed information about urban behaviors, but they're hard to update and might limit results to "snapshots in time. " In the past few years, some innovative approaches have sought to use mobile devices to collect spatiotemporal data. But little research has been done to develop and analyze the much larger samples of existing data generated daily by mobile networks. The most common explanation for this is that the challenge of data-sharing with the telecommunications industry has hampered data access. However, in early 2006, a collaboration between Telecom Italia, which serves 40 percent of the Roman market, and MIT's SKNSEable City Laboratory (http://senseable.mit.edu) allowed unprecedented access to aggregate mobile phone data from Rome. Here, we explore how researchers might be able to use data for an entire metropolitan region to analyze urban dynamics.
The Role of models@run.time in Autonomic Systems: Keynote

Autonomic systems manage their own behaviour in accordance with high-level goals. This paper presents a brief outline of challenges related to Autonomic Computing due to uncertainty in the operational environments, and the role that models@run.time play in meeting them. We argue that the existing progress in Autonomic Computing can be further exploited with the support of runtime models. We briefly discuss our ideas related to the need to understand the extent to which the high-level goals of the autonomic system are being satisfied to support decision-making based on runtime evidence and, the need to support self-explanation.
Upper Bounds for the Connective Constant of Self-Avoiding Walks

We present a method for obtaining upper bounds for the connective constant of self-avoiding walks. The method works for a large class of lattices, including all that have been studied in connection with self-avoiding walks. The bound is obtained as the largest eigenvalue of a certain matrix. Numerical application of the method has given improved bounds for all lattices studied, e.g. μ < 2.696 for the square lattice, μ < 4.278 for the triangular lattice and μ < 4.756 for the simple cubic lattice.
What's in a User Story: IS Development Methods as Communication

This paper challenges claims made by Scrum proponents when characterising the communicative nature of user stories: including being more 'authentic' because they comprise spoken language and that they are stories. We argue and decisively demonstrate that neither can be upheld. By incorrectly characterising user stories, we miss opportunities to understand what they are and how they work during development. User stories are better understood by applying a functional theory of communication that emphasises how language is used. By selecting systemic functional linguistics, we can analyse user stories, and have developed a method for factoring unwanted epics into usable user stories.
Predicted Functional RNAs within Coding Regions Constrain Evolutionary Rates of Yeast Proteins

Functional RNAs (fRNAs) are being recognized as an important regulatory component in biological processes. Interestingly, recent computational studies suggest that the number and biological significance of functional RNAs within coding regions (coding fRNAs) may have been underestimated. We hypothesized that such coding fRNAs will impose additional constraint on sequence evolution because the DNA primary sequence has to simultaneously code for functional RNA secondary structures on the messenger RNA in addition to the amino acid codons for the protein sequence. To test this prediction, we first utilized computational methods to predict conserved fRNA secondary structures within multiple species alignments of Saccharomyces sensu strico genomes. We predict that as much as 5% of the genes in the yeast genome contain at least one functional RNA secondary structure within their protein-coding region. We then analyzed the impact of coding fRNAs on the evolutionary rate of protein-coding genes because a decrease in evolutionary rate implies constraint due to biological functionality. We found that our predicted coding fRNAs have a significant influence on evolutionary rates (especially at synonymous sites), independent of other functional measures. Thus, coding fRNA may play a role on sequence evolution. Given that coding regions of humans and flies contain many more predicted coding fRNAs than yeast, the impact of coding fRNAs on sequence evolution may be substantial in genomes of higher eukaryotes.
Determinants of the exclusion zone in dopaminergic amacrine cell mosaics

A fundamental organizing feature of the retina is the presence of regularly spaced distributions of neurons, yet we have little knowledge of how this patterning emerges during development. Among these retinal mosaics, the spatial organization of the dopaminergic amacrine cells is unique: using nearest‐neighbor and Vornoi domain analysis, we found that the dopaminergic amacrine cells were neither randomly distributed, nor did they achieve the regularity documented for other retinal cell types. Autocorrelation analysis revealed the presence of an exclusion zone surrounding individual dopaminergic amacrine cells and modeling studies confirmed this organization, as the mosaic could be simulated by a minimal distance spacing rule defined by a broad set of parameters. Experimental studies determined the relative contributions of tangential dispersion, fate determination, and cell death in the establishment of this exclusion zone. Clonal boundary analysis and simulations of proximity‐driven movement discount tangential dispersion, while data from bcl‐2 overexpressing mice rule out feedback‐inhibitory fate‐deterministic accounts. Cell death, by contrast, appears to eliminate dopaminergic amacrine cells that are within close proximity, thereby establishing the exclusion zone surrounding individual cells and in turn creating their mosaic regularity. J. Comp. Neurol. 461:123–136, 2003. © 2003 Wiley‐Liss, Inc.
Tiered-Latency DRAM (TL-DRAM)

