Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Epstein-Barr virus in metastatic lymph nodes of patients with nasopharyngeal carcinoma and a primary unknown carcinoma.

BACKGROUND Nasopharyngeal carcinoma is often associated with neck lymph node (LN) metastases, which in many cases is the only manifestation of this disease. The submucosal and infiltrative characteristics of nasopharyngeal carcinoma make this type of cancer difficult to diagnose. Nasopharyngeal carcinoma has also been reported to be strongly associated with the Epstein-Barr virus. METHODS We examined 36 nasopharyngeal carcinomas (from 30 primary sites and from 6 metastasized LNs), 13 metastasized LNs of other head and neck cancers, and 12 primary unknown neck metastases using an in situ hybridization technique. RESULTS In the nasopharyngeal carcinomas, in situ hybridization with an Epstein-Barr virus-encoded small RNA identified the Epstein-Barr virus in 20 (67%) of the 30 primary sites and in 3 (50%) of the 6 metastasized LNs. Epstein-Barr virus was not detected in metastasized LNs of other head and neck cancers, but was detected in 1 of the primary unknown neck metastases. CONCLUSION In situ hybridization using a digoxigenin-labeled Epstein-Barr virus-encoded small RNA probe is useful for the differential diagnosis of metastasized LNs when the primary site is unknown.
Protective Effects of Isoflurane Pretreatment in Endotoxin-induced Lung Injury

Background: The concept of antiinflammatory effects of volatile anesthetics is well established in vitro and in some organ systems. Their protective role in lung injury, however, remains to be elucidated. The authors hypothesized that in the lung, isoflurane pretreatment may attenuate neutrophil infiltration and reduce endotoxin-induced injury. Methods: Male C57Bl/6 mice were exposed to aerosolized lipopolysaccharide. Neutrophil recruitment into the pulmonary vasculature and migration into the different lung compartments (interstitium and alveolar air space) were determined by flow cytometry. Capillary protein leakage, formation of lung edema, and concentration of the chemokines keratinocyte-derived chemokine (CXCL1) and macrophage inflammatory protein 2 (CXCL2/3) in bronchoalveolar lavage were compared in mice with or without isoflurane treatment (1.4% inspired for 30 min) at different times before and after endotoxin exposure. Results: Endotoxin inhalation induced significant neutrophil migration into all lung compartments. Isoflurane pretreatment attenuated both neutrophil recruitment into lung interstitium and alveolar space when given 1 or 12 h before or 1 h after lipopolysaccharide but not at 4, 6, or 24 h before endotoxin exposure. Isoflurane pretreatment 1 or 12 h before lipopolysaccharide also reduced protein leakage and pulmonary edema. Production of CXCL1 and CXCL2/3 in the bronchoalveolar lavage was reduced when isoflurane was given 1 h but not 12 h before lipopolysaccharide, suggesting different mechanisms for early and late protection. Conclusion: Isoflurane pretreatment reduces acute lung injury when given 1 or 12 h before an endotoxin challenge or within the first hour of an already established inflammation.
Comparative studies of quantitative trait and neutral marker divergence: a meta‐analysis

Comparative studies of quantitative genetic and neutral marker differentiation have provided means for assessing the relative roles of natural selection and random genetic drift in explaining among‐population divergence. This information can be useful for our fundamental understanding of population differentiation, as well as for identifying management units in conservation biology. Here, we provide comprehensive review and meta‐analysis of the empirical studies that have compared quantitative genetic (QST) and neutral marker (FST) differentiation among natural populations. Our analyses confirm the conclusion from previous reviews – based on ca. 100% more data – that the QST values are on average higher than FST values [mean difference 0.12 (SD 0.27)] suggesting a predominant role for natural selection as a cause of differentiation in quantitative traits. However, although the influence of trait (life history, morphological and behavioural) and marker type (e.g. microsatellites and allozymes) on the variance of the difference between QST and FST is small, there is much heterogeneity in the data attributable to variation between specific studies and traits. The latter is understandable as there is no reason to expect that natural selection would be acting in similar fashion on all populations and traits (except for fitness itself). We also found evidence to suggest that QST and FST values across studies are positively correlated, but the significance of this finding remains unclear. We discuss these results in the context of utility of the QST–FST comparisons as a tool for inferring natural selection, as well as associated methodological and interpretational problems involved with individual and meta‐analytic studies.
Pain and the Placebo: What We Have Learned

