Miracle-dz/UniFAR-FTUs huggingface dataset:
Kraft fibre and pulp qualities of 29 trees of New Zealand grown Eucalyptus nitens

There is a need to determine the between tree variation in the wood properties and kraft fibre and pulp qualities of softwoods and hardwoods that grow well in New Zealand. This information will be used in the planning and management of end-product directed plantation forests and tree-breeding programs. Variation among 29 individual trees of E. nitens is extremely high; for the individual tree chip samples the basic density range is 390-556kg/m 3 , total lignin content 25.1-29.7%, and kraft pulp yield 54-59%. Between tree variation in some important kraft pulp properties are: fibre length (0.780.95mm), fibre perimeter (19.0-21.6mm), wall area (coarseness) (53-70mm 2 ), and handsheet bulk at 500 PFI mill rev (1.59-1.37cm 3 /g). The fibre width:thickness ratio and length combination (r 2 = 0.67), and the chip density and length combination (r 2 = 0.64) are the best predictors of handsheet bulk. Fibres are curled and consequently 'shortened' by pulp bleaching.
Existence and Uniqueness of Solutions to a Nonlocal Equation with Monostable Nonlinearity

Let $J \in C(\mathbb{R})$, $J\ge 0$, $\int_{\mbox{\tinyR}} J = 1$ and consider the nonlocal diffusion operator $\mathcal{M}[u] = J \star u - u$. We study the equation $\mathcal{M} u + f(x,u) = 0$, $u \ge 0$, in $\mathbb{R}$, where f is a KPP-type nonlinearity, periodic in x. We show that the principal eigenvalue of the linearization around zero is well defined and that a nontrivial solution of the nonlinear problem exists if and only if this eigenvalue is negative. We prove that if, additionally, J is symmetric, then the nontrivial solution is unique.
Reciprocal connections between the medial preoptic area and the midbrain periaqueductal gray in rat: A WGA‐HRP and PHA‐L study

The midbrain periaqueductal gray (PAG) participates in diverse functions such as analgesia, autonomic regulation, sexual behavior, and defense/escape responses. Anatomical studies of the circuits involved in such functions have largely focused on the connections of PAG with the medulla. Projections to PAG from forebrain structures are extensive, but their organization has received little attention. Previous anatomic studies indicate that the medial preoptic area (MPO), involved in a variety of physiological and behavioral functions, is a major source of afferent input to the periaqueductal gray. Here, we have examined the topography of reciprocal connections between these two structures in the rat by using wheat germ agglutinin conjugated horseradish peroxidase (WGA‐HRP) and Phaseolus vulgaris leucoagglutinin (PHA‐L).
Two Dynamin-2 Genes Are Required for Normal Zebrafish Development

Dynamin-2 (DNM2) is a large GTPase involved in clathrin-mediated endocytosis and related trafficking pathways. Mutations in human DNM2 cause two distinct neuromuscular disorders: centronuclear myopathy and Charcot-Marie-Tooth disease. Zebrafish have been shown to be an excellent animal model for many neurologic disorders, and this system has the potential to inform our understanding of DNM2-related disease. Currently, little is known about the endogenous zebrafish orthologs to human DNM2. In this study, we characterize two zebrafish dynamin-2 genes, dnm2 and dnm2-like. Both orthologs are structurally similar to human DNM2 at the gene and protein levels. They are expressed throughout early development and in all adult tissues examined. Knockdown of dnm2 and dnm2-like gene products resulted in extensive morphological abnormalities during development, and expression of human DNM2 RNA rescued these phenotypes. Our findings suggest that dnm2 and dnm2-like are orthologs to human DNM2, and that they are required for normal zebrafish development.
Effect of background electrolyte on the estimation of protein hydrodynamic radius and net charge through capillary zone electrophoresis

