Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of the bovine major histocompatibility complex (BoLA) BoLA-DRB3 gene with fat and protein production and somatic cell score in Brazilian Gyr dairy cattle (Bos indicus)

The effect of the bovine major histocompatibility complex (BoLA) locus on animal health may be due to a direct action of its alleles on immune functions, whereas its indirect effect on production traits might be explained by the better general health conditions of more productive animals. In the present study, the BoLA-DRB3 gene was investigated in 1058 cows belonging to seven Brazilian Gyr Dairy herds (Bos indicus, Zebu cattle). A total of 37 alleles were identified, 15 of them described for the first time in a Zebu breed. A highly significant association (p < 0.02) was observed between allele *54 and a decrease (-26.1 kg) in milk protein yield and there was a significant association (p < 0.05) between this allele and lower (-26.07 kg) milk fat yield. There was also a significant association (p < 0.05) between allele *6 and decreased (-12.47 kg) milk protein and allele *7 and increased (12.72 kg) milk protein. There were also indications of association (p < 0.10) between somatic cell score (SCS) and alleles *3 (SCS increased by 0.54 units) and *31 (SCS increased by 0.46 units). The highly significant association of allele *54 with lower protein yield suggests the possible use of this allele in marker-assisted selection programs.
Medial temporal and prefrontal contributions to working memory tasks with novel and familiar stimuli

Lesions of parahippocampal structures impair performance of delayed matching tasks in nonhuman primates, suggesting a role for these structures in the maintenance of items in working memory and short‐term stimulus matching. However, most human functional imaging studies have not shown medial temporal activation during working memory tasks and have primarily focused on functional magnetic resonance imaging (fMRI) signal intensity changes in the prefrontal and posterior parietal cortex. The goal of this study was to test the hypothesis that the difference between the human and nonhuman primate data results from the use of highly familiar stimuli in human working memory studies and trial‐unique stimuli in nonhuman primate studies. We used fMRI to examine prefrontal and temporal lobe activation during performance of a working memory (two‐back) task, using blocks of novel and highly familiar complex pictures. Performance of the working memory task with novel complex pictures resulted in greater signal change within medial temporal lobe structures than performance of the task with familiar complex pictures. In contrast, the working memory task with highly familiar stimuli resulted in greater prefrontal activation. These results are consistent with‐ out hypothesis that the medial temporal lobe is recruited for the short‐term maintenance of information that has no prior representation in the brain, whereas the prefrontal cortex is important for monitoring familiar stimuli that have a high degree of interference. A second set of tasks examined stimulus matching. Subjects performed a target‐matching task, during which they identified a single target presented in blocks of novel or familiar stimuli. The results provide evidence of hippocampal and parahippocampal recruitment in the target‐matching task with familiar stimuli. These results are consistent with prior animal studies and suggest that prefrontal regions may be important for the monitoring and matching of familiar stimuli which have a high potential for interference, whereas medial temporal regions may become proportionally more important for matching and maintenance of novel stimuli. Hippocampus 2001;11:337–346. © 2001 Wiley‐Liss, Inc.
Histones and nucleosomes in Cancer sperm (Decapod: Crustacea) previously described as lacking basic DNA‐associated proteins: A new model of sperm chromatin

To date several studies have been carried out which indicate that DNA of crustacean sperm is neither bound nor organized by basic proteins and, contrary to the rest of spermatozoa, do not contain highly packaged chromatin. Since this is the only known case of this type among metazoan cells, we have re‐examined the composition, and partially the structure, of the mature sperm chromatin of Cancer pagurus, which has previously been described as lacking basic DNA‐associated proteins. The results we present here show that: (a) sperm DNA of C. pagurus is bound by histones forming nucleosomes of 170 base pairs, (b) the ratio [histones/DNA] in sperm of two Cancer species is 0.5 and 0.6 (w/w). This ratio is quite lower than the proportion [proteins/DNA] that we found in other sperm nuclei with histones or protamines, whose value is from 1.0 to 1.2 (w/w), (c) histone H4 is highly acetylated in mature sperm chromatin of C. pagurus. Other histones (H3 and H2B) are also acetylated, though the level is much lower than that of histone H4. The low ratio of histones to DNA, along with the high level of acetylation of these proteins, explains the non‐compact, decondensed state of the peculiar chromatin in the sperm studied here. In the final section we offer an explanation for the necessity of such decondensed chromatin during gamete fertilization of this species. J. Cell. Biochem. 105: 574–584, 2008. © 2008 Wiley‐Liss, Inc.
Advection-Dominated Accretion, Jets, and the Spectral Energy Distribution of LINERs

