Miracle-dz/UniFAR-FTUs huggingface dataset:
An MND/ALS phenotype associated with C9orf72 repeat expansion: Abundant p62‐positive, TDP‐43‐negative inclusions in cerebral cortex, hippocampus and cerebellum but without associated cognitive decline

The transactive response DNA binding protein (TDP‐43) proteinopathies describe a clinico‐pathological spectrum of multi‐system neurodegeneration that spans motor neuron disease/amyotrophic lateral sclerosis (MND/ALS) and frontotemporal lobar degeneration (FTLD). We have identified four male patients who presented with the clinical features of a pure MND/ALS phenotype (without dementia) but who had distinctive cortical and cerebellar pathology that was different from other TDP‐43 proteinopathies. All patients initially presented with weakness of limbs and respiratory muscles and had a family history of MND/ALS. None had clinically identified cognitive decline or dementia during life and they died between 11 and 32 months after symptom onset. Neuropathological investigation revealed lower motor neuron involvement with TDP‐43‐positive inclusions typical of MND/ALS. In contrast, the cerebral pathology was atypical, with abundant star‐shaped p62‐immunoreactive neuronal cytoplasmic inclusions in the cerebral cortex, basal ganglia and hippocampus, while TDP‐43‐positive inclusions were sparse. This pattern was also seen in the cerebellum where p62‐positive, TDP‐43‐negative inclusions were frequent in granular cells. Western blots of cortical lysates, in contrast to those of sporadic MND/ALS and FTLD‐TDP, showed high p62 levels and low TDP‐43 levels with no high molecular weight smearing. MND/ALS‐associated SOD1, FUS and TARDBP gene mutations were excluded; however, further investigations revealed that all four of the cases did show a repeat expansion of C9orf72, the recently reported cause of chromosome 9‐linked MND/ALS and FTLD. We conclude that these chromosome 9‐linked MND/ALS cases represent a pathological sub‐group with abundant p62 pathology in the cerebral cortex, hippocampus and cerebellum but with no significant associated cognitive decline.
Functional LCAT deficiency in human apolipoprotein A-I transgenic, SR-BI knockout mice Published, JLR Papers in Press, February 1, 2007.

Reduction of plasma LCAT activity has been observed in several conditions in which the size of HDL particles is increased; however, the mechanism of this reduction remains elusive. We investigated the plasma activity, mass, and in vivo catabolism of LCAT and its association with HDL particles in human apolipoprotein A-I transgenic, scavenger receptor class B type I knockout (hA-I Tg SR-BI−/−) mice. Compared with hA-I Tg mice, hA-I Tg SR-BI−/− mice had a 4-fold higher total plasma cholesterol concentration, which occurred predominantly in 13–18 nm diameter HDL particles, a significant reduction in plasma esterified cholesterol-total cholesterol (EC/TC) ratio, and significantly lower plasma LCAT activity, suggesting a decrease in LCAT protein. However, LCAT protein in plasma, hepatic mRNA for LCAT, and in vivo turnover of 35S-radiolabeled LCAT were similar in both genotypes of mice. HDL from hA-I Tg SR-BI−/− mice was enriched in sphingomyelin (SM), relative to phosphatidylcholine, and had less associated [35S]LCAT radiolabel and endogenous LCAT activity compared with HDL from hA-I Tg mice. We conclude that the decreased EC/TC ratio in the plasma of hA-I Tg SR-BI−/− mice is attributed to a reduction in LCAT reactivity with SM-enriched HDL particles.
Pesticide Residues, Heavy Metals, and DNA Damage in Sentinel Oysters Crassostrea gigas From Sinaloa and Sonora, Mexico

