gebhart/patrepeval huggingface dataset:
Advances in Machine Learning for the Behavioral Sciences (2019)

The areas of machine learning and knowledge discovery in databases have considerably matured in recent years. In this article, we briefly review recent developments as well as classical algorithms that stood the test of time. Our goal is to provide a general introduction into different tasks such as learning from tabular data, behavioral data, or textual data, with a particular focus on actual and potential applications in behavioral sciences. The supplemental appendix to the article also provides practical guidance for using the methods by pointing the reader to proven software implementations. The focus is on R, but we also cover some libraries in other programming languages as well as systems with easy-to-use graphical interfaces.
Face database retrieval using pseudo 2D hidden Markov models (2003)

This paper explores the face database retrieval capabilities of a face recognition system based on hidden Markov models (HMMs). A new HMM-based measure to rank images of the database is presented. The method is able to work on a large database. Previous systems for image retrieval based on HMMs were only capable of operating on small databases. The relation of the presented method to confidence measures is pointed out, and five different approximations of the confidence for the task of database retrieval are evaluated. The experiments are carried out on a database of 25,000 different face images, showing that the normalization and filler models are most suitable for retrieval on a large face database.
Sequencing of a 4.3 kbp region of chromosome 2 of <i>Candida albicans</i> reveals the presence of homologues of <i>SHE9</i> from <i>Saccharomyces cerevisiae</i> and of bacterial phosphatidylinositol‐phospholipase C (2001)

The nucleotide sequence of a 4.3 kb fragment downstream of the LIG4 gene of Candida albicans has been determined. This fragment contains two entire ORFs (ORF1 and ORF2) and a truncated one (ORF3). ORF1 (1029 bp; EMBL databank, Accession No. AJ277539) encodes a putative protein of 343 amino acids with a high degree of similarity to phosphatidylinositol-specific phospholipases C (PI-PLC) of bacterial origin and, to a lesser degree, to similar proteins from trypanosome, fly and human. Isolated ORF1 confers PI-PLC activity to Escherichia coli transformants. ORF2 (1572 bp; EMBL databank, Accession No. AJ277538) predicts a protein of 524 amino acids with high similarity along most of the entire length to Ydr393w from Saccharomyces cerevisiae. This protein carries a domain with significant similarity to several cytoskeleton proteins of different origins. YDR393w (SHE9) is an orphan gene whose overexpression compromises cell growth. ORF3 appears to encode the homologue of the well-conserved proteasomal 26S regulatory subunit.
Human Health and Phytoestrogens (1998)

An abundant literature during the last 20-30 years dealing with both epidemiological and migrant studies, suppons the view that the western diet is mainly responsible for the high incidence of chronic and degenerative diseases in Western Europe, the United States, and Canada and now also in many of the East European countries (Dunn, 1975; Trowell and Burkitt, 1981; Reddy and Cohen, l986a, l986b; Rose et al., 1986; Stanford et al., 1995; Griffiths et al., 1996). These diseases include the major hormone-dependent cancers, colon cancer, and coronary heart disease. In the Mediterranean region as well as in Finland, particularly in the east and north, incidence of breast, colon, and prostate cancer is lower than in Western Europe and the United States but higher than in some Asian countries like Japan and China, and this may be at least partly explained by diet (Teppo et al., 1980; Reddy et al., 1985, 1987; Rose et al., 1986; Pukkala et al., 1987; Adlercreutz, 1990b; Rose, 1992; Minami et al., 1993; Kliewer and Smith, 1995; Tominaga and Kuroishi, 1995; Willett et al., 1995; Griffiths et al., 1996). On the basis of epidemiological and animal experimental studies, it has been concluded that high fat and low fiber intake are important contributors to the increased incidence of the above-mentioned diseases. Recently the conclusions have, however, been questioned with regard to breast cancer (Willett et al., 1992). Independent of which position one takes in this debate, it seems that causes other than an abundance of fat and lack of fiber should receive consideration for the high incidence of cancer and coronary heart disease.
Fault injection scan design for enhanced VLSI design verification (2002)