Two physicochemical models are proposed for the estimation of both hydrodynamic radius and net charge of a protein when the capillary zone electrophoretic mobility at a given protocol, the set of pK of charged amino acids, and basic data from Protein Data Bank are available. These models also provide a rationale to interpret appropriately the effects of solvent properties on protein hydrodynamic radius and net charge. To illustrate the numerical predictions of these models, experimental data of electrophoretic mobility available in the literature for well‐defined protocols are used. Five proteins are considered: lysozyme, staphylococcal nuclease, human carbonic anhydrase, bovine carbonic anhydrase, and human serum albumin. Numerical predictions of protein net charges through these models compare well with the results reported in the literature, including those found asymptotically through protein charge ladder techniques. Model calculations indicate that the hydrodynamic radius is sensitive to changes of the protein net charge and hence it cannot be assumed constant in general. Also, several limitations associated with models for estimating protein net charge and hydrodynamic radius from protein structure, amino acid sequence, and experimental electrophoretic mobility are provided and discussed. These conclusions also show clear requirements for further research.
An Analogical Learner for Morphological Analysis

Analogical learning is based on a two-step inference process: (i) computation of a structural mapping between a new and a memorized situation; (ii) transfer of knowledge from the known to the unknown situation. This approach requires the ability to search for and exploit such mappings, hence the need to properly define analogical relationships, and to efficiently implement their computation. In this paper, we propose a unified definition for the notion of (formal) analogical proportion, which applies to a wide range of algebraic structures. We show that this definition is suitable for learning in domains involving large databases of structured data, as is especially the case in Natural Language Processing (NLP). We then present experimental results obtained on two morphological analysis tasks which demonstrate the flexibility and accuracy of this approach.
Roles of Major Histocompatibility Complex Class II in Inducing Protective Immune Responses to Influenza Vaccination

ABSTRACT Major histocompatibility complex class II-deficient (MHC-II KO; Aβ−/−) mice were used to assess the roles of MHC-II molecules in inducing protective immune responses to vaccination. After vaccination with influenza A/PR8 virus-like particle (VLP) vaccine, in vivo and in vitro vaccine antigen-specific IgG isotype antibodies were not detected in MHC-II KO mice, which is quite different from CD4 T cell-deficient mice that induced vaccine-specific IgG antibodies. The deficiency in MHC-II did not significantly affect the induction of antigen-specific IgM antibody in sera. MHC-II KO mice that were vaccinated with influenza VLP, whole inactivated influenza virus, or live attenuated influenza virus vaccines were not protected against lethal infection with influenza A/PR8 virus. Adoptive transfer of fractionated spleen cells from wild-type mice to MHC-II KO mice indicated that CD43+ cell populations with MHC-II contributed more significantly to producing vaccine-specific IgG antibodies than CD43− B220+ conventional B cell or CD4 T cell populations, as well as conferring protection against lethal infection. Bone marrow-derived dendritic cells from MHC-II KO mice showed a significant defect in producing interleukin-6 and tumor necrosis factor alpha cytokines. Thus, results indicate that MHC-II molecules play multiple roles in inducing protective immunity to influenza vaccination. IMPORTANCE Major histocompatibility complex class II (MHC-II) has been known to activate CD4 T helper immune cells. A deficiency in MHC-II was considered to be equivalent to the lack of CD4 T cells in developing host immune responses to pathogens. However, the roles of MHC-II in inducing protective immune responses to vaccination have not been well understood. In the present study, we demonstrate that MHC-II-deficient mice showed much more significant defects in inducing protective antibody responses to influenza vaccination than CD4 T cell-deficient mice. Further analysis showed that CD43 marker-positive immune cells with MHC-II, as well as an innate immunity-simulating adjuvant, could rescue some defects in inducing protective immune responses in MHC-II-deficient mice. These results have important implications for our understanding of host immunity-inducing mechanisms to vaccination, as well as in developing effective vaccines and adjuvants.
Perceptual Learning in Children With Infantile Nystagmus: Effects on Visual Performance.

