Miracle-dz/UniFAR-FTUs huggingface dataset:
Neutrophil Gelatinase-Associated Lipocalin (NGAL) Predicts Response to Neoadjuvant Chemotherapy and Clinical Outcome in Primary Human Breast Cancer

In our previous work we showed that NGAL, a protein involved in the regulation of proliferation and differentiation, is overexpressed in human breast cancer (BC) and predicts poor prognosis. In neoadjuvant chemotherapy (NACT) pathological complete response (pCR) is a predictor for outcome. The aim of this study was to evaluate NGAL as a predictor of response to NACT and to validate NGAL as a prognostic factor for clinical outcome in patients with primary BC. Immunohistochemistry was performed on tissue microarrays from 652 core biopsies from BC patients, who underwent NACT in the GeparTrio trial. NGAL expression and intensity was evaluated separately. NGAL was detected in 42.2% of the breast carcinomas in the cytoplasm. NGAL expression correlated with negative hormone receptor (HR) status, but not with other baseline parameters. NGAL expression did not correlate with pCR in the full population, however, NGAL expression and staining intensity were significantly associated with higher pCR rates in patients with positive HR status. In addition, strong NGAL expression correlated with higher pCR rates in node negative patients, patients with histological grade 1 or 2 tumors and a tumor size <40 mm. In univariate survival analysis, positive NGAL expression and strong staining intensity correlated with decreased disease-free survival (DFS) in the entire cohort and different subgroups, including HR positive patients. Similar correlations were found for intense staining and decreased overall survival (OS). In multivariate analysis, NGAL expression remained an independent prognostic factor for DFS. The results show that in low-risk subgroups, NGAL was found to be a predictive marker for pCR after NACT. Furthermore, NGAL could be validated as an independent prognostic factor for decreased DFS in primary human BC.
Comparison of uninterrupted warfarin and bridging therapy using low-molecular weight heparin with respect to the severity of bleeding after dental extractions in patients with prosthetic valves

Objective: The management of anticoagulated patients with warfarin during dental extraction is an intricate issue. We carefully designed the current study so that the amount of bleeding was measured with objective methods and the data from the same patient in different dental extraction appointments could be compared, eliminating the bleeding diathesis differences of patients. Methods: This prospective and controlled study was conducted in 36 adult patients with prosthetic valve requiring multiple tooth extractions. The first dental extraction was performed without the discontinuation of warfarin therapy, and the second procedure was performed with a discontinuation of warfarin and bridging with low-molecular weight heparin (LMWH). The two dental extraction protocols in the same patient group were compared. The total amount of bleeding was calculated as the difference between the weights of gauze swabs used before and after the tamponade; the number of gauze swabs used for bleeding control in the first 48 h was recorded. Result: The median number of used gauze swabs was 2.5 (IQR: 1–5) and 3.0 (IQR: 2–7) in the first and second dental extraction procedures, respectively. The median bleeding time was 50.0 (IQR: 20–100) in the first procedure compared with 60.0 (IQR: 40–140) min in the second procedure. The mean amounts of bleeding were 2194±1418 mg in the first dental extraction procedure and 2950±1694 mg in the second dental extraction procedure. The median number of used gauze swabs, the median bleeding time, and the mean amount of bleeding were statistically higher in the second dental extraction procedure (p<0.001). Conclusion: Continued warfarin treatment at the time of dental extractions reduces the total amount of bleeding compared with bridging therapy in patients with prosthetic valves.
CHRONIC LYMPHOCYTIC LEUKEMIA : TAKING A BIG LEAP FORWARD Monoclonal B-cell lymphocytosis and early-stage chronic lymphocytic leukemia : diagnosis , natural history , and risk strati fi cation