Abstract Low-luminosity active galactic nuclei (LLAGNs) represent the bulk of the AGN population in the present-day universe and they trace low-level accreting supermassive black holes. The observational properties of LLAGNs suggest that their central engines are intrinsically different from those of more luminous AGNs. It has been suggested that accretion in LLAGNs occurs via an advection-dominated accretion flow (ADAF) associated with strong jets. In order to probe the accretion physics in LLAGNs as a class, we model the multiwavelength spectral energy distributions (SEDs) of 24 LINERs (taken from a recent compilation by Eracleous et al.) with a coupled accretion-jet model. The accretion flow is modeled as an inner ADAF outside of which there is a truncated standard thin disk. These SEDs include radio, near-IR to near-UV HST data, and Chandra X-ray data. We find that the radio emission is severely underpredicted by ADAF models but can be explained by the relativistic jet. The origin of the X-ray radiation in most sources can be explained by three distinct scenarios: the X-rays can be dominated by emission from the ADAF, the jet, or from both components contributing at similar levels. From the model fits, we estimate important parameters of the central engine of LINERs, such as the mass accretion rate — relevant for studies of the feeding of AGNs — and the mass-loss rate in the jet and the jet power — relevant for studies of the kinetic feedback from jets.
Structural basis for T cell recognition of altered peptide ligands: a single T cell receptor can productively recognize a large continuum of related ligands

T cells recognize short linear peptides bound to major histocompatibility complex (MHC)-encoded molecules. Subtle molecular changes in peptide antigens produce altered peptide ligands (APLs), which induce different T cell responses from those induced by the antigenic ligand. A molecular basis for how these slight molecular variations lead to such different consequences for the T cell has not been described. To address this issue, we have made amino acid substitutions at the primary T cell receptor (TCR) contact residue of the murine hemoglobin determinant, Hb(64-76)/I-Ek and produced 12 peptides that interact with the TCR of the T cell clone 3.L2. The 3.L2 T cell responds to these peptides, which vary 1 million-fold in their activity, and enables them to be ranked according to their relative ability to signal through the 3.L2 TCR. Such a ranking reveals that the ability of the 3.L2 T cell to respond to these peptides depends on how well the structure of the side chain at the primary TCR contact site mimics that of the Asn residue present in the antigenic ligand. The reactivity of the 3.L2 T cell also depends on an MHC contact residue that is next to the primary TCR contact residue, suggesting that conformation of the Asn side chain is also important. By using nonnatural amino acids at a TCR contact residue, we have demonstrated that APLs can be rationally designed based on structure. These data are consistent with a model in which the affinity of a peptide-MHC complex for the TCR determines how the T cell will respond.
Inhibition of Lyn is a promising treatment for mantle cell lymphoma with bortezomib resistance

Although proteasome inhibition with bortezomib (BTZ) is a validated treatment for relapsed or refractory mantle cell lymphoma (MCL), many patients show resistance to BTZ. However, the molecular mechanism of BTZ resistance in MCL has not been elucidated. In the present study, we investigated BTZ-resistant MCL cells in vitro and in vivo. We demonstrate that BTZ-resistant MCL cells showed highly increased expression of the B-cell receptor (BCR) components CD79A and CD19. Activation of the BCR signaling pathway enhanced the activity of Src family kinases (SFKs), especially Lyn, and downstream kinases PI3K/AKT/mTOR in BTZ-resistant MCL cells. Depletion of CD79A and Lyn significantly reduced several kinase activities involved in PI3K signaling, leading to inhibition of proliferation. In addition, the SFKs inhibitor dasatinib inhibited the proliferation of BTZ-resistant cells, preventing the binding of CD19 with Lyn and PI3K p85. We also verified our findings with the mouse xenograft tumor model. Dasatinib treatment significantly decreased tumor size in the mouse bearing BTZ-resistant MCL cells, but not in the mouse bearing BTZ-sensitive MCL cells. Collectively, our data show that overexpression of the BCR and its activated signaling confers BTZ resistance in MCL cells. Thus, targeting BCR signaling with dasatinib could be a novel therapeutic approach for patients with MCL that has relapsed or is refractory to treatment with BTZ.
The Lifespan of Time Intervals in Reference Memory

To further explore how memory influences time judgments, we conducted two experiments on the lifespan of temporal representations in memory. Penney et al (2000, Journal of Experimental Psychology: Human Perception and Performance 26 1770 – 1787) reported that the perceived duration of auditorily and visually marked intervals differs only when both marker-type intervals are compared directly. This finding can be explained by a ‘memory-mixing’ process, whereby the memory trace of previous intervals influences the perception of upcoming ones, which are then added to the memory content. In the experiments discussed here, we manipulated the mixing mode of auditory/visual signal presentations. In experiment 1, signals from the same modality were either grouped by blocks or randomised within blocks. The results showed that the auditory/visual difference decreased but remained present when modalities were grouped by blocks. In experiment 2, we used a line-segmentation task. The results showed that, after a training block was performed in one modality, the perceived duration of signals from the other modality was distorted for at least 30 trials and that the magnitude of the difference decreased as the block went on. The results of both experiments highlight the influence of memory on time judgments, providing empirical support to, and quantitative portrayal of, the memory-mixing process.
A Parametric Bootstrap for Heavy Tailed Distributions by Adriana Cornea