Despite the recent blossoming of rigorous research into placebo mechanisms and the long-standing use of placebos in clinical trials, there remains widespread and profound misunderstanding of the placebo response among both practicing physicians and clinical researchers. This review identifies and clarifies areas of current confusion about the placebo response (including whether it exists at all), describes its phenomenology, and outlines recent advances in our knowledge of its underlying psychological and neural mechanisms. The focus of the review is the placebo analgesic response rather than placebo responses in general, because much of the best established clinical and experimental work to date has been done on this type of placebo response. In addition, this subfield of placebo research offers a specific neural circuit hypothesis capable of being integrated with equally rigorous experimental work on the psychological (including social psychological) and clinical levels. In this sense, placebo analgesia research bears all the marks of a genuine multilevel interdisciplinary research paradigm in the making, one that could serve as a model for research into other kinds of placebo responses, as well as into other kinds of mind-body responses.
Discrete time congestion controllers for multi-source connection-oriented communication networks

In this article, a new, discrete time, non-linear flow control strategy for a connection-oriented, multi-source communication network is proposed. The strategy effectively exploits the Smith principle in order to avoid data loss in the network, and to ensure full utilisation of the bottleneck link available bandwidth. The desirable properties of the proposed control strategy are preserved, even though the connection round trip times may be determined imprecisely. Furthermore, an enhanced strategy, which employs extra feed-forward bandwidth compensation, and reduces the influence of the available bandwidth variations on the steady state queue length in the network, is introduced. Finally, the proposed strategy is modified to be appropriate for application when the number of active connections changes during the control process, and new conditions for no data loss and full bandwidth utilisation are formulated and strictly proved. Since the modified strategy allows for arbitrary resource allocation among the controlled virtual circuits, the max–min fairness criteria can be satisfied.
Equitable Coloring of Sparse Planar Graphs

A proper vertex coloring of a graph $G$ is equitable if the sizes of color classes differ by at most one. The equitable chromatic threshold $\chi_{eq}^*(G)$ of $G$ is the smallest integer $m$ such that $G$ is equitably $n$-colorable for all $n\geq m$. We show that for planar graphs $G$ with minimum degree at least two, $\chi_{eq}^*(G)\leq4$ if the girth of $G$ is at least 10, and $\chi_{eq}^*(G)\leq3$ if the girth of $G$ is at least 14.
THE STRATIGRAPHY OF THE OFFSHORE GIPPSLAND BASIN

The Gippsland Basin in south-eastern Australia mainly underlies the continental shelf between eastern Victoria and Tasmania. It is filled with Lower Cretaceous-Recent sediment and has become a major source of hydrocarbons for the Australian market. Forty-two wildcat and stepout wells, additional development wells and over 7,000 miles of seismic lines provide a framework on which to build the region's geological history. The time-stratigraphy of the basin is derived from extensive use of spore-pollen assemblages in the mainly non-marine Cretaceous-Eocene and foraminifera in the marine Oligocene-Pliocene, largely complemented by seismic and to a lesser extent electric log correlations. Ten Cretaceous and five Paleocene-Eocene spore-pollen zones and fourteen Oligocene-Pliocene foraminiferal zonules are recognized. Only broad-scale lithostratigraphic units, initially recognized along the northern, onshore margin of the basin are traceable offshore. The Lower Cretaceous is represented by at least 10,000 feet of non-marine greywacke of the Strzelecki Group. The Upper Cretaceous-Eocene, with a cumulative thickness of 15,000 feet is termed the Latrobe Group and consists mainly of lacustrine and fluviatile elastics. Channels dissected the top of the Latrobe Group during the Eocene and were filled with sediments recognizable as distinct sequences within the group and termed the Flounder and Turrum Formations. A destructive marine phase during latest Eocene time left the glauconitic Gurnard Formation as the youngest member of the Group. Subsequent marine inundation of the basin resulted in deposition of up to 1,500 feet of calcareous mudstone referred to the Lakes Entrance Formation and up to 5,000 feet of marl, calcarenite and limestone of the Gippsland Limestone during the Oligocene and Miocene. Up to 1,000 feet of Pliocene- Recent calcarenite, micrite and marl complete the sedimentary sequence.
Assessing land use/cover change in Costa Rica