Chronic lymphocytic leukemia (CLL) is a clonal lymphoproliferative disorder characterized by . 5 3 10/L peripheral B-lymphocytes coexpressing CD5, CD19, and CD23 and a weak expression of CD20, CD79b, and surface immunoglobulin (sIg). When such a population is detected in enlarged lymph nodes of patients without peripheral lymphocytes, the term small lymphocytic lymphoma (SLL) is used, indicating a clinical variant of the same histopathological and molecular entity. The possibility of a precursor state to CLLwas first identified in the early 1990s when a series of cross-sectional population-based studies was conducted in the United States to determine the health risks of living near hazardous waste sites. Using a 2-color panel (CD19 and CD5), 11out of 1926 (0.6%) individualsolder than40yearswere found to have a clonal population of CD5CD19 B cells, an immunophenotype classically associated with CLL. However, none of them met the diagnostic criteria for CLL or SLL. In particular, none had an absolute lymphocyte count (ALC) . 5000/mL, as originally required by the diagnostic criteria for CLL. This phenomenon, later categorized monoclonal B-cell lymphocytosis (MBL), opened a new chapter in the field of B-cell lymphoproliferative disorders, suggesting that a precursor state of these lymphoid malignancies may occur at high prevalence in the general population.
Transecting Security and Space in Phnom Penh

Our paper examines everyday interactions of money, power, and security in Cambodia's capital city of Phnom Penh, informed by a series of transects and interviews. When Phnom Penh hosted the Association of the Southeast Asian Nations (ASEAN) Summit in April 2012, Prime Minister Hun Sen declared that “Cambodia is not for sale” in an angry exchange with journalists who had quizzed him about China's influence. However, the sale and enclosure of Cambodian land and property have yielded both profit and tensions. These are connected with the meanings and operation of security. The most powerful ‘security’ agency in Phnom Penh is neither wholly ‘public’ nor fully ‘private’, but hybrid; where public police and military personnnel and their equipment are purchased. We argue that this is symptomatic of circulation/operation of state/capital in Cambodia.
Exemplar Dynamics in Phonetic Convergence of Speech Rate

We motivate and test an exemplar-theoretic view of phonetic convergence, in which convergence effects arise because exemplars just perceived in a conversation are stored in a speaker’s memory, and used subsequently in speech production. Most exemplar models assume that production targets are established using stored exemplars, taking into account their frequencyand recency-influenced level of activation. Thus, convergence effects are expected to arise because the exemplars just perceived from a partner have a comparably high activation. However, in the case of frequent exemplars, this effect should be countered by the high frequency of already stored, older exemplars. We test this assumption by examining speech rate convergence in spontaneous speech by female German speakers. We fit two linear mixed models, calculating speech rate on the basis of either infrequent, or frequent, syllables, and predict a speaker’s speech rate in a phrase by the partner’s speech rate in the preceding phrase. As anticipated, we find a significant main effect indicating convergence only for the infrequent syllables. We also find an unexpected significant interaction of the partner’s speech rate and the speaker’s assessment of the partner in terms of likeability, indicating divergence, but again, only for the infrequent case.
Different Questions, Different Answers

Carroll and Fennema (2004) raise a number of concerns about our research on the expansion of the global business community (Kentor and Jang, 2004). We find little merit in the issues they raise. We begin with a brief overview of the differences between our two efforts and then address their critique. We preface this response by restating that we do find merit in Carrol and Fennema’s original (2002, hereafter C&F) article. There are, as they point out, many similarities in our findings. The discrepancies between our works, however, are also significant. At the core of these differences is a conflict over the appropriate unit of analysis for the global processes in question. Carroll and Fennema use a sampling design based upon countries as the units of analysis, while our sample is drawn from the global economy as a whole, irrespective of geographic location. These conflicting perspectives lead to disparate findings. Different questions, different answers. Carroll and Fennema (2002) examine the possible emergence of a transnational business community between 1976 and 2002, as evidenced by an increase in interlocking boards of directors across national boundaries. To do so, they used a disproportionate stratified sample design of 176 firms, which oversampled European firms to avoid the dominance of US corporations in the global economy in the 1970s. Their longitudinal analysis of this sample failed to find any significant growth in international linkages over this time period. We, too, were interested in examining change in the integration of transnational corporations over time. But our focus was on understanding changes in the global economy as a whole, rather than with changes within
CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data