This paper summarizes the idea of Tiered-Latency DRAM, which was published in HPCA 2013. The key goal of TL-DRAM is to provide low DRAM latency at low cost, a critical problem in modern memory systems. To this end, TL-DRAM introduces heterogeneity into the design of a DRAM subarray by segmenting the bitlines, thereby creating a low-latency, low-energy, low-capacity portion in the subarray (called the near segment), which is close to the sense amplifiers, and a high-latency, high-energy, high-capacity portion, which is farther away from the sense amplifiers. Thus, DRAM becomes heterogeneous with a small portion having lower latency and a large portion having higher latency. Various techniques can be employed to take advantage of the low-latency near segment and this new heterogeneous DRAM substrate, including hardware-based caching and software based caching and memory allocation of frequently used data in the near segment. Evaluations with simple such techniques show significant performance and energy-efficiency benefits.
The Enabling Role of Information Technology for Business Performance Management

As a consequence of various shortcomings of traditional, isolated support concepts, the IT industry has developed several new concepts and tools to meet business requirements for a highly integrated, low-latency, adaptive performance management support. In this paper, recent trends in the IT market are analysed. Certain convergence trends are identified which contribute to an appropriate IT support for business performance management. As a conceptual foundation of performance management system implementations, it support processes for business performance management proposed. All findings are based on a large-scale cooperation project of a business school and five large service companies.
Approximation in Stochastic integer programming

Approximation algorithms are the prevalent solution methods in the field of stochastic programming. Problems in this field are very hard to solve. Indeed, most of the research in this field has concentrated on designing solution methods that approximate the optimal solutions. However, efficiency in the complexity theoretical sense is usually not taken into account. Quality statements mostly remain restricted to convergence to an optimal solution without accompanying implications on the running time of the algorithms for attaining more and more accurate solutions. However, over the last twenty years also some studies on performance analysis of approximation algorithms for stochastic programming have appeared. In this direction we find both probabilistic analysis and worst-case analysis. There have been studies on performance ratios and on absolute divergence from optimality. Only recently the complexity of stochastic programming problems has been addressed, indeed confirming that these problems are harder than most combinatorial optimization problems.
The Case-Based Matchmaker

Matchmaking of human beings is recognized as a difficult task requiring great insight and sensitivity. In this paper, we present a case-based model that enlarges the number of relevant matches for any applicant. This model has been implemented in a working system for matches among either religious or traditional Jews in Israel. One implemented idea is the regular case-based retrieval, i.e. retrieving proposals similar to previous successful proposals. In addition, we implement a more complex case-based retrieval, which retrieves proposals in a few case-based steps. The model has been implemented in a working system intended for use in real life. Examples of the experiment we carried out show that casebased retrieval helps the majority of people by proposing new proposals in addition to those proposed in the regular kinds of retrieval. We think that these case-based retrieval methods, in principle, can be generalized to a certain extent to other matching tasks. Another future idea is to evaluate the potential of the case-based matchmaker as an intelligent support system for matchmakers.
Automatically classifying benign and harmful data races using replay analysis

Many concurrency bugs in multi-threaded programs are due to dataraces. There have been many efforts to develop static and dynamic mechanisms to automatically find the data races. Most of the prior work has focused on finding the data races and eliminating the false positives. In this paper, we instead focus on a dynamic analysis technique to automatically classify the data races into two categories - the dataraces that are potentially benign and the data races that are potentially harmful. A harmful data race is a real bug that needs to be fixed. This classification is needed to focus the triaging effort on those data races that are potentially harmful. Without prioritizing the data races we have found that there are too many data races to triage. Our second focus is to automatically provide to the developer a reproducible scenario of the data race, which allows the developer to understand the different effects of a harmful data race on a program's execution. To achieve the above, we record a multi-threaded program's execution in a replay log. The replay log is used to replay the multi-threaded program, and during replay we find the data races using a happens-before based algorithm. To automatically classify if a data race that we find is potentially benign or potentially harmful, were play the execution twice for a given data race - one for each possible order between the conflicting memory operations. If the two replays for the two orders produce the same result, then we classify the data race to be potentially benign. We discuss our experiences in using our replay based dynamic data race checker on several Microsoft applications.
Multi-resolution RASTA filtering for TANDEM-based ASR

New speech representation based on multiple filtering of temporal trajectories of speech energies in frequency sub-bands is proposed and tested. The technique extends earlier works on delta features and RASTA filtering by processing temporal trajectories by a bank of band-pass filters with varying resolutions. In initial tests on OGI Digits database the technique yields about 30% relative improvement in word error rate over the conventional PLP features. Since the applied filters have zero-mean impulse responses, the technique is inherently robust to linear distortions.
Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.
A parallel architecture for fast computation of elliptic curve scalar multiplication over GF(2/sup m/)

Summary form only given. We present a generic parallel architecture for fast elliptic curve scalar multiplication over binary extension fields. We show how the parallel strategy followed in this work leads to high performance designs. We also implemented the proposed architecture on reconfigurable hardware devices where the predicted expeditious performance figures were actually obtained. The results achieved show that our proposed design is able to compute GF(2/sup 191/) elliptic curve scalar multiplication operations in 56.44 /spl mu/Secs.