ASSESSING LAND USE/COVER CHANGE IN COSTARICA By Gerardo-Arturo Sanchez-Azofeifa University of New Hampshire, September 1996 The need for accurate estimates of forest cover and forest fragmentation is a critical issue for developing countries such as Costa Rica. Accurate estimates of forest cover can help in several sectors related to the environment and economic development. This dissertation focuses on providing an accurate and precise estimate of forest cover in Costa Rica. The year 1991 was use as a baseline. Landsat Thematic Mapper was the remote sensing sensor used in this analysis. This dissertation concludes that: (1) Twenty-nine percent (-1,400,000 ha) of the country was under primary forest (80% canopy closure) in 1991. Of the total forest cover, 71% is outside national parks and 29% is protected by the national parks. (2) Forest loss (for scene path 15 / row 53) during five years period (1986-1991) was 224,970 ha, and it was estimated that the rate was -44,994 ha/yr. (3) Deforestation produced an increase in island fragments during the study period. Between 1986 and 1991, the total number of islands between three and 50 ha, and 50 and 100 ha increased by 524 and 45, respectively. Fifteen new islands with areas greater than 500 ha were created. (4) Results suggest that the extent of tropical deforestation go beyond estimations of total forest loss at the national level. The impacts at the national level have greater roots deeper roots when the
Personality moderates the links of social identity with work motivation and job searching

Work motivation is critical for successful school-to-work transitions, but little is known about its determinants among labor market entrants. Applying a social identity framework, we examined whether work motivation and job searching are social-contextually determined. We expected that some job seekers are more sensitive to contextual influence, depending on their personality. Mediation analyses on 591 Dutch vocational training students indicate that the perception of more positive work norms in someone's social context was related to higher levels of intrinsic motivation, which in turn predicted higher preparatory job search behavior and job search intentions. Multi-group analysis shows that perceived work norms more strongly predict work motivation among overcontrollers compared to resilients and undercontrollers. In conclusion, work motivation and job searching appear contextually determined: especially among those sensitive to contextual influence, people seem to work when they believe that is what people like them do.
Summary of the published Indian data on chronic myeloid leukemia

Abstract Chronic myelogenous leukemia (LML) was recognized as a distinct entity in the mid-1800s. Since Nowell and Hunagerford initiated their research on CML in1960 our understanding in CML has been increasing. Imatinib became the preferred treatment from 2000 onwards as a result of its unprecedented success. The lack of structured Indian data on CML led to the formation of a CML data cansortuim which invited CML data albiet retro spartive form around the country including major cancer service providers both government and private. We provide a summary of published Indian data on CML here.
Mining and reasoning on workflows

Today's workflow management systems represent a key technological infrastructure for advanced applications that is attracting a growing body of research, mainly focused in developing tools for workflow management, that allow users both to specify the "static" aspects, like preconditions, precedences among activities, and rules for exception handling, and to control its execution by scheduling the activities on the available resources. This paper deals with an aspect of workflows which has so far not received much attention even though it is crucial for the forthcoming scenarios of large scale applications on the Web: providing facilities for the human system administrator for identifying the choices performed more frequently in the past that had lead to a desired final configuration. In this context, we formalize the problem of discovering the most frequent patterns of executions, i.e., the workflow substructures that have been scheduled more frequently by the system. We attacked the problem by developing two data mining algorithms on the basis of an intuitive and original graph formalization of a workflow schema and its occurrences. The model is used both to prove some intractability results that strongly motivate the use of data mining techniques and to derive interesting structural properties for reducing the search space for frequent patterns. Indeed, the experiments we have carried out show that our algorithms outperform standard data mining algorithms adapted to discover frequent patterns of workflow executions.
Developmental Expression and Hypoxic Induction of Hypoxia Inducible Transcription Factors in the Zebrafish

