Miracle-dz/UniFAR-FTUs huggingface dataset:
Proximal tubular cytochrome c efflux: determinant, and potential marker, of mitochondrial injury.

BACKGROUND Cytochrome c (cyt c) is released from mitochondria after tissue injury, but little is known of its subsequent fate. This study was undertaken to ascertain: (1) does cyt c readily gain access to the extracellular space; (2) if so, what are some determinants of this process; and (3) might cyt c release be a potentially useful marker of in vivo tissue damage. METHODS Isolated mouse proximal tubules (PT) were subjected to site 1 (rotenone; Rot), site 2 (antimycin A, AA), or site 3 (hypoxic) respiratory chain blockade (+/- 2 mmol/L glycine, to prevent plasma membrane disruption/cell death). Alternatively, oxidant injury was imposed (Fe(2+) or cholesterol oxidase). Extra- and intracellular cyt c levels were quantified by Western blot. Plasma or urine cyt c levels were also determined after rhabdomyolysis or ischemic acute renal failure (ARF) (in mice), or clinical ARF. RESULTS AA, Rot, and hypoxia caused variable degrees of PT cyt c release (AA >> rot approximately hypoxia), but at most, <20% of total cell content was involved. In contrast, Fe(2+) evoked approximately 65% cyt c efflux, and cholesterol oxidation caused approximately 100% cyt c release. Glycine did not block cyt c efflux, dissociating this process from plasma membrane disruption/necrotic cell death. After rhabdomyolysis, plasma cyt c levels rose and correlated with the severity of ARF (r, 0.93 vs. BUNs). Cyt c was detected in urine after both experimental and clinical ARF. CONCLUSION Cell cyt c release is dependent on the site and the type of mitochondrial injury sustained. Oxidative injury, in general, and cholesterol oxidation, in particular, seem particularly relevant in this regard. After mitochondrial release, cyt c traverses plasma membranes, eventuating in the extracellular space. The data suggest that plasma and/or urine cyt c appearance might function as a clinically useful in vivo marker of mitochondrial stress and the tissue injury sustained.
Wild-type Drosophila melanogaster as an alternative model system for investigating the pathogenicity of Candida albicans

SUMMARY Candida spp. are opportunistic pathogens in humans, and their systemic infections display upwards of 30% mortality in immunocompromised patients. Current mammalian model systems have certain disadvantages in that obtaining results is time consuming owing to the relatively long life spans and these results have low statistical resolution because sample sizes are usually small. We have therefore evaluated the potential of Drosophila melanogaster as an additional model system with which to dissect the host-pathogen interactions that occur during Candida albicans systemic infection. To do this, we monitored the survival of wild-type flies infected with various C. albicans clinical isolates that were previously ranked for murine virulence. From our lifetime data we computed two metrics of virulence for each isolate. These correlated significantly with murine survival, and were also used to group the isolates, and this grouping made relevant predictions regarding their murine virulence. Notably, differences in virulence were not predictably resolvable using immune-deficient spz−/− flies, suggesting that Toll signalling might actually be required to predictably differentiate virulence. Our analysis reveals wild-type D. melanogaster as a sensitive and relevant model system; one that offers immense genetic tractability (having an extensive RNA interference library that enables tissue-specific gene silencing), and that is easy to manipulate and culture. Undoubtedly, it will prove to be a valuable addition to the model systems currently used to study C. albicans infection.
De novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research