PURPOSE To evaluate whether computerized training with a crowded or uncrowded letter-discrimination task reduces visual impairment (VI) in 6- to 11-year-old children with infantile nystagmus (IN) who suffer from increased foveal crowding, reduced visual acuity, and reduced stereopsis. METHODS Thirty-six children with IN were included. Eighteen had idiopathic IN and 18 had oculocutaneous albinism. These children were divided in two training groups matched on age and diagnosis: a crowded training group (n = 18) and an uncrowded training group (n = 18). Training occurred two times per week during 5 weeks (3500 trials per training). Eleven age-matched children with normal vision were included to assess baseline differences in task performance and test-retest learning. Main outcome measures were task-specific performance, distance and near visual acuity (DVA and NVA), intensity and extent of (foveal) crowding at 5 m and 40 cm, and stereopsis. RESULTS Training resulted in task-specific improvements. Both training groups also showed uncrowded and crowded DVA improvements (0.10 ± 0.02 and 0.11 ± 0.02 logMAR) and improved stereopsis (670 ± 249″). Crowded NVA improved only in the crowded training group (0.15 ± 0.02 logMAR), which was also the only group showing a reduction in near crowding intensity (0.08 ± 0.03 logMAR). Effects were not due to test-retest learning. CONCLUSIONS Perceptual learning with or without distractors reduces the extent of crowding and improves visual acuity in children with IN. Training with distractors improves near vision more than training with single optotypes. Perceptual learning also transfers to DVA and NVA under uncrowded and crowded conditions and even stereopsis. Learning curves indicated that improvements may be larger after longer training.
Can Automatic Speech Transcripts Be Used for Large Scale TV Stream Description and Structuring?

The increasing quantity of TV material requires methods to help users navigate such data streams. Automatically associating a short textual description to each program in a stream, is a first stage to navigating or structuring tasks. Speech contained in TV broadcasts---accessible by means of automatic speech recognition systems in the absence of closed caption---is a highly valuable semantic clue that might be used to link existing textual description such as program guides, with video segments corresponding to program. However, high word error rates are to be expected on some programs, likely to jeopardize the usefulness of transcripts. The goal of this article is to determine to what extent automatic transcripts of TV streams, for various types of programs, can be used for structuring or navigating tasks. To this end, word-based and phonetic-based automatic association between video segments and program descriptions is used as a case study. We show that descriptions from a program guide can be associated with video segments with an accuracy of up to 65% and provide a valuable description to validate existing program labels. Such associations constitute a first stage for structuring task as they enable video segment textual characterization.
Histopathology of Chronic Rejection in a Nonhuman Primate Model of Vascularized Composite Allotransplantation

Background Chronic rejection of vascularized composite allografts (VCA) is an emerging phenomenon that may decrease long-term allograft survival and impair allograft function. Although intimal hyperplasia has been reported in human hand transplants, chronic changes in VCAs remain poorly described. Methods We developed a nonhuman primate model of face transplantation to evaluate the effect of various immunosuppressive regimens on allograft survival that we have previously reported. Nineteen grafts were successfully transplanted and serially biopsied to assess for rejection. Five VCA grafts with long-term survival (>200 days) were weaned off immunosuppression. We performed additional histologic and immunohistochemical studies on previously collected samples. Results All five grafts developed features consistent with chronic rejection, including neointimal proliferation, transplant vasculopathy, vessel wall fibrosis, progressive luminal occlusion, and tertiary lymphoid follicles. Review of 186 serial allograft skin and subcutaneous tissue biopsies revealed that tertiary follicles and vascular changes developed in the absence of acute skin rejection. No relationship was found between alloantibody production and these changes. Conclusions Recognition of these characteristics of VCA chronic rejection is important for diagnosis in clinical hand and face transplantation. Studies directed towards minimizing VCA chronic rejection responses may be required to improve long-term outcomes.
RNase P-Mediated Sequence-Specific Cleavage of RNA by Engineered External Guide Sequences

The RNA cleavage activity of RNase P can be employed to decrease the levels of specific RNAs and to study their function or even to eradicate pathogens. Two different technologies have been developed to use RNase P as a tool for RNA knockdown. In one of these, an external guide sequence, which mimics a tRNA precursor, a well-known natural RNase P substrate, is used to target an RNA molecule for cleavage by endogenous RNase P. Alternatively, a guide sequence can be attached to M1 RNA, the (catalytic) RNase P RNA subunit of Escherichia coli. The guide sequence is specific for an RNA target, which is subsequently cleaved by the bacterial M1 RNA moiety. These approaches are applicable in both bacteria and eukaryotes. In this review, we will discuss the two technologies in which RNase P is used to reduce RNA expression levels.
Towards spoken clinical-question answering: evaluating and adapting automatic speech-recognition systems for spoken clinical questions