It is known that Efron’s resampling bootstrap of the mean of random variables with common distribution in the domain of attraction of the stable laws with infinite variance is not consistent, in the sense that the limiting distribution of the bootstrap mean is not the same as the limiting distribution of the mean from the real sample. Moreover, the limiting distribution of the bootstrap mean is random and unknown. The conventional remedy for this problem, at least asymptotically, is either the m out of n bootstrap or subsampling. However, we show that both these procedures can be quite unreliable in other than very large samples. We introduce a parametric bootstrap that overcomes the failure of Efron’s resampling bootstrap and performs better than the m out of n bootstrap and subsampling. The quality of inference based on the parametric bootstrap is examined in a simulation study, and is found to be satisfactory with heavy-tailed distributions unless the tail index is close to 1 and the distribution is heavily skewed.
Men Connecting and Changing–Stages of Relational Growth in Men's Groups

ABSTRACT A revised model of group development for all-male groups is presented. The purpose of such groups is the restoration of relational connection. The model emphasizes the creation of a safe environment as a necessary first stage, with conflict and difference occurring at a later stage. The author builds on ideas from the “Boston model” and Linda Schiller's work on group developmental stages. The model is based on practice experience with over sixty men's groups, led by more than two dozen practitioners.
A TDOA Gaussian mixture model for improving acoustic source tracking

Traditionally, time difference of arrival (TDOA) based acoustic source tracking consists of two stages, more precisely, estimation of TDOAs followed by a tracking algorithm. In general, these two stages are performed separately and presume that (1) TDOAs can be estimated reliably; and (2) the errors in detection behave in a well-defined fashion. The presence of noise and reverberation, however, leads to multimodal TDOA distributions and causes larger errors in the estimates, which ultimately lowers the tracking performance. To counteract this effect, we propose an approach that enhances TDOA estimation by (1) accounting for the multimodal aspect through a Gaussian mixture model and (2) integrating knowledge that has been obtained in the tracking stage. In doing so, this approach tightly couples the two stages. Experimental results on the AV16.3 corpus show that the proposed approach significantly improves the tracking performance compared to various other tracking algorithms.
Papers on psychoanalysis

This volume brings together many of the important writings of Hans Loewald, one of the major theoreticians of psychoanalysis today. Among other subjects, Dr. Loewald discusses the nature of the internalization processes and structure building, the nature and role of reality, pre oedipal modes of perceiving and the permanence of a "psychotic core" in every personality, the relationship of psychoanalysis to culture, mastery and defense, and the nature of time. "[Loewald's] writing is stimulating and challenging, and his work contains some profound psychoanalytic insights. "-Steven J. Ellman, Contemporary Psychology "Loewald belongs securely in the ranks of major psychoanalytic thinkers. [His book] contains memorable contributions to our theoretical and clinical understanding of a broad range of topics, and should be read by anyone interested in human psychology. "-Sydney E. Pulver, M.D., Review of Psychoanalytic Books "A pleasure to read. "-F. H. G. Balfour, British Journal of Psychiatry
Health state utilities: a framework for studying the gap between the imagined and the real.

OBJECTIVES Health state utilities play an important role in decision analysis and cost-utility analysis. The question whose utilities to use at various levels of health-care decision-making has been subject of considerable debate. The observation that patients often value their own health, but also other health states, higher than members of the general public raises the question what underlies such differences? Is it an artifact of the valuation methods? Is it adaptation versus poor anticipated adaptation? This article describes a framework for the understanding and study of potential mechanisms that play a role in health state valuation. It aims at connecting research from within different fields so that cross-fertilization of ideas may occur. METHODS The framework is based on stimulus response models from social judgment theory. For each phase, from stimulus, through information interpretation and integration, to judgment, and, finally, to response, we provide evidence of factors and processes that may lead to different utilities in patients and healthy subjects. RESULTS Examples of factors and processes described are the lack of scope of scenarios in the stimulus phase, and appraisal processes and framing effects in the information interpretation phase. Factors that play a role in the judgment phase are, for example, heuristics and biases, adaptation, and comparison processes. Some mechanisms related to the response phase are end aversion bias, probability distortion, and noncompensatory decision-making. CONCLUSIONS The framework serves to explain many of the differences in valuations between respondent groups. We discuss some of the findings as they relate to the field of response shift research. We propose issues for discussion in the field, and suggestions for improvement of the process of utility assessment.
Dimensions of the heterosexual bond : culture, personality and cycle effects