Vicia faba (L.) is an important cool-season grain legume species used widely in agriculture but also in plant physiology research, particularly as an experimental model to study transfer cell (TC) development. TCs are specialized nutrient transport cells in plants, characterized by invaginated wall ingrowths with amplified plasma membrane surface area enriched with transporter proteins that facilitate nutrient transfer. Many TCs are formed by trans-differentiation from differentiated cells at apoplasmic/symplasmic boundaries in nutrient transport. Adaxial epidermal cells of isolated cotyledons can be induced to form functional TCs, thus providing a valuable experimental system to investigate genetic regulation of TC trans-differentiation. The genome of V. faba is exceedingly large (ca. 13 Gb), however, and limited genomic information is available for this species. To provide a resource for future transcript profiling of epidermal TC differentiation, we have undertaken de novo assembly of a genome-wide transcriptome map for V. faba. Illumina paired-end sequencing of total RNA pooled from different tissues and different stages, including isolated cotyledons induced to form epidermal TCs, generated 69.5 M reads, of which 65.8 M were used for assembly following trimming and quality control. Assembly using a De-Bruijn graph-based approach generated 21,297 contigs, of which 80.6% were successfully annotated against GO terms. The assembly was validated against known V. faba cDNAs held in GenBank, including transcripts previously identified as being specifically expressed in epidermal cells across TC trans-differentiation. This genome-wide transcriptome map therefore provides a valuable tool for future transcript profiling of epidermal TC trans-differentiation, and also enriches the genetic resources available for this important legume crop species.
Restoration of photosystem II photochemistry and carbon assimilation and related changes in chlorophyll and protein contents during the rehydration of desiccated Xerophyta scabrida leaves

Recovery of photosynthesis in rehydrating desiccated leaves of the poikilochlorophyllous desiccation-tolerant plant Xerophyta scabrida was investigated. Detached leaves were remoistened under 12 h light/dark cycles for 96 h. Water, chlorophyll (Chl), and protein contents, Chl fluorescence, photosynthesis–CO2 concentration response, and the amount and activity of Rubisco were measured at intervals during the rehydration period. Leaf relative water contents reached 87% in 12 h and full turgor in 96 h. Chl synthesis was slower before than after 24 h, and Chla:Chlb ratios changed from 0.13 to 2.6 in 48 h. The maximum quantum efficiency recovered faster during rehydration than the photosystem II operating efficiency and the efficiency factor, which is known to depend mainly on the use of the electron transport chain products. From 24 h to 96 h of rehydration, net carbon fixation was Rubisco limited, rather than electron transport limited. Total Rubisco activity increased during rehydration more than the Rubisco protein content. Desiccated leaves contained, in a close to functional state, more than half the amount of the Rubisco protein present in rehydrated leaves. The results suggest that in X. scabrida leaves Rubisco adopts a special, protective conformation and recovers its activity during rehydration through modifications in redox status.
Typing of Clostridium difficile strains by PCR-amplification of variable length 16S-23S rDNA spacer regions.

To develop a rapid and accurate method of typing large numbers of clinical isolates of Clostridium difficile, four regions of the rRNA operon [A, 15-1407 and B, 907-1407 (16S-16S); C, 1392-507 and D, 907-507 (16S-23S)] were enzymically amplified from 24 strains. When region A was hybridized to HindIII-digested genomic DNA isolated from C. difficile strains, all of the variable length restriction fragments hybridized. When region B was hybridized to HindIII-digested genomic DNA isolated from C. difficile strains, a set of variable length restriction fragments (Group II) hybridized predominantly. When region C was separated by agarose gel electrophoresis, a series of products ranging in size from approximately 800-1300 bp was obtained. When regions C and D were digested with HindIII, a constant region of 430 bp was found in both products and in all strains. From the above experiments it was concluded that the variable length Group II restriction fragments and the variable length region C amplification products were due to variable length 16S-23S spacer regions between alleles of the one strain. When region C amplification products were separated by denaturing PAGE, 16 variable length rRNA alleles (rrnA-P) were demonstrated from 24 C. difficile strains ranging in size from 852-1210 bp. After analysis with maximum parsimony, the 24 strains were divided into 14 ribotypes. (ABSTRACT TRUNCATED AT 250 WORDS)
Comparative Effects of α-, β-, and γ-Carbolines on Platelet Aggregation and Lipid Membranes

Cigarette smoking and alcohol consumption possibly affect platelet functions. To verify the hypothesis that some α-, β-, and γ-carboline components in cigarette smoke and alcoholic beverages may change platelet aggregability, their effects on human platelets were determined by aggregometry together with investigating their membrane effects by turbidimetry. Carbolines inhibited platelet aggregation induced by five agents with the potency being 3-amino-1,4-dimethyl-5H-pyrido[4,3-b]indole > 3-amino-1-methyl-5H-pyrido[4,3-b]indole > 1-methyl-9H-pyrido[3,4-b]indole. The most potent 3-amino-1,4-dimethyl-5H-pyrido[4,3-b]indole showed 50% aggregation-inhibitory concentrations of 6–172 μM. Both γ-carbolines interacted with phosphatidylcholine membranes to lower the lipid phase transition temperature with the potency correlating to the antiplatelet activity, suggesting that the interaction with platelet membranes to increase their fluidity underlies antiplatelet effects. Given their possible concentration and accumulation in platelets, γ- and β-carbolines would provide cigarette smokers and alcohol drinkers with reduced platelet aggregability, and they may be responsible for the occurrence of hemorrhagic diseases associated with heavy smoking and alcoholics.
Induction of Apoptosis in Leukemic Cells by Homovanillic Acid Derivative, Capsaicin, through Oxidative Stress

Capsaicin (N-vanillyl-8-methyl-1-nonenamide) is a homovanillic acid derivative found in pungent fruits. Several investigators have reported the ability of capsaicin to inhibit events associated with the promotion of cancer. However, the effects of capsaicin on human leukemic cells have never been investigated. We investigated the effects of capsaicin on leukemic cells in vitro and in vivo and further examined the molecular mechanisms of capsaicin-induced apoptosis in myeloid leukemic cells. Capsaicin suppressed the growth of leukemic cells, but not normal bone marrow mononuclear cells, via induction of G0-G1 phase cell cycle arrest and apoptosis. Capsaicin-induced apoptosis was in association with the elevation of intracellular reactive oxygen species production. Interestingly, capsaicin-sensitive leukemic cells were possessed of wild-type p53, resulting in the phosphorylation of p53 at the Ser-15 residue by the treatment of capsaicin. Abrogation of p53 expression by the antisense oligonucleotides significantly attenuated capsaicin-induced cell cycle arrest and apoptosis. Pretreatment with the antioxidant N-acetyl-l-cystein and catalase, but not superoxide dismutase, completely inhibited capsaicin-induced apoptosis by inhibiting phosphorylation of Ser-15 residue of p53. Moreover, capsaicin effectively inhibited tumor growth and induced apoptosis in vivo using NOD/SCID mice with no toxic effects. We conclude that capsaicin has potential as a novel therapeutic agent for the treatment of leukemia.
The Delphi technique: myths and realities.

AIMS To outline the key concepts and principles of the Delphi technique. METHODS Reference is made to a selection of studies that illustrate a variety of methodological interpretations. Drawing on Heshusius's concept of 'goodness criteria', particular emphasis is given to the question of scientific merit and means of evaluation. CONCLUSIONS Although the technique should be used with caution, it appears to be an established method of harnessing the opinions of an often diverse group of experts on practice-related problems.
Association between Lameness and Indicators of Dairy Cow Welfare Based on Locomotion Scoring, Body and Hock Condition, Leg Hygiene and Lying Behavior