Pesticides and heavy metals were analyzed in sentinel Crassostrea gigas oysters placed in six aquaculture sites close to a contaminated agricultural region. Each site was sampled twice. Tests revealed the presence of organochlorine (OC) pesticides in the oysters at concentrations varying from 31.8 to 72.5 μg/kg for gamma-hexachlorocyclohexane (γ-HCH); from 1.2 to 3.1 μg/kg for dichlorodiphenyldichloroethylene (4,4-DDE); from 1.6 to 2.3 μg/kg for endosulfan I; and from 1.4 to 41.2 μg/kg for endosulfan II, as well as heavy metals in concentrations that exceeded Mexican tolerance levels (405.5 to 987.8 μg/g for zinc; 4.2 to 7.3 μg/g for cadmium; and 7.2 to 9.9 μg/g for lead). Significant levels of DNA damage in oyster hemocytes were also detected. There was a significant, positive correlation between genotoxic damage and concentration of nickel or the presence of endosulfan II. Cellular viability evaluated by cytotoxic analyses was found to be high at 80%. Marked inhibition in activity of acetylcholinesterase (AChE ) and induction of glutathione S-transferase (GST) activity was noted. Data demonstrated a significant relation between AChE activity inhibition and presence of endosulfan II, γ-HCH, copper, lead, and 4,4-DDE, as well as between AChE and GST activity at different sites.
Horseradish peroxidase‐catalysed in situ‐forming hydrogels for tissue‐engineering applications

In situ‐forming hydrogels are an attractive class of implantable biomaterials that are used for biomedical applications. These injectable hydrogels are versatile and provide a convenient platform for delivering cells and drugs via minimally invasive surgery. Although several crosslinking methods for preparing in situ forming hydrogels have been developed over the past two decades, most hydrogels are not sufficiently versatile for use in a wide variety of tissue‐engineering applications. In recent years, enzyme‐catalysed crosslinking approaches have been emerged as a new approach for developing in situ‐forming hydrogels. In particular, the horseradish peroxidase (HRP)‐catalysed crosslinking approach has received increasing interest, due to its highly improved and tunable capacity to obtain hydrogels with desirable properties. The HRP‐catalysed crosslinking reaction immediately occurs upon mixing phenol‐rich polymers with HRP and hydrogen peroxide (H2O2) in aqueous media. Based on this unique gel‐forming feature, recent studies have shown that various properties of formed hydrogels, such as gelation time, stiffness and degradation rate, can be easily manipulated by varying the concentrations of HRP and H2O2. In this review, we outline the versatile properties of HRP‐catalysed in situ‐forming hydrogels, with a brief introduction to the crosslinking mechanisms involved. In addition, the recent biomedical applications of HRP‐catalysed in situ‐forming hydrogels for tissue regeneration are described. Copyright © 2014 John Wiley & Sons, Ltd.
Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae).

BACKGROUND AND AIMS The Arecoideae is the largest and most diverse of the five subfamilies of palms (Arecaceae/Palmae), containing >50 % of the species in the family. Despite its importance, phylogenetic relationships among Arecoideae are poorly understood. Here the most densely sampled phylogenetic analysis of Arecoideae available to date is presented. The results are used to test the current classification of the subfamily and to identify priority areas for future research. METHODS DNA sequence data for the low-copy nuclear genes PRK and RPB2 were collected from 190 palm species, covering 103 (96 %) genera of Arecoideae. The data were analysed using the parsimony ratchet, maximum likelihood, and both likelihood and parsimony bootstrapping. KEY RESULTS AND CONCLUSIONS Despite the recovery of paralogues and pseudogenes in a small number of taxa, PRK and RPB2 were both highly informative, producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Simultaneous analyses of the combined data sets provided additional resolution and support. Two areas of incongruence between PRK and RPB2 were strongly supported by the bootstrap relating to the placement of tribes Chamaedoreeae, Iriarteeae and Reinhardtieae; the causes of this incongruence remain uncertain. The current classification within Arecoideae was strongly supported by the present data. Of the 14 tribes and 14 sub-tribes in the classification, only five sub-tribes from tribe Areceae (Basseliniinae, Linospadicinae, Oncospermatinae, Rhopalostylidinae and Verschaffeltiinae) failed to receive support. Three major higher level clades were strongly supported: (1) the RRC clade (Roystoneeae, Reinhardtieae and Cocoseae), (2) the POS clade (Podococceae, Oranieae and Sclerospermeae) and (3) the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae and Pelagodoxeae). However, new data sources are required to elucidate ambiguities that remain in phylogenetic relationships among and within the major groups of Arecoideae, as well as within the Areceae, the largest tribe in the palm family.
Depression Treatment With Selective Serotonin Reuptake Inhibitors for the Postacute Coronary Syndrome Population: A Literature Review