Proposes a design technique called the fault injection scan register (FISR) for fault injection that has much higher fault coverage than the traditional pin-level fault injection for systems using complex VLSI components. The FISR utilizes the scan-in-scan-out design inject faults to the internal circuits of a VLSI chip. The fault injection is accomplished by loading a pair of fault vectors to a set of fault latches via the scan registers. The fault latches are then enabled so that the target signals will be forced to high or low during the normal operation. the delivery of injected faults via the scan registers and the concept of fault vector are the major innovations in the design. An innovative three stage flip-flop is also used to reduce the implementation overhead of the FISR.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Do Behavioral Biases Affect Prices? (2005)

ABSTRACT This paper documents strong evidence for behavioral biases among Chicago Board of Trade proprietary traders and investigates the effect these biases have on prices. Our traders appear highly loss‐averse, regularly assuming above‐average afternoon risk to recover from morning losses. This behavior has important short‐term consequences for afternoon prices, as losing traders actively purchase contracts at higher prices and sell contracts at lower prices than those that prevailed previously. However, the market appears to distinguish these risk‐seeking trades from informed trading. Prices set by loss‐averse traders are reversed significantly more quickly than those set by unbiased traders.
Skin Toxicity of propranolol in guinea pigs. (1999)

The skin toxicities of propranolol were studied in guinea pigs. In the primary and cumulative skin irritation studies, the skin reactions and the histopathological changes were observed in all animals treated with propranolol, and those tended to increase with the increase of propranolol dosage. The skin reactions increased with the application times of propranolol up to 7 days in the cumulative skin irritation study. In the skin sensitization, the phototoxicity and the skin photosensitization studies, no skin reactions were observed in any animals used in the studies. These results indicate that propranolol caused skin irritation, but was negative for skin sensitization, phototoxicity and skin photosensitization in guinea pigs.
Penman: An Open-Source Library and Tool for AMR Graphs (2020)

Meaning Representation (AMR) The format is simple enough that users of AMR data often write small scripts or libraries for parsing it into an internal graph representation, but there is enough complexity that these users could benefit from a more sophisticated and well-tested solution. The open-source Python library Penman provides a robust parser, functions for graph inspection and manipulation, and functions for formatting graphs into PENMAN notation. Many functions are also available in a command-line tool, thus extending its utility to non-Python setups.
Enhancement of Precise Gene Editing by the Association of Cas9 With Homologous Recombination Factors (2019)

The CRISPR-Cas9 system is used for genome editing in mammalian cells by introducing double-strand breaks (DSBs) which are predominantly repaired via non-homologous end joining (NHEJ) or to lesser extent by homology-directed repair (HDR). To enhance HDR for improving the introduction of precise genetic modifications, we tested fusion proteins of Cas9 nuclease with HDR effectors to enforce their localization at DSBs. Using a traffic-light DSB repair reporter (TLR) system for the quantitative detection of HDR and NHEJ events in human HEK cells we found that Cas9 fusions with CtIP, Rad52, and Mre11, but not Rad51C promote HDR up to twofold in human cells and significantly reduce NHEJ events. We further compared, as an alternative to the direct fusion with Cas9, two components configurations that associate CtIP fusion proteins with a Cas9-SunTag fusion or with guide RNA that includes MS2 binding loops. We found that the Cas9-CtIP fusion and the MS2-CtIP system, but not the SunTag approach increase the ratio of HDR/NHEJ 4.5-6-fold. Optimal results are obtained by the combined use of Cas9-CtIP and MS2-CtIP, shifting the HDR/NHEJ ratio by a factor of 14.9. Thus, our findings provide a simple and effective tool to promote precise gene modifications in mammalian cells.
HAQ: Hardware-Aware Automated Quantization with Mixed Precision (2018)

Model quantization is a widely used technique to compress and accelerate deep neural network (DNN) inference. Emergent DNN hardware accelerators begin to support mixed precision (1-8 bits) to further improve the computation efficiency, which raises a great challenge to find the optimal bitwidth for each layer: it requires domain experts to explore the vast design space trading off among accuracy, latency, energy, and model size, which is both time-consuming and sub-optimal. Conventional quantization algorithm ignores the different hardware architectures and quantizes all the layers in a uniform way. In this paper, we introduce the Hardware-Aware Automated Quantization (HAQ) framework which leverages the reinforcement learning to automatically determine the quantization policy, and we take the hardware accelerator's feedback in the design loop. Rather than relying on proxy signals such as FLOPs and model size, we employ a hardware simulator to generate direct feedback signals (latency and energy) to the RL agent. Compared with conventional methods, our framework is fully automated and can specialize the quantization policy for different neural network architectures and hardware architectures. Our framework effectively reduced the latency by 1.4-1.95x and the energy consumption by 1.9x with negligible loss of accuracy compared with the fixed bitwidth (8 bits) quantization. Our framework reveals that the optimal policies on different hardware architectures (i.e., edge and cloud architectures) under different resource constraints (i.e., latency, energy and model size) are drastically different. We interpreted the implication of different quantization policies, which offer insights for both neural network architecture design and hardware architecture design.
Relative Distribution of Gb <sub>3</sub> Isoforms/Analogs in Nod/Scid/Fabry Mice Tissues Determined by Tandem Mass Spectrometry (2016)

The devised method is sensitive and useful for the evaluation of biomarker profiles in Fabry mice.
530. The reaction of carbonyl chloride with 1 : 2-epoxides (1957)

J. I. Jones, J. Chem. Soc., 1957, 2735 DOI: 10.1039/JR9570002735
Voucher funds in transitional economies : the Czech and Slovak experience (1994)

Voucher funds have arisen in the transitional economies of Eastern and Central Europe that have used voucher privatization. These funds collect vouchers from citizens and use them to buy shares in enterprises. In the Czech and Slovak Republics, voucher funds are typically organized as corporations owned by the citizens who contributed their vouchers. Recently, they have also been organized as unit trusts (either open-ended or closed). A management company manages the funds under a contract that specifies the management fee. The management company is typically owned by the initial sponsor of the fund - for example, a bank. Voucher funds can give owners a diversified and professionally managed portfolio. More important, the funds select who sits on an enterprise's governance boards (which oversee management and profitability). Although experience is limited, the funds in these two countries have probably stopped most fraud and self-serving by enterprise mangers and are beginning to encourage the restructuring needed for profitability. A few funds have replaced poorly performing or dishonest managers; more often, because qualified replacements are few, they encourage managers to improve performance. There have been complaints about funds'performance. Some have made unrealistic promises to voucher holders and have appointed poorly qualified members to management boards. There is concern about conflicts of interest in the bank-sponsored funds and excessive control of enterprises. Funds typically lack capital or expertise to undertake restructuring - but few other potential owners are likely to be better qualified. The author examines 27 regulations that have been proposed for funds. Regulations in transitional economies, unlike regulations in most western countries, should encourage funds to play a strong role in corporate governance, he contends, as few potential owners have this ability. Most important, regulations should require that funds disclose information about their operations so their owners can monitor and control fund managers. The regulatory regime, the author says, should discourage monopolies and anticompetitive behavior; create incentives for fund managers to improve fund performance; discourage self-serving or fraudulent behavior by fund managers, and conflicts of interest; and eliminate high-risk investments unacceptable to fund owners. Because there is so little experience with these funds, the regulatory regime should not be unduly restrictive. As problems arise, regulations to deal with them can be added.
A simple design methodology for testable flash A/D converter output encoding (1988)

A Boolean matrix technique is presented for the design of easily tested digital-encoding circuits to follow a flash analog-to-digital converter. The digital encoding is performed using a form of Reed-Muller network. The Reed-Muller configuration is known to be easily tested, but the design of this type of network to implement arbitrary logic equations is very difficult. The author demonstrates that the unique structure of the comparator outputs in a flash converter permits the highly testable Reed-Muller network to be designed easily with arbitrary encoding. The testability implications are discussed and a design example is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
LAV Revisited: Origins of the Early HIV-1 Isolates from Institut Pasteur (1991)