Simple Summary Lameness is a major welfare issue in dairy cows. Locomotion scoring (LS) is mostly used in identifying lame cows based on gait and postural changes. However, lameness shares some important associations with body condition, hock condition, leg hygiene and behavioral changes such as lying behavior. These measures are considered animal-based indicators in assessing welfare in dairy cows. This review discusses lameness as a welfare problem, the use of LS, and the relationship with the aforementioned welfare assessment protocols. Such information could be useful in depicting the impact on cow welfare as well as in reducing the occurrence of lameness in dairy herds. Abstract Dairy cow welfare is an important consideration for optimal production in the dairy industry. Lameness affects the welfare of dairy herds by limiting productivity. Whilst the application of LS systems helps in identifying lame cows, the technique meets with certain constraints, ranging from the detection of mild gait changes to on-farm practical applications. Recent studies have shown that certain animal-based measures considered in welfare assessment, such as body condition, hock condition and leg hygiene, are associated with lameness in dairy cows. Furthermore, behavioural changes inherent in lame cows, especially the comfort in resting and lying down, have been shown to be vital indicators of cow welfare. Highlighting the relationship between lameness and these welfare indicators could assist in better understanding their role, either as risk factors or as consequences of lameness. Nevertheless, since the conditions predisposing a cow to lameness are multifaceted, it is vital to cite the factors that could influence the on-farm practical application of such welfare indicators in lameness studies. This review begins with the welfare consequences of lameness by comparing normal and abnormal gait as well as the use of LS system in detecting lame cows. Animal-based measures related to cow welfare and links with changes in locomotion as employed in lameness research are discussed. Finally, alterations in lying behaviour are also presented as indicators of lameness with the corresponding welfare implication in lame cows.
Inapproximability of Truthful Mechanisms via Generalizations of the VC Dimension

Algorithmic mechanism design (AMD) studies the delicate interplay between computational efficiency, truthfulness, and optimality. We focus on AMD's paradigmatic problem: combinatorial auctions. We present a new generalization of the VC dimension to multivalued collections of functions, which encompasses the classical VC dimension, Natarajan dimension, and Steele dimension. We present a corresponding generalization of the Sauer-Shelah Lemma and harness this VC machinery to establish inapproximability results for deterministic truthful mechanisms. Our results essentially unify all inapproximability results for deterministic truthful mechanisms for combinatorial auctions to date and establish new separation gaps between truthful and non-truthful algorithms.
Semantic Relation Classification: Task Formalisation and Refinement

The identification of semantic relations between terms within texts is a fundamental task in Natural Language Processing which can support applications requiring a lightweight semantic interpretation model. Currently, semantic relation classification concentrates on relations which are evaluated over open-domain data. This work provides a critique on the set of abstract relations used for semantic relation classification with regard to their ability to express relationships between terms which are found in a domain-specific corpora. Based on this analysis, this work proposes an alternative semantic relation model based on reusing and extending the set of abstract relations present in the DOLCE ontology. The resulting set of relations is well grounded, allows to capture a wide range of relations and could thus be used as a foundation for automatic classification of semantic relations.
Determining is-a relationships for Textual Entailment

The Textual Entailment task has become inﬂuential in NLP and many researchers have become interested in applying it to other tasks. However, the two major issues emerging from this body of work are the fact that NLP applications need systems that (1) attain results which are not corpus dependent and (2) assume that the text for entailment cannot be incorrect or even contradictory. In this paper we pro-pose a system which decomposes the text into chunks via a shallow text analysis
Rule extraction from neural networks — A comparative study

Though neural networks have achieved highest classification accuracy for many classification problems, the obtained results may not be interpretable as they are often considered as black box. To overcome this drawback researchers have developed many rule extraction algorithms. This paper has discussed on various rule extraction algorithms based on three different rule extraction approaches namely decompositional, pedagogical and eclectic. Also it evaluates the performance of those approaches by comparing different algorithms with these three approaches on three real datasets namely Wisconsin breast cancer, Pima Indian diabetes and Iris plants.
Characterization of solid airborne particles deposited in snow in the vicinity of urban fossil fuel thermal power plant (Western Siberia)

ABSTRACT Recognition and detailed characterization of solid particles emitted from thermal power plants into the environment is highly important due to their potential detrimental effects on human health. Snow cover is used for the identification of anthropogenic emissions in the environment. However, little is known about types, physical and chemical properties of solid airborne particles (SAP) deposited in snow around thermal power plants. The purpose of this study is to quantify and characterize in detail the traceable SAP deposited in snow near fossil fuel thermal power plant in order to identify its emissions into the environment. Applying the scanning electron microscopy-energy dispersive spectroscopy, and X-ray diffraction, mineral and anthropogenic phase groups in SAP deposited in snow near the plant and in fly ash were observed. We identified quartz, albite and mullite as most abundant mineral phases and carbonaceous matter, slag and spherical particles as dominate anthropogenic phases. This is the first study reporting that zircon and anthropogenic sulphide-bearing, metal oxide-bearing, intermetallic compound-bearing and rare-earth element-bearing particles were detected in snow deposits near thermal power plant. The identified mineral and anthropogenic phases can be used as tracers for fossil fuel combustion emissions, especially with regard to their possible effect on human health.
Advances in geometric modeling and feature extraction on pots