Objective: After acute coronary syndrome (ACS), patients have a significantly higher incidence of depression compared to the average healthy adult. Depression is independently associated with poorer outcomes and heightens the morbidity and mortality risk in this susceptible population. Selective serotonin reuptake inhibitors (SSRIs) are a newer class of antidepressants recently investigated for use in this population. This article reviews the current research on the safety, efficacy, possible benefits, and limitations of this class of antidepressants for patients with post-ACS. Data Sources: Information was obtained through a literature search of the electronic databases CINAHL, EMBASE, Ovid Medline (R), and PubMed Plus during the months of January and February of 2007. Keywords searched included acute coronary syndrome, myocardial infarction, selective serotonin reuptake inhibitors, sertraline, paroxetine, fluoxetine, depressive disorder, major depression, and depression. Results were then limited to the English language, adult population, publication years 2002-2007, and primary research articles. The search was broadened to include years 2000-2002. Study Selection: Abstracts were reviewed for applicability. All studies meeting the criteria for research articles of SSRI use in depressed patients with post-ACS were included. This amounted to 6 articles. Data Extraction: Independent extraction was conducted by a single observer. Conclusions: Recent research shows positive outcomes associated with the use of SSRIs for depressed patients with post-ACS. The greatest benefit from these medications appears to be in the recurrently and severely depressed subpopulations. Although the use of SSRIs in patients with post-ACS appears to be associated with a decrease in morbidity and mortality rates, large, randomized control trials are still needed to support this finding.
The diffusion of policy innovations -an experimental investigation

Abstract.What causes a government to adopt a new program or policy? Despite a large number of empirical studies available to date, the relative importance of various determinants remains obscure because of difficulties of statistical identification. We present an experimental setting to study the diffusion of policy innovations in the laboratory. Our approach discriminates between experimentation, experience, and emulation as determinants of policy adoption. The policy innovation we study is an internalization tax to mitigate a local market externality. Our results demonstrate the importance of information about innovations in other states in the diffusion of policy innovations.
RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

Reduced representation genome‐sequencing approaches based on restriction digestion are enabling large‐scale marker generation and facilitating genomic studies in a wide range of model and nonmodel systems. However, sampling chromosomes based on restriction digestion may introduce a bias in allele frequency estimation due to polymorphisms in restriction sites. To explore the effects of this nonrandom sampling and its sensitivity to different evolutionary parameters, we developed a coalescent‐simulation framework to mimic the biased recovery of chromosomes in restriction‐based short‐read sequencing experiments (RADseq). We analysed simulated DNA sequence datasets and compared known values from simulations with those that would be estimated using a RADseq approach from the same samples. We compare these ‘true’ and ‘estimated’ values of commonly used summary statistics, π, θw, Tajima's D and FST. We show that loci with missing haplotypes have estimated summary statistic values that can deviate dramatically from true values and are also enriched for particular genealogical histories. These biases are sensitive to nonequilibrium demography, such as bottlenecks and population expansion. In silico digests with 102 completely sequenced Drosophila melanogaster genomes yielded results similar to our findings from coalescent simulations. Though the potential of RADseq for marker discovery and trait mapping in nonmodel systems remains undisputed, our results urge caution when applying this technique to make population genetic inferences.
A Composite Kernel to Extract Relations between Entities with Both Flat and Structured Features

This paper proposes a novel composite kernel for relation extraction. The composite kernel consists of two individual kernels: an entity kernel that allows for entity-related features and a convolution parse tree kernel that models syntactic information of relation examples. The motivation of our method is to fully utilize the nice properties of kernel methods to explore diverse knowledge for relation extraction. Our study illustrates that the composite kernel can effectively capture both flat and structured features without the need for extensive feature engineering, and can also easily scale to include more features. Evaluation on the ACE corpus shows that our method outperforms the previous best-reported methods and significantly out-performs previous two dependency tree kernels for relation extraction.
Prehospital deaths in the Yorkshire Health Region.