Two of the first human immunodeficiency virus type-1 (HIV-1) strains isolated were authenticated by reanalyzing original cultured samples stored at the Collection Nationale de Culture des Microorganismes as well as uncultured primary material. Cloned polymerase chain reaction products were used to analyze coding sequences of the V3 loop in the gp120 glycoprotein. The original isolate HIV-1 Bru, formerly called LAV, was derived from patient BRU. HIV-1 Lai was derived from patient LAI and contaminated a HIV-1 Bru culture between 20 July and 3 August 1983. The culture became, in effect, HIV-1 Lai, identifiable by a unique motif in the V3 loop. Because of this contamination two, rather than one, HIV-1 isolates were sent to the Laboratory of Tumor Cell Biology at the National Cancer Institute on 23 September 1983. Original HIV-1 Bru was indeed present in the sample marked JBB/LAV. However the M2T-/B sample harbored HIV-1 Lai, a strain capable of growing on established cell lines. The striking similarity between HIV-1 Lai (formerly LAV-Bru) and HTLV-3B sequences remains.
The <i>ica</i> Operon and Biofilm Production in Coagulase-Negative Staphylococci Associated with Carriage and Disease in a Neonatal Intensive Care Unit (2002)

Coagulase-negative staphylococci (CoNS) are a major cause of sepsis in the neonatal intensive care unit (NICU). We evaluated the hypothesis that the ica operon and biofilm production are associated with CoNS disease in this setting. CoNS associated with bacteremia or blood culture contamination and from the skin of infants with CoNS bacteremia or healthy controls were obtained during a prospective case-control study on a busy NICU. A total of 180 strains were identified, of which 122 (68%) were Staphylococcus epidermidis and the remainder were S. capitis (n = 29), S. haemolyticus (n = 11), S. hominis (n = 9), S. warneri (n = 8), and S. auricularis (n = 1). The presence of the genes icaA, icaB, icaC, and icaD was determined by PCR, and biofilm production was examined using qualitative (Congo red agar [CRA]) and quantitative (microtiter plate) techniques. There were no significant differences in the presence of the ica operon or CRA positivity among the four groups of strains. However, quantitative biofilm production was significantly greater in strains isolated from either the blood or the skin of neonates with S. epidermidis bacteremia. We conclude that the quantity of biofilm produced may be associated with the ability to cause CoNS infection. This conclusion suggests that the regulation of biofilm expression may play a central role in the disease process.
Brassinosteroid Regulates Fiber Development on Cultured Cotton Ovules (2005)

Our current understanding of the role of phytohormones in the development of cotton fibers is derived largely from an amenable culture system in which cotton ovules, collected on the day of anthesis, are floated on liquid media. Under these conditions, supplemental auxin and gibberellin were found to promote fiber initiation and elongation. More recently, addition of low concentrations of the brassinosteroid brassinolide (BL) were also found to promote fiber elongation while a brassinosteroid biosynthesis inhibitor brassinazole2001 (Brz) inhibited fiber development. In order to elucidate the role of brassinosteroid in cotton fiber development further, we have performed a more detailed analysis of the effects of these chemicals on cultured cotton ovules. Our results confirm that exogenous BL promotes fiber elongation while treatment with Brz inhibits it. Furthermore, treatment of cotton floral buds with Brz results in the complete absence of fiber differentiation, indicating that BR is required for fiber initiation as well as elongation. Expression of fiber genes associated with cell elongation increased in ovules treated with BL and was suppressed by Brz treatment, establishing a correlation between brassinosteroid-regulated gene expression and fiber elongation. These results establish a clear connection between brassinosteroid and fiber development and open the door for genetic analysis of cotton development through direct modification of the brassinosteroid signal transduction pathway.
[Hematopoietic inhibitors elaborated by bone marrow endothelial cells]. (2002)

