Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional neuroanatomy of the parahippocampal region in the rat: The perirhinal and postrhinal cortices

The parahippocampal region in the rodent brain includes the perirhinal, postrhinal, and entorhinal cortices, the presubiculum, and the parasubiculum. In recent years, the perirhinal and postrhinal cortices have been a focus in memory research because they supply highly processed, polymodal sensory information to the hippocampus, both directly and via the entorhinal cortex. Available evidence indicates that these cortices receive different complements of cortical information, which are then forwarded to the hippocampus via parallel pathways.Here we have summarized the cortical, subcortical, and hippocampal connections of the perirhinal and postrhinal cortices in order to provide further insight into the nature of the information that is processed by these regions prior to arriving in the hippocampus. As has been previously described, the cortical afferents of the rodent postrhinal cortex are dominated by structures known to be involved in the processing of visual and spatial information, whereas the cortical afferents of the perirhinal cortex result in remarkable convergence of polymodal sensory information. The two regions are also differentiated by their cortical efferents. The perirhinal cortex projects more strongly to piriform, frontal, and insular regions, whereas the postrhinal cortex projects preferentially to visual and visuospatial regions. The subcortical connections of the two regions provide further evidence that they have different functions. For example, the perirhinal cortex has strong reciprocal connections with the amygdala, which suggest involvement in processing affective stimuli. Subcortical input to the postrhinal cortex is dominated by projections from dorsal thalamic structures, particularly the lateral posterior nucleus. Although the perirhinal and postrhinal cortices are considered to contribute to the episodic memory system, many questions remain about their particular roles. A detailed description of the anatomical connections of the perirhinal and postrhinal cortices will permit the generation of new, anatomically guided, hypotheses about their role in episodic memory and other cognitive processes. © 2007 Wiley‐Liss, Inc.
Identification and Analysis of Genome-Wide SNPs Provide Insight into Signatures of Selection and Domestication in Channel Catfish (Ictalurus punctatus)

Domestication and selection for important performance traits can impact the genome, which is most often reflected by reduced heterozygosity in and surrounding genes related to traits affected by selection. In this study, analysis of the genomic impact caused by domestication and artificial selection was conducted by investigating the signatures of selection using single nucleotide polymorphisms (SNPs) in channel catfish (Ictalurus punctatus). A total of 8.4 million candidate SNPs were identified by using next generation sequencing. On average, the channel catfish genome harbors one SNP per 116 bp. Approximately 6.6 million, 5.3 million, 4.9 million, 7.1 million and 6.7 million SNPs were detected in the Marion, Thompson, USDA103, Hatchery strain, and wild population, respectively. The allele frequencies of 407,861 SNPs differed significantly between the domestic and wild populations. With these SNPs, 23 genomic regions with putative selective sweeps were identified that included 11 genes. Although the function for the majority of the genes remain unknown in catfish, several genes with known function related to aquaculture performance traits were included in the regions with selective sweeps. These included hypoxia-inducible factor 1β· HIFιβ ¨ and the transporter gene ATP-binding cassette sub-family B member 5 (ABCB5). HIF1β· is important for response to hypoxia and tolerance to low oxygen levels is a critical aquaculture trait. The large numbers of SNPs identified from this study are valuable for the development of high-density SNP arrays for genetic and genomic studies of performance traits in catfish.
DNA-Dependent Protein Kinase and Ataxia Telangiectasia Mutated (ATM) Promote Cell Survival in Response to NK314, a Topoisomerase IIα Inhibitor