The hypoxia inducible transcription factor (HIF) has been shown to coordinate the hypoxic response of vertebrates and is expressed in three different isoforms, HIF-1α, HIF-2α and HIF-3α. Knock down of either Hif-1α or Hif-2α in mice results in lethality in embryonic or perinatal stages, suggesting that this transcription factor is not only controlling the hypoxic response, but is also involved in developmental phenomena. In the translucent zebrafish embryo the performance of the cardiovascular system is not essential for early development, therefore this study was designed to analyze the expression of the three Hif-isoforms during zebrafish development and to test the hypoxic inducibility of these transcription factors. To complement the existing zfHif-1α antibody we expressed the whole zfHif-2α protein and used it for immunization and antibody generation. Similarly, fragments of the zfHif-3α protein were used for immunization and generation of a zfHif-3α specific antibody. To demonstrate presence of the Hif-isoforms during development [between 1 day post fertilization (1 dpf) and 9 dpf] affinity-purified antibodies were used. Hif-1α protein was present under normoxic conditions in all developmental stages, but no significant differences between the different developmental stages could be detected. Hif-2α was also present from 1 dpf onwards, but in post hatching stages (between 5 and 9 dpf) the expression level was significantly higher than prior to hatching. Similarly, Hif-3α was expressed from 1 dpf onwards, and the expression level significantly increased until 5 dpf, suggesting that Hif-2α and Hif-3α play a particular role in early development. Hypoxic exposure (oxygen partial pressure = 5 kPa) in turn caused a significant increase in the level of Hif-1α protein even at 1 dpf and in later stages, while neither Hif-2α nor Hif-3α protein level were affected. In these early developmental stages Hif-1α therefore appears to be more important for the coordination of hypoxic responsiveness.
An introduction to Causal Inference

In Causation, Prediction, and Search (CPS hereafter), Peter Spirtes, Clark Glymour and I developed a theory of statistical causal inference. In his presentation at the Notre Dame conference (and in his paper, this volume), Glymour discussed the assumptions on which this theory is built, traced some of the mathematical consequences of the assumptions, and pointed to situations in which the assumptions might fail. Nevertheless, many at Notre Dame found the theory difficult to understand and/or assess. As a result I was asked to write this paper to provide a more intuitive introduction to the theory. In what follows I shun almost all formality and avoid the numerous and complicated qualifiers that typically accompany definitions or important philosophical concepts. They can be all be found in Glymour's paper or in CPS, which are clear although sometimes dense. Here I attempt to fix intuitions by highlighting a few of the essential ideas and by providing extremely simple examples throughout. The route I take is a response to the core concern of many I talked to at the Notre Dame conference. Our techniques take statistical data and output sets of directed graphs. Most everyone saw how that worked-but they could not easily assess the additional assumptions necessary to give such output a causal interpretation, that is an interpretation that would inform us about how systems would respond to interventions. I will try to present in the simplest terms the assumptions that allow us to move from probabilistic independence relations to the kind of causal relations that involve counterfactuals about manipulations and interventions. I first separate out the various parts of the theory: directed graphs, probability, and causality, and then clarify the assumptions that connect causal structure to probability. Finally, I discuss the additional assumptions needed to make inferences from statistical data to causal structure.
B Cell Activation Is Regulated by the Stiffness Properties of the Substrate Presenting the Antigens