Romantic love, sexual desire, and adult attachment mechanisms were proposed to be universal adaptations which initiate and maintain a pair-bond relationship with a selected partner. The main goal of the thesis was to explore the functions of the pair-bond mechanisms from an evolutionary perspective and to test whether these proposed mechanisms showed the characteristics expected of psychological systems designed to initiate and maintain a pair-bond. The life history theory assumes that, as the available resources and lifespan are limited, decisions regarding resource allocation (e.g., energy) involve trade-offs among life history tasks (e.g., reproduction, parenting). The theory implies that individuals in different circumstances should deal with trade-offs differently, and this may be reflected in the experiences of pair-bond relationships. I first selected prospective items in order to construct self-report measurements of pair-bond relationships (Chapter Two). These items were administered to Occidental and Japanese participants. Their responses were entered in a series of factor analyses in order to confirm factor structure underlying pair-bond relationships, and to develop and refine measurements to assess relationships dimensions (Chapter Three). For both cultural groups, six factors were generated: a romantic love related factor (obsession); three attachment-related factors (care-receiving, care-giving, separation distress); and two sexual desire-related factors (partner- and other-directed sexual desire). The developed scales and/or some of the selected items were used to assess whether individuals differed in the intensity of relationship dimensions as a function of sex (Chapters Four and Five), age (Chapter Four), relationship stage (Chapter Four), cultural background (Chapter Four), personality (Chapter Five) and female conception probability (Chapter Six). Results showed that the intensity of relationship dimensions differed between sexes, different age groups, relationship stages, cultural backgrounds, personalities, and menstrual phases. In fact, culture had a major impact on pair-bond relationship dimensions. The strong cultural influence found on the relationship dimensions suggests that this should not be ignored by evolutionary psychologists.
A Comparison of Alignment Models for Statistical Machine Translation

In this paper, we present and compare various alignment models for statistical machine translation. We propose to measure the quality of an alignment model using the quality of the Viterbi alignment compared to a manually-produced alignment and describe a refined annotation scheme to produce suitable reference alignments. We also compare the impact of different alignment models on the translation quality of a statistical machine translation system.
Evidence for depletion of Ia+ macrophages and associated immunosuppression in African trypanosomiasis

The percentage of Ia antigen-bearing (Ia+) macrophages was significantly lower in mice infected with Trypanosoma rhodesiense than in normal controls. The degree of difference varied with the source of macrophages and time course of infection. The percentage of Ia+ macrophages isolated from spleens 10 days after infection was 71% of that in the controls, and depletion continued until Ia+ macrophages were almost undetectable 30 days after infection. The rate of depletion was slower in the peritoneal cavity. In contrast, Ia+ macrophages were not significantly depleted from the lymph nodes until 30 days after infection. The ability of macrophages from trypanosome-infected mice to present listerial antigen to sensitized T cells was significantly lower than in controls. Immune T cells had significantly less ability (43% of controls) to incorporate thymidine when exposed to splenic macrophages from infected mice during the early stage of disease. This loss of antigen presentation increased during the course of infection. Peritoneal macrophages also exhibited an early loss of ability to present antigen, but no significant decline occurred thereafter. No significant loss of antigen had occurred in the lymph node macrophages 10 days after infection, but during the later stages of the disease a significant loss was detected. Treatment of macrophages from infected and control mice with anti-Iab serum and complement inhibited their ability to present antigen. Our results demonstrate that Ia+ macrophages and their distribution can influence the ability of infected animals to process antigens and may therefore account in part for the immunosuppression observed in trypanosomiasis.
Erv14 family cargo receptors are necessary for ER exit during sporulation in Saccharomyces cerevisiae

Sporulation of Saccharomyces cerevisiae is a developmental process in which four haploid spores are created within a single mother cell. During this process, the prospore membrane is generated de novo on the spindle pole body, elongates along the nuclear envelope and engulfs the nucleus. By screening previously identified sporulation-defective mutants, we identified additional genes required for prospore membrane formation. Deletion of either ERV14, which encodes a COPII cargo receptor, or the meiotically induced SMA2 gene resulted in misshapen prospore membranes. Sma2p is a predicted integral membrane that localized to the prospore membrane in wild-type cells but was retained in the ER in erv14 cells, suggesting that the prospore membrane morphology defect of erv14 cells is due to mislocalization of Sma2p. Overexpression of the ERV14 paralog ERV15 largely suppressed the sporulation defect in erv14 cells. Although deletion of ERV15 alone had no phenotype, erv14 erv15 double mutants displayed a complete block of prospore membrane formation. Plasma membrane proteins, including the t-SNARE Sso1p, accumulated in the ER upon transfer of the double mutant cells to sporulation medium. These results reveal a developmentally regulated change in the requirements for ER export in S. cerevisiae.