High-throughput bisulfite sequencing is widely used to measure cytosine methylation at single-base resolution in eukaryotes. It permits systems-level analysis of genomic methylation patterns associated with gene expression and chromatin structure. However, methods for large-scale identification of methylation patterns from bisulfite sequencing are lacking. We developed a comprehensive tool, CpG_MPs, for identification and analysis of the methylation patterns of genomic regions from bisulfite sequencing data. CpG_MPs first normalizes bisulfite sequencing reads into methylation level of CpGs. Then it identifies unmethylated and methylated regions using the methylation status of neighboring CpGs by hotspot extension algorithm without knowledge of pre-defined regions. Furthermore, the conservatively and differentially methylated regions across paired or multiple samples (cells or tissues) are identified by combining a combinatorial algorithm with Shannon entropy. CpG_MPs identified large amounts of genomic regions with different methylation patterns across five human bisulfite sequencing data during cellular differentiation. Different sequence features and significantly cell-specific methylation patterns were observed. These potentially functional regions form candidate regions for functional analysis of DNA methylation during cellular differentiation. CpG_MPs is the first user-friendly tool for identifying methylation patterns of genomic regions from bisulfite sequencing data, permitting further investigation of the biological functions of genome-scale methylation patterns.
Speech-Based Interaction in Multitask Conditions: Impact of Prompt Modality

Speech-based interaction is often recognized as appropriate for hands-busy, eyes-busy multitask situations. The objective of this study was to explore prompt-guided speech-based interaction and the impact of prompt modality on overall performance in such situations. A dual-task paradigm was employed, with tracking as a primary task and speech-based data input as a secondary task. There were three tracking conditions: no tracking, basic, and difficult tracking. Two prompt modalities were used for the speech interaction: a dialogue with spoken prompts and a dialogue with visual prompts. Data entry duration was longer with the speech prompts than with the visual prompts, regardless of whether or not there was tracking or its level of difficulty. However, when tracking was difficult, data entry duration was similar for both spoken and visual prompts. Tracking performance was also affected by the prompt modality, with poorer performance obtained when the prompts were visual. The findings are discussed in terms of multiple resource theory and the possible implications for speech-based interactions in multitask situations. Actual or potential applications of this research include the design of speech-based dialogues for multitask situations such as driving and other hands-busy, eyes-busy situations.
Different Effects of Regional Species Pool on Plant Diversity between Forest and Grassland Biomes in Arid Northwest China

Species pool hypothesis is broadly known and frequently tested in various regions and vegetation types. However it has not been tested in the arid Xinjiang region of China due to lack of data. Here with systematic data from references and field survey, we comprehensively examined species pool hypothesis in this region. Took species richness in 0.1° × 0.1° grid cells as regional species richness (RSR) which were obtained from the distribution maps of vascular plant species, and took species diversity of 190 and 103 plots in forest and grassland biomes across Xinjiang as local species richness (LSR), together with the digitalized soil pH and climate data, we tested the species pool hypothesis in this region. We found that: (1) the average RSR was higher in mountains than that in basins and it was negatively correlated with soil pH in mountains while positively correlated with soil pH in basins in Xinjiang; (2) RSR showed a positive correlation with mean annual precipitation (MAP) while showed a hump-shaped pattern with mean annual temperature (MAT); and the changing patterns of LSR were different for forest and grassland along the geographical and climate gradients; (3) LSR of forest was more affected by RSR than by climate, while on the contrary, LSR of grassland was more affected by climate than by RSR. Our results validated the species pool hypothesis in revealing that RSR had a significant role in shaping LSR patterns in addition to climate. We concluded that the relative effects of climate vs. RSR on LSR differed markedly between the forest and grassland communities across Xinjiang. Our results also showed that RSR revealed a contrasting relationship with soil pH in mountains and in basins, which might reflect differences in evolutionary processes of various habitats. In summary, our research systematically analyzed the correlation of species richness in regional and local scales in Xinjiang which provides more insights into the understanding of species pool hypothesis.
Reactive Oxygen Species Production Is Involved in Quercetin-Induced Apoptosis in Human Hepatoma Cells

Abstract: Hepatocellular carcinoma (HCC) is the leading cause of cancer mortality in Asia. The aim of this study was to examine whether reactive oxygen species production is involved in quercetin-induced apoptosis in human HCC cell lines. Quercetin inhibited the growth of hepatoma cells in dose and time dependent manners. Quercetin treatment of hepatoma cells resulted in changes of cell cycle progression. The G0/G1phase was decreased and S phase was increased in HA22T/VGH cells after treatment with quercetin. The levels of apoptotic sub-G0/G1, reactive oxygen species and annexin V were increased prior to cell death and concurrent with lipid peroxidation in two human hepatoma cells after treatment with quercetin. Quercetin also enhanced the apoptotic effect of the chemotherapeutic agent, paclitaxel, in HA22T/VGH cells. Quercetin has therapeutic potential as an anti-cancer drug. These results provide basis for further study into the potential use of quercetin in combination with paclitaxel for treatment of hepatoma.
Metal Complexes of Diisopropylthiourea: Synthesis, Characterization and Antibacterial Studies

Co(II), Cu(II), Zn(II) and Fe(III) complexes of diisopropylthiourea have been synthesized and characterized by elemental analyses, molar conductivity, magnetic susceptibility, FTIR and electronic spectroscopy. The compounds are non-electrolytes in solution and spectroscopic data of the complexes are consistent with 4-coordinate geometry for the metal(II) complexes and six coordinate octahedral for Fe(III) complex. The complexes were screened for their antibacterial activities against six bacteria: Escherichia coli, Pseudomonas auriginosa, Klebsiella pneumoniae, Bacillus cereus, Staphylococcus aureus and Bacillus pumilus. The complexes showed varied antibacterial activities and their minimum inhibitory concentrations (MICs) were determined.
Emotion Science in the Twenty-First Century. Time, Sex, and Behavior in Emotion Science: Over and Above

With the advent of sophisticated tools and techniques over the past three decades, brain imaging has energized the rapidly developing field of Social Neuroscience, and has sparked a wide range of research in Emotion Science. Since its launch in 2010, Frontiers in Emotion Science has published more than 400 articles, many of them utilizing brain imaging tools. However, the question arises: Are we on the way to real progress? It is reasonable, and healthy, to reflect on how brain imaging has helped to elucidate our understanding of socio-emotional functioning, and how its contributions can be enriched and improved in the future. As a neuroscientist who has conducted many brain imaging studies, I wrestle with several doubts and concerns. In this piece of work, I will discuss the critical importance of behavior, time, and sex/gender not only for Emotion Science, but also “over and above” this specific area of investigation. I will focus on the ways in which these key constructs represent a grand (and very exciting) challenge for neuroscience. I elaborate on three of these here.
Distribution of non-LEE-encoded type 3 secretion system dependent effectors in enteropathogenic Escherichia coli

Enteropathogenic Escherichia coli (EPEC) are important human gastroenteritis agents. The prevalence of six non-LEE genes encoding type 3 translocated effectors was investigated. The nleC, cif and nleB genes were more prevalent in typical than in atypical EPEC, although a higher diversity of genes combinations was observed in atypical EPEC.
Hoop Housing for Feeder Pigs Offers a Welfare-Friendly Environment Compared to a Nonbedded Confinement System

Total confinement systems of swine production offer several benefits and costs in terms of animal welfare. Swine raised in total confinement are protected from environmental extremes and predators; however, welfare concerns stem from observations of stereotypic behavior and lameness of pigs, common in some of these systems. Because total confinement systems are expensive to build and maintain compared to less intensive systems, producers have become interested in an inexpensive alternative: hoop structures (Hoop). Open-ended Quonsets shaped like a half cylinder lying on its flat side, the Hoop use bedding to keep the pigs dry and allow this bedding to compost beneath the pigs to keep them warm in winter. This project compared the behavior and physiology of pigs in a nonbedded confinement system (NBCS) with those in the Hoop. Two experiments, 1 in the winter and 1 in the summer, assessed the welfare of pigs based on the incidence of aberrant behavior, physiologic response to handling, incidence of lameness, and the performance of play behavior. Pigs raised in the NBCS performed more aberrant behaviors and less play behavior, had greater plasma cortisol in response to handling (but fewer vocalizations), and a greater incidence of injuries than did the pigs raised in the Hoop. Based on these data, pigs in the Hoop were adjudged to have enhanced welfare as compared to pigs raised in the NBCS. Because the welfare of pigs in the Hoop appears to be greater than the welfare of pigs raised in the NBCS, future research should determine which factors are most important to pigs and then try to incorporate these into production systems.
Personality as an indirect predictor of academic achievement via student course experience and approach to learning

How personality traits predict students’ course experience, approaches to learning (SAL), and academic achievement were investigated. A path analysis showed that personality traits predicted course experience, which, in turn, predicted SAL and academic achievement. Personality traits accounted for 27% of the variance in teaching quality, and 18% of the variance in appropriate workload. Furthermore, personality traits and course experience accounted for 19% of the variance in deep SAL, 55% of the variance in surface SAL, and 48% of the variance in strategic SAL. The whole model accounted for 13% of the variance in examination grades. It was concluded that individual differences in personality should be taken into account when investigating learning in terms of students’ course experience and SAL.
Distilling Knowledge from an Ensemble of Models for Punctuation Prediction

This paper proposes an approach to distill knowledge from an ensemble of models to a single deep neural network (DNN) student model for punctuation prediction. This approach makes the DNN student model mimic the behavior of the ensemble. The ensemble consists of three single models. Kullback-Leibler (KL) divergence is used to minimize the difference between the output distribution of the DNN student model and the behavior of the ensemble. Experimental results on English IWSLT2011 dataset show that the ensemble outperforms the previous state-of-the-art model by up to 4.0% absolute in overall F1-score. The DNN student model also achieves up to 13.4% absolute overall F1-score improvement over the conventionally-trained baseline models.
Trust within organisations: Introduction to a special issue.

Introduces six empirical studies on trust within organisations which were originally presented at a workshop on “Trust within and between organisations”, organised by the European Institute for Advanced Studies in Management at the Free University Amsterdam, in November 2001. Areas covered include: the legitimacy of the field of study; common understandings and disagreements in theoretical ideas; and directions for future research.
The assembly of ionic currents in a thalamic neuron III. The seven-dimensional model

We replace our earlier three-dimensional ha-model of a thalamic neuron (Rose & Hindmarsh, Proc. R. Soc. Lond. B 237, 289–312 (1989b)) by a seven-dimensional ha-model. The stability and state diagrams for this seven-dimensional model are shown to be similar to those of the three-dimensional system with which it is compared. Two examples that illustrate how the seven-dimensional model can be related to experimental recordings are then discussed in detail. In each case we show the state and stability diagrams and the time courses of the different ionic currents during the burst response. We discuss how the various components of the state diagram could be determined experimentally. These experiments are illustrated by using our model to simulate the results of actual experiments. Finally the state and stability diagrams are transferred to a current–voltage diagram. This shows the advantage of the state diagram compared with the current–voltage diagram for representing the dynamics of the firing of a thalamic neuron.