B lymphocytes are activated upon Ag sensing by BCRs. The substrate presenting the Ag can show different degrees of stiffness. It is not clear whether B cells can respond to changes in substrate stiffness. In this study we use high-resolution, high-speed live cell imaging techniques to capture the molecular events in B cell activation after the recognition of Ags tethered to polyacrylamide gel substrates with variable degrees of stiffness as quantified by Young’s modulus (2.6–22.1 kPa). We show that the initiation of B cell activation is extremely sensitive to substrate stiffness. B cells exhibit much stronger activation responses when encountering Ags tethered to substrates with a high degree of stiffness as measured by the accumulation of BCR, phospho-spleen tyrosine kinase, and phosphotyrosine molecules into the B cell immunological synapse. Ags tethered to stiff substrates induce the formation of more prominent BCR and phospho-spleen tyrosine kinase microclusters with significantly enhanced colocalization as compared with Ags tethered to soft substrates. Moreover, the expression of the B cell activation marker CD69 is enhanced in B cells encountering Ags on stiffer substrates. Through time-lapse live cell imaging, we find that the different responses of B cells to substrate stiffness are only demonstrated 5 min after BCR and Ag recognition. Using a series of cytoskeleton inhibitors, we determine that the mechanosensing ability of B cells is dependent on microtubules, and only mildly linked to the actin cytoskeleton. These results suggest the importance of the mechanical properties mediated by substrate stiffness in B cell activation.
Ethnic Identity and Substance Use Among Mexican-Heritage Preadolescents

This study examined interactive relationships among ethnic identity, gender, time in the US, and changes in substance use outcomes among a school-based sample of 1,731 Mexican-heritage preadolescents (ages 9-13). Residual change multilevel models adjusting for school clustering and using multiply imputed data assessed changes from beginning to end of fifth grade in use of alcohol, cigarettes, marijuana and inhalants, and four substance use antecedents. Effects of ethnic identity were conditional on time in the US, and in opposite directions by gender. Among males living longer in the US, stronger ethnic identity predicted desirable changes in all but one outcome (substance offers). Among females living longer in the US, stronger ethnic identity predicted undesirable changes in alcohol use, pro-drug norms, and peer substance use. Interpretations focus on differential exposure to substance use opportunities and the erosion of traditional gender role socialization among Mexican-heritage youth having lived longer in the US.
Bias vs structure of polynomials in large fields, and applications in effective algebraic geometry and coding theory

Let $f$ be a polynomial of degree $d$ in $n$ variables over a finite field $\mathbb{F}$. The polynomial is said to be unbiased if the distribution of $f(x)$ for a uniform input $x \in \mathbb{F}^n$ is close to the uniform distribution over $\mathbb{F}$, and is called biased otherwise. The polynomial is said to have low rank if it can be expressed as a composition of a few lower degree polynomials. Green and Tao [Contrib. Discrete Math 2009] and Kaufman and Lovett [FOCS 2008] showed that bias implies low rank for fixed degree polynomials over fixed prime fields. This lies at the heart of many tools in higher order Fourier analysis. In this work, we extend this result to all prime fields (of size possibly growing with $n$). We also provide a generalization to nonprime fields in the large characteristic case. However, we state all our applications in the prime field setting for the sake of simplicity of presentation. As an immediate application, we obtain improved bounds for a suite of problems in effective algebraic geometry, including Hilbert nullstellensatz, radical membership and counting rational points in low degree varieties. Using the above generalization to large fields as a starting point, we are also able to settle the list decoding radius of fixed degree Reed-Muller codes over growing fields. The case of fixed size fields was solved by Bhowmick and Lovett [STOC 2015], which resolved a conjecture of Gopalan-Klivans-Zuckerman [STOC 2008]. Here, we show that the list decoding radius is equal the minimum distance of the code for all fixed degrees, even when the field size is possibly growing with $n$.
Encapsulating peritoneal sclerosis and other aspects of long-term peritoneal dialysis

Bij peritoneale dialyse (PD) wordt het peritoneum (buikvlies) gebruikt als dialyse-membraan. Langdurige PD kan leiden tot afwijkingen in het buikvlies. Anniek Vlijm deed onderzoek naar encapsulerende peritoneale sclerose (EPS), de ernstigste complicatie van PD. Bij deze aandoening zijn de darmen ingekapseld in verhard weefsel. Dit verhoogt het sterfterisico aanzienlijk. Met behulp van een CT-scan kan de diagnose betrouwbaar worden gesteld.