OBJECTIVE To evaluate existing automatic speech-recognition (ASR) systems to measure their performance in interpreting spoken clinical questions and to adapt one ASR system to improve its performance on this task. DESIGN AND MEASUREMENTS The authors evaluated two well-known ASR systems on spoken clinical questions: Nuance Dragon (both generic and medical versions: Nuance Gen and Nuance Med) and the SRI Decipher (the generic version SRI Gen). The authors also explored language model adaptation using more than 4000 clinical questions to improve the SRI system's performance, and profile training to improve the performance of the Nuance Med system. The authors reported the results with the NIST standard word error rate (WER) and further analyzed error patterns at the semantic level. RESULTS Nuance Gen and Med systems resulted in a WER of 68.1% and 67.4% respectively. The SRI Gen system performed better, attaining a WER of 41.5%. After domain adaptation with a language model, the performance of the SRI system improved 36% to a final WER of 26.7%. CONCLUSION Without modification, two well-known ASR systems do not perform well in interpreting spoken clinical questions. With a simple domain adaptation, one of the ASR systems improved significantly on the clinical question task, indicating the importance of developing domain/genre-specific ASR systems.
Flavopiridol-related proinflammatory syndrome is associated with induction of interleukin-6.

BACKGROUND Flavopiridol is a flavonoid with antiproliferative effects mediated, in part, by inhibition of cyclin-dependent kinases. Clinical manifestations in a previous Phase I trial in patients with refractory malignancies treated with a 72-h flavopiridol infusion included a proinflammatory syndrome consisting of fever, fatigue, and "local" tumor pain with concomitant alterations in plasma acute-phase reactant proteins. PURPOSE The aim of this study was to determine whether the proinflammatory syndrome observed in this trial was associated with modulation of plasma cytokines. METHODS Patients receiving flavopiridol (n = 76) had serial plasma samples drawn preinfusion and during the infusion for evaluation of interleukin (IL)-6, IL-10, IL-12, granulocyte macrophage colony-stimulating factor, basic-fibroblast growth factor, transforming growth factor-beta, and tumor necrosis factor-alpha levels by standard ELISA assays. The Wilcoxon signed rank test was used to test the significance of the difference between the baseline (time 0) plasma cytokine levels compared with the values of each subsequent data collection time points (8, 24, 48, and 72 h). RESULTS There was a significant and sustained increase in plasma IL-6 levels at all time points when compared with baseline values. Paired values were used in the statistical analysis. Median plasma (interquartile range) values of IL-6 were elevated from 15.5 (9-52) pg/ml at baseline to 23 (4-48) pg/ml (P < 0.01) at 8 h; from 15 (2-48) pg/ml at baseline to 46 (21-105) pg/ml (P < 0.001) at 24 h; from 16 (9-52) pg/ml at baseline to 61 (32-170) pg/ml (P < 0.001) at 48 h; and from 15.5 (6-48) pg/ml to 68 (40-200) pg/ml (P < 0.001) at 72 h. Significance was maintained even when adjusted for multiple comparisons. The relative increase in IL-6 concentration was dose-dependent. Moreover, IL-6 elevation had a direct correlation with flavopiridol peak plasma concentration, flavopiridol area under the curve, and plasma C-Reactive protein levels. A significant decrease in plasma granulocyte macrophage colony-stimulating factor occurred at the 8-h sampling point: 50 pg/ml (interquartile range 10-205 pg/ml, P < 0.01) when compared with baseline plasma levels and 71 pg/ml (interquartile range 5-152 pg/ml, P < 0.01). No changes in the other pro or anti-inflammatory cytokines were observed. Immunohistochemistry studies in bone marrow aspirates from a prospective group of patients in this trial demonstrated approximately 4-fold induction of IL-6 (compared with baseline), mostly in non-T cells. CONCLUSION Biochemical analysis of plasma in patients undergoing infusional flavopiridol found a significant dose-dependent induction of IL-6. IL-6 elevation could be a marker for the process leading to the appearance of the proinflammatory syndrome observed in patients treated with infusional flavopiridol. The mechanism(s) underlying IL-6 induction and its significance are still unknown but may influence strategies to modulate flavopiridol's clinical effects.
The Importance of Drains for the Larval Development of Lymphatic Filariasis and Malaria Vectors in Dar es Salaam, United Republic of Tanzania