(1) When BME C-CM and its components directly were added to CFU-GM and HPP-CFC culture system, BMEC-CM had no effect on colony formation, > 10 kD component enhanced and < 10 kD component inhibited the formation of CFU-GM and HPP-CFC. (2) When BMEC-C M and its components were added to liquid culture system of marrow cells, after 24 hours incubation, CFU-GM decreased and HPP-CFC increased significantly in B MEC-CM group, CFU-GM increased and HPP-CFC had no significant change in > 10 kD component group; and both CFU-GM and HPP-CFC reduced in < 10 kD group. (3) MIP-2, MIP-1 alpha, MSP, TGF-beta, TNF-alpha, IFN-gamma and T beta 4 were expressed in murine marrow endothelial cells, and MIP-2, MIP-1 alpha, MSP, TGF-beta, TNF-alpha and T beta 4 were existed in BMEC-CM. (4) Antibody neutralization test results demonstrated that TGF-beta, MSP, MIP-1 alpha, IFN-gamma and T beta 4 existed in BMEC-CM had significant suppressive effects on CFU-GM and HPP-CFC. (5) T beta 4 combined with 5 hematopoietic cytokines (SCF, IL-3, IL-6, GM-CSF and EPO) added to CD34(+) cells expansion culture system, HPP-CFC significantly increased compared with 5 cytokines group. T beta 4 could downregulated the expression of proliferation and differentiation-related genes and signal transduction-related genes. It is concluded that BM EC-CM promotes the proliferation of early hematopoietic progenitor cells, and this effect is related with the inhibitors existed in BMEC-CM and it could be executed via influencing cell proliferation and differentiation-related genes and signal-related genes.
Prescient mode selection for robust video coding (2002)

In standard predictive video coders, intra-mode coding of macroblocks (MBs) provides packet loss resilience, at the cost of reduced compression efficiency. Conventional mode selection algorithms are "greedy" as they focus on minimization of distortion of current MB, while ignoring the effect of this selection on subsequent frames. This paper proposes an algorithm for prescient mode selection: the coding modes of MBs are chosen while taking into account the distortion of subsequent frames. The problem is formulated as one of joint selection of MB coding modes, for a group of pictures, so as to minimize the rate-distortion cost. The straightforward solution based on dynamic programming requires enormous computational complexity. We propose an iterative algorithm which obtains a locally optimal solution at feasible complexity. The total decoder distortion is computed using recursive optimal per-pixel estimate (ROPE) which accurately accounts for the effects of quantization, packet loss, error propagation, and error concealment. Simulation results show consistent improvement over our previous "greedy" ROPE-RD mode selection, and substantial gains over other (non-ROPE) mode selection schemes.
A computation procedure for the exact solution of location‐allocation problems with rectangular distances (1975)

Abstract A method is presented to locate and allocate p new facilities in relation to n existing facilities. Each of the n existing facilities has a requirement flow which must be supplied by the new facilities. Rectangular distances are assumed to exist between all facilities. The algorithm proceeds in two stages. In the first stage a set of all possible optimal new facility locations is determined by a set reduction algorithm. The resultant problem is shown to be equivalent to finding the p ‐median of a weighted connected graph. In the second stage the optimal locations and allocations are obtained by using a technique for solving the p ‐median problem.
Dynamics of loading the Escherichia coli sliding clamp (2006)

Sliding clamps are ring‐shaped protein complexes that encircle DNA to tether DNA polymerases to the template being copied and increase the processivity of synthesis. Clamp loaders assemble these ring‐shaped sliding clamps onto DNA in an ATP‐dependent reaction. Binding and hydrolysis of ATP promote conformational changes in the clamp loaders that modulate their affinities for clamps and DNA so that the clamp loaders can catalyze this mechanical reaction. Our laboratory has been investigating the mechanism by which the Escherichia coli γ complex clamp loader assembles the β‐sliding clamp onto DNA. We are using real time fluorescence‐based techniques to measure the kinetics of DNA binding, clamp loader·clamp binding, and ATP hydrolysis directly in solution to correlate the timing of these events. Our results demonstrated that primed template DNA specifically triggers the γ complex to hydrolyze ATP and release the clamp on DNA. All molecules of ATP are hydrolyzed in the same global step, releasing the clamp onto DNA, but ATP binding and hydrolysis at individual sites modulates the affinity of different interactions. ATP binding and hydrolysis at one subset of sites regulates interactions with the clamp whereas binding and hydrolysis at another modulates interactions with DNA. Our current efforts are aimed at defining the number of molecules of ATP hydrolyzed by different forms of the clamp loader and in the presence of SSB to further delineate the mechanism by which ATP binding and hydrolysis are coupled to mechanical work.