A bstract: This paper outlines progress on the 3D Knowledge and Distributed Intelligence project (3DK) at A rizona State University. Three of the six 3 DK pilot projects involve archaeological and biological material, namely ceramic vessels, lithic artifacts, and bones. These projects are: (1) "3D Morphology of Ceramic Vessels " which aims to learn about vessel uniformity and proportionality as indicators of developing craft specialization and complex social organization among prehistoric cultures; (2) "Lithic Refitting" which intends to develop the algorithms required to (partially) automate the refitting process through 3D scanning and surface modeling: and (3) "3D Topography of Joint Surfaces " which investigates the ability of human ancestors to make tools and walk upright. This paper discusses underlying research aspects common to all three pilot projects: data acquisition, modeling, feature recognition, database construction, and development of a visual query interface aimed at making 3D models of these artifacts available online for query.
During automatic program animation, explanations after animations have greater impact than before animations

Little is known about the effectiveness of automatic explanations in educational program visualization. We designed a study in which the order of animations and related explanations was manipulated. Two groups of a total of 18 participants interacted with either animation-first or explanation-first version of a tool. The results indicate that animation-first approach is significantly more effective. On the grounds of these findings and students' input about the explanation generation and layout, we discuss the design implications of the findings.
The Development and Establishment of a Care Map in Children with Asthma in Taiwan

Background. It is often difficult to predict the timing and frequency of asthma attacks. In addition to interrupting the daily life of both the affected child and his/her family, asthma can also pose sudden danger to a child. Based on clinical observations, many asthma‐affected children and their parents must constantly adjust themselves to the uncertainty of the disease, which leads to increased stress on the family. The use of care maps has demonstrated increased efficiency and effectiveness in the care of asthma patients from a variety of settings. Objective. We designed this study to construct and evaluate a care map for asthmatic children in Taiwan. Specific attention was placed on comparing the study and control subjects by parental knowledge of asthma, medication used for asthma, hospital readmission, and health care resource usage. Subjects and Methods. The care map was constructed by in‐depth interviews with eight sets of parents of children with asthma. Forty‐four parents of 42 asthma children were randomized into two groups in the Allergic Clinic of the Chang Gung Children's Hospital. The experimental group of 22 parents received individual instruction and training sessions in addition to the regular care provided to the control group of 22 parents. Results. Forty‐two children with asthma were surveyed in this study. To examine the reliability and validity of a care map for children with asthma, a quantitative survey was conducted with 42 outpatient parents with asthmatic children. There was less emergency room attending rate in experimental group (6/month; p < 0.05) The understanding of the disease was much improved in parents of experimental group (13.85 ± 1.04 vs. 10.91 ± 2.14; p < 0.01). Furthermore, parents acquired a more positive attitude to asthma, and almost all of the control group had irregular follow‐ups by a physician and had irregular use of medication. Conclusion. This study emphasizes that a care map in children with asthma (CACM) can be used to educate parents in how to provide the best treatment plan for their children. This study also shows how a CACM can help parents train their children in the best behaviors during asthma attacks. Empathetic assessment and elimination of cultural barriers, a well‐designed educational program, and a mutually developed treatment plan could significantly improve the quality of life for families and specific asthma outcomes.
Email reciprocity and personal communication bias

In this paper, we discuss differences in reciprocity in core networks in email inboxes using data from 538 cases at a hightech organization. We highlight the fact that reciprocity in email behavior is different between multi-recipient and dyadic mail and that a consistent number of alters send disproportionate volumes of mail.