OBJECTIVES: To estimate the proportion of prehospital deaths in a British population of trauma victims which may be preventable, and to investigate the effect of death at the scene and death in transit on potential survivorship. METHODS: Blinded review, by four specialists with an interest in trauma, of necropsy results and details of age, sex, and mechanism of injury for prehospital trauma deaths in the Yorkshire Health Region in a 12 month period. RESULTS: Complete records were traced on 305 of 337 trauma deaths, 190 being recorded as dead on arrival of emergency services and 115 dead on arrival at hospital. In the group declared dead at the scene, three of the four assessors considered 93% of deaths to have been inevitable and only 2% as potential survivors (25% of this group sustaining inevitably fatal injuries such as brain avulsion or decapitation). In the group dead on arrival 81% were felt to be inevitable deaths and 5% potential survivors. CONCLUSIONS: There seems to be less scope for salvage of victims of trauma death in a British population than has been recorded in America, possibly due to a higher proportion of blunt trauma deaths here. Those who die in transit consist of a less severely injured group with a higher potential for survival.
Professional practice among woman dentist

Objective: This review aims to give an inside view of professional career of a women dentist, addresses the unique demands of being a woman dentist, and highlight ways to address these issues. Materials and Methods: The Medline database, scholarly literature, and informal literature were considered for this review. Results: Working hours of female dentists do not differ significantly from the working hours of their male counterparts, until they have children. The female dentists’ working hours showed a distinct drop as soon as they started a family. It was also found that women dentists are more likely to take career break. It is clear that childrearing and family responsibilities have a great impact on women's working life. Significant differences between males and females in work title and specialization were evident in an academic institution. Due to the societal orientation which regards women as primarily home makers, the responsibilities for family caretaking continues to fall disproportionately on women, and this fact could explain why women abandon their careers in the advanced stages. Conclusions: Efforts should be made to identify and reduce barriers to women's advancement in dentistry.
Rate- and Accuracy-Disabled Subtype Profiles Among Adults With Dyslexia in the Hebrew Orthography

This study examined a subtyping scheme rooted in the dissociation between reading rate and accuracy in an exceptionally large sample of adult readers with dyslexia using a wide variety of behavioral and event-related potential (ERP) measures. Stage 1 was a behavioral study, in which basic reading skill, reading comprehension, linguistic and cognitive tasks were administered to 661 learning-disabled university students (n = 382) and their non-learning-disabled peers (n = 279). Based on a word reading measure, accuracy-disabled and rate-disabled subgroups were identified, as was a subgroup with deficits in both rate and accuracy. The results support the persistence of a rate versus accuracy dissociation into adulthood. Accuracy disability was related to a broad range of deficits affecting phonological, orthographic, and morphological processing, verbal memory, attention, and reading comprehension. Rate disability appeared to be associated with slower processing of printed material, alongside largely intact functioning resembling those of skilled readers. In stage 2, electroencephalogram (EEG)–ERP measurements were obtained from 140 participants recruited from the larger sample. Activation in visual association cortex, indicated by the N170 amplitude, was found to be lower for accuracy-disabled than skilled readers, and comparable between rate-disabled and skilled readers. The lowest amplitude was found in the double-deficit subgroup. The findings support the existence of distinctive reading disability profiles, based on selective deficits in reading rate versus accuracy and associated with different basic reading, linguistic, and cognitive skills as well as electrophysiological responses.
Intermittent tapping control

Control using a sequence of ‘taps’, in contrast to the usual smooth control, is shown to fit within the established intermittent control framework. In particular, a specially designed generalised hold gives rise to tapping behaviour optimised according to the underlying linear-quadratic design. Both fixed-interval and event-driven tapping are included in this approach and some basic stability analysis is given. Illustrative examples are presented and the advantages of tapping in the context of electromechanical servo systems with friction are explored using a laboratory experiment.
1-Syntrophin–deficient skeletal muscle exhibits hypertrophy and aberrant formation of neuromuscular junctions during regeneration