Background Dar es Salaam has an extensive drain network, mostly with inadequate water flow, blocked by waste, causing flooding after rainfall. The presence of Anopheles and Culex larvae is common, which is likely to impact the transmission of lymphatic filariasis and malaria by the resulting adult mosquito populations. However, the importance of drains as larval habitats remains unknown. Methodology Data on mosquito larval habitats routinely collected by the Urban Malaria Control Program (UMCP) and a special drain survey conducted in 2006 were used to obtain a typology of habitats. Focusing on drains, logistic regression was used to evaluate potential factors impacting the presence of mosquito larvae. Spatial variation in the proportion of habitats that contained larvae was assessed through the local Moran's I indicator of spatial association. Principal Findings More than 70% of larval habitats in Dar es Salaam were human-made. Aquatic habitats associated with agriculture had the highest proportion of Anopheles larvae presence and the second highest of Culex larvae presence. However, the majority of aquatic habitats were drains (42%), and therefore, 43% (1,364/3,149) of all culicine and 33% (320/976) of all anopheline positive habitats were drains. Compared with drains where water was flowing at normal velocity, the odds of finding Anopheles and Culex larvae were 8.8 and 6.3 (p<0.001) times larger, respectively, in drains with stagnant water. There was a positive association between vegetation and the presence of mosquito larvae (p<0.001). The proportion of habitats with mosquito larvae was spatially correlated. Conclusion Restoring and maintaining drains in Dar es Salaam has the potential to eliminate more than 40% of all potential mosquito larval habitats that are currently treated with larvicides by the UMCP. The importance of human-made larval habitats for both lymphatic filariasis and malaria vectors underscores the need for a synergy between on-going control efforts of those diseases.
Health consequences of reduced daily cigarette consumption

Objective: To determine the risk of dying from specified smoking-related diseases and from any cause in heavy smoking men and women (⩾15 cigarettes/day), who reduced their daily cigarette consumption by >50%. Design: A prospective cohort study. Setting: Three counties in Norway. Participants: 24 959 men and 26 251 women, aged 20–49 years, screened for risk factors of cardiovascular disease in the mid-1970s, screened again after 3–13 years, and followed up throughout 2003. Outcomes: Absolute mortality and relative risks adjusted for confounding variables, of dying from all causes, cardiovascular disease, ischaemic heart disease, all smoking-related cancer and lung cancer. Results: With sustained heavy smokers as reference, the smokers of both sexes who reduced their daily consumption (reducers) had the following adjusted relative risks (95% confidence interval (CI)): of dying from any cause, 1.02 (0.84 to 1.22); cardiovascular disease, 1.02 (0.75 to 1.39); ischaemic heart disease, 0.96 (0.65 to 1.41); smoking-related cancer, 0.86 (0.57 to 1.29); and lung cancer, 0.66 (0.36 to 1.21). The difference in cigarette consumption between two examinations was not a significant predictor of death from any of the causes. A follow-up from a third screening of the subgroup who were reducers at both second and third examinations (sustained reducers) did not have a lower risk than those who were heavy smokers at all three examinations. Conclusions: Long-term follow-up provides no evidence that heavy smokers who cut down their daily cigarette consumption by >50% reduce their risk of premature death significantly. In health education and patient counselling, it may give people false expectations to advise that reduction in consumption is associated with reduction in harm.
Using Semantic Roles to Improve Question Answering

Shallow semantic parsing, the automatic identification and labeling of sentential constituents, has recently received much attention. Our work examines whether semantic role information is beneficial to question answering. We introduce a general framework for answer extraction which exploits semantic role annotations in the FrameNet paradigm. We view semantic role assignment as an optimization problem in a bipartite graph and answer extraction as an instance of graph matching. Experimental results on the TREC datasets demonstrate improvements over state-of-the-art models.