4-Hydroxy-5-methoxy-2,3-dihydro-1H-[1,3]benzodioxolo[5,6-c]pyrrolo[1,2-f]-phenanthridium chloride (NK314) is a benzo[c] phenanthridine alkaloid that inhibits topoisomerase IIα, leading to the generation of DNA double-strand breaks (DSBs) and activating the G2 checkpoint pathway. The purpose of the present studies was to investigate the DNA intercalating properties of NK314, to evaluate the DNA repair mechanisms activated in cells that may lead to resistance to NK314, and to develop mechanism-based combination strategies to maximize the antitumor effect of the compound. A DNA unwinding assay indicated that NK314 intercalates in DNA, a property that likely cooperates with its ability to trap topoisomerase IIα in its cleavage complex form. The consequence of this is the formation of DNA DSBs, as demonstrated by pulsed-field gel electrophoresis and H2AX phosphorylation. Clonogenic assays demonstrated a significant sensitization in NK314-treated cells deficient in DNA-dependent protein kinase (DNA-PK) catalytic subunit, Ku80, ataxia telangiectasia mutated (ATM), BRCA2, or XRCC3 compared with wild-type cells, indicating that both nonhomologous end-joining and homologous recombination DNA repair pathways contribute to cell survival. Furthermore, both the DNA-PK inhibitor 8-(4-dibenzothienyl)-2-(4-morpholinyl)-4H-1-benzopyran-4-one (NU7441) and the ATM inhibitor 2-(4-morpholinyl)-6-(1-thianthrenyl)-4H-pyran-4-one (KU55933) significantly sensitized cells to NK314. We conclude that DNA-PK and ATM contribute to cell survival in response to NK314 and could be potential targets for abrogating resistance and maximizing the antitumor effect of NK314.
Accompaniment separation and karaoke application based on automatic melody transcription

We propose a method for separating accompaniment from polyphonic music and its karaoke application, both based on automatic melody transcription. First, the method transcribes the lead-vocal melody of an existing polyphonic music piece, where the transcription consists of a MIDI note sequence and a detailed fundamental frequency (F0) trajectory for each note. Based on the note F0 trajectories, the method uses sinusoidal modeling to estimate, synthesize, and remove the lead vocals in the piece, thus producing separated accompaniment of the piece. User sings along with the separated accompaniment similar to karaoke while the user singing can be tuned to the transcribed melody. This will help non-professional singers to produce more appealing karaoke performances. The quality of separated accompaniments was quantitatively evaluated with approximately one hour of polyphonic music, including material from a commercial karaoke DVD.
Using unreliable data for creating more reliable online learners

Some machine learning applications involve the question of whether or not to use unreliable data for the learning. Previous work shows that learners trained using unreliable data in addition to reliable data present either similar or worse performance than learners trained solely on reliable data. Such learners frequently use unreliable data as if they were reliable and consider only the offline learning scenario. The present paper shows that it is possible to use unreliable data to improve the performance in online learning scenarios with a pre-existing set of unreliable data. We propose an approach called Dynamic Un+Reliable data learners (DUR) able to determine when unreliable data could be useful by maintaining a fixed size weighted memory of unreliable data learners. The weights represent how well learners perform for the current concept and are updated throughout DUR's lifetime. This approach manages not only to outperform an approach which uses only reliable data, but also an approach which uses unreliable data as if they were reliable. Moreover, the variance in performance is reduced in comparison to the approach which uses only reliable data. In other words, DUR is a more reliable learner.
Sip4, a Snf1 kinase‐dependent transcriptional activator, binds to the carbon source‐responsive element of gluconeogenic genes

The carbon source‐responsive element (CSRE) mediates transcriptional activation of the gluconeogenic genes during growth of the yeast Saccharomyces cerevisiae on non‐fermentable carbon sources. Previous studies have suggested that the Cat8 protein activates the expression of CSRE‐binding factors. We show here that one of these factors is Sip4, a glucose‐regulated C6 zinc cluster activator which was identified by its interaction with the Snf1 protein kinase. We present genetic evidence that Sip4 contributes to transcriptional activation by the CSRE and biochemical evidence that Sip4 binds to the CSRE. Binding was detected in electrophoretic mobility shift assays with both yeast nuclear extracts and a bacterially expressed Sip4 fusion protein. Evidence suggests that Sip4 also activates the expression of other CSRE‐binding proteins. Finally, we show that Cat8 regulates SIP4 expression and that overexpression of Sip4 compensates for loss of Cat8. We propose a model for activation by the CSRE in which Sip4 and Cat8 have related functions, but Cat8 is the primary regulator because it controls Sip4 expression.
On the Information Loss of the Max-Log Approximation in BICM Systems

We present a comprehensive study of the information rate loss of the max-log approximation for M-ary pulse-amplitude modulation (PAM) in a bit-interleaved coded modulation (BICM) system. It is widely assumed that the calculation of L-values using the max-log approximation leads to an information loss. We prove that this assumption is correct for all M-PAM constellations and labelings with the exception of a symmetric 4-PAM constellation labeled with a Gray code. We also show that for max-log L-values, the BICM generalized mutual information (GMI), which is an achievable rate for a standard BICM decoder, is too pessimistic. In particular, it is proved that the so-called harmonized GMI, which can be seen as the sum of bit-level GMIs, is achievable without any modifications to the decoder. We then study how bit-level channel symmetrization and mixing affect the MI and the GMI for max-log L-values. Our results show that these operations, which are often used when analyzing BICM systems, preserve the GMI. However, this is not necessarily the case when the MI is considered. Necessary and sufficient conditions under which these operations preserve the MI are provided.
Dynamic Software Testing of MPI Applications with Umpire

As evidenced by the popularity of MPI (Message Passing Interface), message passing is an effective programming technique for managing coarse-grained concurrency on distributed computers. Unfortunately, debugging message-passing applications can be difficult. Software complexity, data races, and scheduling dependencies can make programming errors challenging to locate with manual, interactive debugging techniques. This article describes Umpire, a new tool for detecting programming errors at runtime in message passing applications. Umpire monitors the MPI operations of an application by interposing itself between the application and the MPI runtime system using the MPI profiling layer. Umpire then checks the application’s MPI behavior for specific errors. Our initial collection of programming errors includes deadlock detection, mismatched collective operations, and resource exhaustion. We present an evaluation on a variety of applications that demonstrates the effectiveness of this approach.
Keynote Lecture: Residual Stress Gradient Analysis by Multiple Diffraction Line Methods

The paper deals with methods for X-ray stress analysis (XSA), which allow for the evaluation of near surface in-plane residual stress gradients σ||(τ) and σ||(z) in the LAPLACE- and the real space, respectively. Since the ‘robustness’ of residual stress gradient analysis strongly depends on both, the quality of the measured strain data and the number of experimental data points, the discussion aims at those approaches which are based on processing various diffraction lines or even complete diffraction patterns. It is shown that these techniques, which were originally developed for angle-dispersive (AD) diffraction, can be adapted and enhanced for energy-dispersive (ED) diffraction employing high-energy synchrotron radiation. With the example of a shot-peened ferritic steel it is demonstrated, that sin²ψ-data measured in the Ψ-mode of XSA employing the ED diffraction technique can be analyzed on different levels of approximation.
The morphology and properties of melt-mixed polyoxymethylene/monosilanolisobutyl-POSS composites

In this study, the morphology and thermo-mechanical behavior of composites formed by a polyoxymethylene (POM) matrix and monosilanolisobutyl polyhedral oligomeric silsesquioxane (msib-POSS) filler have been studied. The msib-POSS molecules were added to the POM by direct melt blending at loadings between 0 and 10 wt. %. Hydrogen bonding interactions were detected between POM and msib-POSS Si-OH groups, increasing their mutual compatibility and leading to nanometer-size dispersion of some msib-POSS molecules. These interactions do not prevent POSS aggregation during blending, but lead to micron-scale msib-POSS domains. The thermal decomposition temperature of the composites remained practically constant under inert and oxidative conditions. The low temperature thermal transition (γ) and glass transition temperature (Tg) of POM were found to move to higher temperatures only when 2.5 wt. % of msib-POSS was added, indicating that POSS is physically linked to the POM chains, restricting their motion under those conditions. Low content (2.5 wt.%) of msib-POSS results in antiplastization, whereas higher levels of POSS lead to a decrease in the storage modulus of the polymer. The relationships among these effects and the morphological characteristics of the systems will be discussed herein.
Automatic compiler-inserted I/O prefetching for out-of-core applications

Current operating systems offer poor performance when a numeric application’s working set does not fit in main memory. As a result, programmers who wish to solve “out-of-core” problems efficiently are typically faced with the onerous task of rewriting an application to use explicit I/O operations (e.g., read/write). In this paper, we propose and evaluate a fully-automatic technique which liberates the programmer from this task, provides high performance, and requires only minimal changes to current operating systems. In our scheme, the compiler provides the crucial information on future access patterns without burdening the programmer, the operating system supports non-binding prefetch and release hints for managing I/O, and the operating system cooperates with a run-time layer to accelerate performance by adapting to dynamic behavior and minimizing prefetch overhead. This approach maintains the abstraction of unlimited virtual memory for the programmer, gives the compiler the flexibility to aggressively move prefetches back ahead of references, and gives the operating system the flexibility to arbitrate between the competing resource demands of multiple applications. We have implemented our scheme using the SUIF compiler and the Hurricane operating system. Our experimental results demonstrate that our fully-automatic scheme effectively hides the I/O latency in out-ofcore versions of the entire NAS Parallel benchmark suite, thus resulting in speedups of roughly twofold for five of the eight applications, with one application speeding up by over threefold.
New Characterizations in Turnstile Streams with Applications

Recently, [Li, Nguyen, Woodruff, STOC'2014] showed any 1-pass constant probability streaming algorithm for computing a relation f on a vector x ∈ {−m, − (m − 1), . , m}n presented in the turnstile data stream model can be implemented by maintaining a linear sketch A · × mod q, where A is an r × n integer matrix and q = (q1, ., qr) is a vector of positive integers. The space complexity of maintaining A · × mod q, not including the random bits used for sampling A and q, matches the space of the optimal algorithm. We give multiple strengthenings of this reduction, together with new applications. In particular, we show how to remove the following shortcomings of their reduction: 1. The Box Constraint. Their reduction applies only to algorithms that must be correct even if ∥;x∥;∞ = maxi∈[n] |xi| is allowed to be much larger than m at intermediate points in the stream, provided that x ∈ {−m, −(m − 1), . , m}n at the end of the stream. We give a condition under which the optimal algorithm is a linear sketch even if it works only when promised that x ∈ {−m, −(m − 1), . , m}n at all points in the stream. Using this, we show the first super-constant Ω(log m) bits lower bound for the problem of maintaining a counter up to an additive em error in a turnstile stream, where e is any constant in (0, ½). Previous lower bounds are based on communication complexity and are only for relative error approximation; interestingly, we do not know how to prove our result using communication complexity. More generally, we show the first super-constant Ω(log m) lower bound for additive approximation of ep-norms; this bound is tight for 1 ≤ p ≤ 2. 2. Negative Coordinates. Their reduction allows xi to be negative while processing the stream. We show an equivalence between 1-pass algorithms and linear sketches A · x mod q in dynamic graph streams, or more generally, the strict turnstile model, in which for all i ∈ [n], xi ≥ 0 at all points in the stream. Combined with [Assadi, Khanna, Li, Yaroslavtsev, SODA'2016], this resolves the 1-pass space complexity of approximating the maximum matching in a dynamic graph stream, answering a question in that work. 3. 1-Pass Restriction. Their reduction only applies to 1-pass data stream algorithms in the turnstile model, while there exist algorithms for heavy hitters and for low rank approximation which provably do better with multiple passes. We extend the reduction to algorithms which make any number of passes, showing the optimal algorithm is to choose a new linear sketch at the beginning of each pass, based on the output of previous passes.
Development of a dry-reagent mix-based polymerase chain reaction as a novel tool for the identification of Acinetobacter species and its comparison with conventional polymerase chain reaction

BACKGROUND: Nosocomial infections are often caused by multidrug-resistant bacteria and the incidence is increasing. Acinetobacter, a Gram-negative bacillus, is commonly associated with the use of intravascular catheterization and airway intubation. Polymerase chain reaction (PCR) for identification of Acinetobacter baumannii from samples has been standardized that use conventional wet-reagent mix. We have designed and optimized a dry-reagent mix for identification of Acinetobacter species by PCR. The dry-reagent mix can be stored at room temperature, has less chances of contamination, and thus can be used at point-of-care diagnosis. AIM AND OBJECTIVE: The present work was focused on comparing the sensitivity and specificity of dry-reagent PCR mix over conventional wet-reagent PCR mix for identification of Acinetobacter species. MATERIALS AND METHODS: Conventional wet-reagent mix based and dry-reagent mix based PCR were carried out for the DNA isolated from Acinetobacter species. The latter was also applied directly on bacterial growth without prior DNA extraction process. Equal numbers of bacterial isolates other than Acinetobacter species were also subjected to identification by the same protocols for determining the sensitivity and specificity of the test. RESULTS: The Acinetobacter species showed amplification of the target rpoB gene and the band was observed at 397 bp. The dry-reagent PCR mix results matched completely with the conventional wet-reagent PCR mix assay. All the non-Acinetobacter isolates were negative for the PCR. This indicates that the test is highly specific. The dry-reagent mix also contained an enzyme resistant to PCR inhibitors and capable of amplifying DNA directly from cells. CONCLUSION: Performance of dry-reagent PCR mix without the need for DNA extraction and preparation of a PCR mix proved to be more sensitive and reduce the handling error, minimizes the time, manual work, and skilled labor.
Diversity of Metabolically Active Bacteria in Water-Flooded High-Temperature Heavy Oil Reservoir

The goal of this work was to study the overall genomic diversity of microorganisms of the Dagang high-temperature oilfield (PRC) and to characterize the metabolically active fraction of these populations. At this water-flooded oilfield, the microbial community of formation water from the near-bottom zone of an injection well where the most active microbial processes of oil degradation occur was investigated using molecular, cultural, radiotracer, and physicochemical techniques. The samples of microbial DNA and RNA from back-flushed water were used to obtain the clone libraries for the 16S rRNA gene and cDNA of 16S rRNA, respectively. The DNA-derived clone libraries were found to contain bacterial and archaeal 16S rRNA genes and the alkB genes encoding alkane monooxygenases similar to those encoded by alkB-geo1 and alkB-geo6 of geobacilli. The 16S rRNA genes of methanogens (Methanomethylovorans, Methanoculleus, Methanolinea, Methanothrix, and Methanocalculus) were predominant in the DNA-derived library of Archaea cloned sequences; among the bacterial sequences, the 16S rRNA genes of members of the genus Geobacillus were the most numerous. The RNA-derived library contained only bacterial cDNA of the 16S rRNA sequences belonging to metabolically active aerobic organotrophic bacteria (Tepidimonas, Pseudomonas, Acinetobacter), as well as of denitrifying (Azoarcus, Tepidiphilus, Calditerrivibrio), fermenting (Bellilinea), iron-reducing (Geobacter), and sulfate- and sulfur-reducing bacteria (Desulfomicrobium, Desulfuromonas). The presence of the microorganisms of the main functional groups revealed by molecular techniques was confirmed by the results of cultural, radioisotope, and geochemical research. Functioning of the mesophilic and thermophilic branches was shown for the microbial food chain of the near-bottom zone of the injection well, which included the microorganisms of the carbon, sulfur, iron, and nitrogen cycles.
Multi-stream spectro-temporal features for robust speech recognition

A multi-stream approach to utilizing the inherently large number of spectro-temporal features for speech recognition is investigated in this study. Instead of reducing the featurespace dimension, this method divides the features into streams so that each represents a patch of information in the spectrotemporal response field. When used in combination with MFCCs for speech recognition under both clean and noisy conditions, multi-stream spectro-temporal features provide roughly a 30% relative improvement in word-error rate over using MFCCs alone. The result suggests that the multi-stream approach may be an effective way to handle and utilize spectro-temporal features for speech applications.