1 Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8502, Tokyo, Japan 2 Department of Neurology, Nakadori General Hospital, Akita 010-8577, Japan 3 Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-8654, Japan 4 Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan 5 Department of Pharmacology, Saitama Medical School, Moroyama-machi, Saitama 350-0495, Japan 6 Department of Ophthalmology, Akita University, Akita 010-8543, Japan
Gastrointestinal nematodes and anthelmintic resistance in Danish goat herds☆

The prevalence of gastrointestinal parasites in Danish goats and the presence of anthelmintic resistance (AR) in 10 selected herds were investigated during April–September 2012. All Danish herds (n = 137) with 10 or more adult goats were invited to participate, and of these 27 herds met the inclusion criterion of more than 10 young kids never treated with anthelmintics. Questionnaire data on management were collected, and faecal samples from 252 kids were analysed by the McMaster technique. From all herds with a mean faecal egg count (FEC) above 300 eggs per g of faeces, pooled samples were stained with peanut agglutinin (PNA) for specific detection of Haemonchus contortus. Strongyle eggs were detected with an individual prevalence of 69%, including Nematodirus battus (3.6%) and other Nematodirus species (15.0%). Eimeria spp. were observed in 99.6% of the kids. H. contortus was found in 11 of 12 (92%) tested herds. Anthelmintics were used in 89% of the herds with mean treatment frequencies of 0.96 and 0.89 treatments per year for kids and adults, respectively. In 2011, new animals were introduced into 44% of the herds of which 25% practised quarantine anthelmintic treatments. In 10 herds the presence of AR was analysed by egg hatch assay and FEC reduction tests using ivermectin (0.3 mg/kg) or fenbendazole (10.0 mg/kg). AR against both fenbendazole and ivermectin was detected in seven herds; AR against fenbendazole in one herd, and AR against ivermectin in another herd. In conclusion, resistance to the most commonly used anthelmintics is widespread in larger goat herds throughout Denmark.
Animal Consciousness

Only philosophers question whether other people are conscious, though presumably philosophers assume their listeners are conscious of their wise words. Like the rest of us, philosophers will talk to their dogs without expecting verbal answers, a bark or a tail wag being enough to bridge the metaphysical gap for practical purposes; though recent electronic toy dogs are impressively canine, although presumably unaware. Loss of speech in people is disturbing and deeply puzzling. It is hard, even for experienced neurologists, to know what goes on in the inner world of prolonged coma where speech is lost. Absence of speech, or other behaviour, does not necessarily mean absence of consciousness. In sleepwalking there may be behaviour without related consciousness, and in acting consciousness can be decoupled from what is spoken. Helmholtz, then of course Freud, stressed the importance of unconscious processes of brain and mind for behaviour and perception. This, now frequently stated separation, is the basis of the philosophical conundrum: How do we recognise consciousness from behaviour? The problem is that either can occur without the other, though intelligence is limited without consciousness. Although we are generally confident that `higher' animals have consciousness, not entirely different from ours, confidence fades for very different organisms, such as fish or birds or spiders. Wonderful as the skills of a spider are, it is far from clear that spiders build their webs consciously. Our compunction at destroying a spider is different from guilt associated with mistreating a dog or a cat or a horse, though the spider ends up dead. Most of us think of the horse feeling the whip and remembering the sting, while we assume the intricate circuits of the spider feel nothing up to or through its door of death, when its circuits fail. Although we are sure `higher' animals are conscious, this is far from clear for `lower' creatures such as spiders. Yet where is the evidence? For us there is all the difference in the world between loss of behaviour (as with the arrow poison, muscle relaxant curare) and switching off consciousness with an anesthetic such as ether. The question is: How far down the evolutionary tree does this behaviour ^ consciousness distinction go? Is this an empirical question that might be answered experimentally? While idling a passing hour reading New Scientist, as is my weekly wont, I came across a Comment and Analysis piece by Joyce D'Silva (Chief Executive of Compassion in World Farming) called ``Faster, cheaper, sicker'' (New Scientist 15 November 2003, page 19). D'Silva writes of the `discomfort' of chickens, made to grow abnormally fast: