Miracle-dz/UniFAR-FTUs huggingface dataset:
Herbivory-induced changes in the small-RNA transcriptome and phytohormone signaling in Nicotiana attenuata

Phytohormones mediate the perception of insect-specific signals and the elicitation of defenses during insect attack. Large-scale changes in a plant's transcriptome ensue, but how these changes are regulated remains unknown. Silencing of RNA-directed RNA polymerase 1 (RdR1) makes Nicotiana attenuata highly susceptible to insect herbivores, suggesting that defense elicitation is under the direct control of small-RNAs (smRNAs). Using 454-sequencing, we characterized N. attenuata's smRNA transcriptome before and after insect-specific elicitation in wild-type (WT) and RdR1-silenced (irRdR1) plants. We predicted the targets of N. attenuata smRNAs in the genes related to phytohormone signaling (jasmonic acid, JA-Ile, and ethylene) known to mediate resistance responses, and we measured the elicited dynamics of phytohormone biosynthetic transcripts and phytohormone levels in time-course experiments with field- and glasshouse-grown plants. RdR1 silencing severely altered the induced transcript accumulation of 8 of the 10 genes, reduced JA, and enhanced ethylene levels after elicitation. Adding JA completely restored the insect resistance of irRdR1 plants. irRdR1 plants had photosynthetic rates, growth, and reproductive output indistinguishable from that of WT plants, suggesting unaltered primary metabolism. We conclude that the susceptibility of irRdR1 plants to herbivores is due to altered phytohormone signaling and that smRNAs play a central role in coordinating the large-scale transcriptional changes that occur after herbivore attack. Given the diversity of smRNAs that are elicited after insect attack and the recent demonstration of the ability of ingested smRNAs to silence transcript accumulation in lepidopteran larvae midguts, the smRNA responses of plants may also function as direct defenses.
Implementing Document-based Lessons in High School Classrooms: A Case Study of World History Teachers' Perspectives and Practices

The purpose of this study is to explore teachers' philosophical and pedagogical views regarding their definitions of historical thinking. Staff development intended to train teachers in this method of instruction is also reflected upon by the participants. The goal of the study is to investigate how teachers create opportunities for practice through their own understanding of the phenomena of the construction of historical knowledge through their pre-service education and current classroom experience, the application of that understanding to their pedagogy, and what they consider to be beneficial staff development. The research design for this study is a phenomenological case study centering on three teachers’ stories. The phenomenon of historical thinking is investigated through analysis of interviews and focus groups conducted with three world history teachers – the goal is to determine how teachers interact with skills and knowledge necessary to grasp historical thinking and literacy and how they approach instructing students in this skill. The teachers interviewed stated varying levels of comfort in using historical thinking in their classrooms. All participants saw value in historical literacy and document analysis, though they differed in incorporating these activities in their classroom activities. All teachers interviewed stated that they had concerns about the time available to teach the content. Teachers expressed frustration with the amount and quality of world history professional development available. Participants stressed the importance of integrating PRD analysis strategies into lessons, and stated that they would benefit from development activities that demonstrated how to effectively work with students across all ability levels on honing this potentially unfamiliar skill.
Demonstration of in situ product recovery of butyric acid via CO2‐facilitated pH swings and medium development in two‐phase partitioning bioreactors

Production of organic acids in solid–liquid two‐phase partitioning bioreactors (TPPBs) is challenging, and highly pH‐dependent, as cell growth occurs near neutral pH, while acid sorption occurs only at low pH conditions. CO2 sparging was used to achieve acidic pH swings, facilitating undissociated organic acid uptake without generating osmotic stress inherent in traditional acid/base pH control. A modified cultivation medium was formulated to permit greater pH reduction by CO2 sparging (pH 4.8) compared to typical media (pH 5.3), while still possessing adequate nutrients for extensive cell growth. In situ product recovery (ISPR) of butyric acid (pKa = 4.8) produced by Clostridium tyrobutyricum was achieved through intermittent CO2 sparging while recycling reactor contents through a column packed with absorptive polymer Hytrel® 3078. This polymer was selected on the basis of its composition as a polyether copolymer, and the use of solubility parameters for predicting solute polymer affinity, and was found to have a partition coefficient for butyric acid of 3. Total polymeric extraction of 3.2 g butyric acid with no CO2 mediated pH swings was increased to 4.5 g via CO2‐facilitated pH shifting, despite the buffering capacity of butyric acid, which resists pH shifting. This work shows that CO2‐mediated pH swings have an observable positive effect on organic acid extraction, with improvements well over 150% under optimal conditions in early stage fermentation compared to CO2‐free controls, and this technique can be applied other organic acid fermentations to achieve or improve ISPR. Biotechnol. Bioeng. 2014;111: 537–544. © 2013 Wiley Periodicals, Inc.
Free Tissue Transfer versus Pedicled Flap Cost in Head and Neck Cancer

OBJECTIVE: We sought to compare the overall 1-year management costs for patients receiving a free tissue transfer with those of patients receiving a pedicled flap reconstruction as a component of their primary head and neck cancer treatment. STUDY DESIGN AND SETTING: Case-control, cost identification analysis of 21 matched pairs of patients and multivariate analysis of variables associated with treatment costs was conducted in a tertiary referral academic institution. RESULTS: No significant difference in total 1-year charges between the pedicled and free tissue transfer groups was found. A structured measure of patient comorbidity was the only variable significantly associated with total 1-year charges. CONCLUSIONS: Total 1-year treatment costs of primary upper aerodigestive tract cancers are similar for patients reconstructed with free tissue transfer or a pedicled flap. SIGNIFICANCE: Within the context of overall 1-year management costs, the primary determinants of health care expense for these patients are comorbidity and extent of disease, not reconstructive technique.
The Propionic Acids: A Personal Perspective

In searching during the early 1950s for new drugs for the treatment of rheumatoid arthritis, little information was available to allow a rational approach. The mode of action of the few drugs available was unknown and even the analgesic action of aspirin could not be demonstrated in animals. A speculative concept was developed that aspirin possessed a specific unidentified action in rheumatoid arthritis and that this and its analgesic properties were related to its ability to delay the development of ultraviolet (UV) erythema in the guinea pig. A series of substituted phenoxypropionic acids proved to be active as antierythemic agents, but the most potent was inactive clinically in rheumatoid arthritis. Refinements to the testing systems led to a series of substituted phenylacetic acids, three of which although active in rheumatoid arthritis produced unacceptable adverse reactions (ADRs). Attempts to relate laboratory data to clinical ADRs suggested that the substituted phenylpropionic acids (originally rejected because of concerns about toxicity) might be better tolerated than we had anticipated. Ibuprofen was selected from this large group. It was proven to be effective and well tolerated and became “the first of the propionics” when it was launched in 1969. In the 1970s, ibuprofen proved to be effective as a prescription drug in a range of painful nonrheumatic conditions and on the basis of its good safety record was approved as an OTC analgesic in 1983 in the United Kingdom and in 1984 in the USA. It has proven to be popular and effective and much safer than aspirin or acetaminophen in overdosage.
Late Miocene episodic lakes in the arid Tarim Basin, western China

Significance The relative roles of the two plausible causes, Cenozoic global cooling and Tibetan Plateau uplift, for the Asian interior aridification/desertification are often difficult to disentangle. High-quality terrestrial records from the Tarim Basin document how enhanced aridification occurred over the last 7 my, from episodic lacustrine environments to the currently prevailing desert environments. During the Late Miocene–Early Pliocene period, episodic occurrences of great lakes and thus wetter climate closely corresponded to periods of high eccentricity and possibly high obliquity, suggesting that the uplifted plateau by then did not effectively block the moisture availability at optimum climatic conditions. The finally irreversible drying up of great lakes at ∼4.9 Ma could be attributed to the plateau uplift. The Tibetan Plateau uplift and Cenozoic global cooling are thought to induce enhanced aridification in the Asian interior. Although the onset of Asian desertification is proposed to have started in the earliest Miocene, prevailing desert environment in the Tarim Basin, currently providing much of the Asian eolian dust sources, is only a geologically recent phenomenon. Here we report episodic occurrences of lacustrine environments during the Late Miocene and investigate how the episodic lakes vanished in the basin. Our oxygen isotopic (δ18O) record demonstrates that before the prevailing desert environment, episodic changes frequently alternating between lacustrine and fluvial-eolian environments can be linked to orbital variations. Wetter lacustrine phases generally corresponded to periods of high eccentricity and possibly high obliquity, and vice versa, suggesting a temperature control on the regional moisture level on orbital timescales. Boron isotopic (δ11B) and δ18O records, together with other geochemical indicators, consistently show that the episodic lakes finally dried up at ∼4.9 million years ago (Ma), permanently and irreversibly. Although the episodic occurrences of lakes appear to be linked to orbitally induced global climatic changes, the plateau (Tibetan, Pamir, and Tianshan) uplift was primarily responsible for the final vanishing of the episodic lakes in the Tarim Basin, occurring at a relatively warm, stable climate period.
Functional complementation between bacterial MDR-like export systems: colicin V, alpha-hemolysin, and Erwinia protease

The antibacterial protein Colicin V (ColV) is secreted from gram-negative bacteria by a signal sequence-independent pathway. The proteins that mediate the export of ColV share sequence similarities with components from other signal sequence-independent export systems such as those for alpha-hemolysin (Hly) and Erwinia protease (Prt). We report here that the intact HlyBD export system can export active ColV from Escherichia coli strains lacking the ColV export proteins CvaA and CvaB. The individual Hly export genes complement mutations in their respective ColV homologs, but do so at a lower efficiency. When CvaA or CvaB is expressed along with the intact HlyBD exporter, the Cva export protein interferes with export of ColV through the HlyBD system. Gene fusions and point mutations in the ColV structural gene were used to define signals in ColV recognized by the Hly exporter. An export signal in ColV recognized by HlyBD is localized to the amino-terminal 57 amino acids of the protein. In addition, mutations in the ColV export signal differentially affect export through CvaAB and HlyBD, suggesting differences in signal specificity between the Cva and Hly systems. The three Erwinia protease export proteins can also export active ColV, and interference is seen when CvaA or CvaB is expressed along with the intact Prt exporter. Functional complementation is not reciprocal; alpha-hemolysin is not exported through either the ColV system or the Prt system.
Transient or persistent asthma-like symptoms and lung growth over 2-year follow-up in pre-adolescent children.

BACKGROUND The main purpose of this study was to assess the effect of transient and continued asthma-like symptoms on lung function growth in preadolescent children. METHODS The follow-up respiratory health survey has been conducted on the sample of 1,129 children aged 9 years over 2 years follow-up. The basic health end-points were the occurrence of asthma-like symptoms and slower lung function growth (SLFG), which was defined as the lung function gain over 2 years within the lowest quintile of the distribution of a given spirometric test. RESULTS Adjusted odds ratios (OR) for SLFG [forced vital capacity (FVC)] were significantly higher only in the children having continued symptoms [OR = 3.39: 95% confidence interval (CI) = 1.39-8.27]. There was a consistent trend of adjusted ORs for SLFG [forced expiratory volume (FEV,) with the category of symptoms, where OR was 2.00 (95% Cl = 1.17-3.42) in children with transient symptoms: while 4.10 (95% Cl = 1.71-9.86) in children who had persistent symptoms. The corresponding ORs for SLFG [maximal mid-expiratory flow (FEF25_75c)] were 2.27 (95% Cl = 1.37-3.76); and 5.43 (95% Cl = 2.38-12.40). DISCUSSION The association between asthma-like symptoms and lung function gain in preadolescent children confirmed the clinical significance of the symptoms in question. The observed slower lung function gain in preadolescence may have implications for the development of chronic lung disease later in adulthood.
Building bridges or deepening divides: Resources and formal volunteering in post-apartheid South Africa

This study investigates volunteering in a highly unequal society. It uses post-apartheid South Africa as a case study: the enduring apartheid legacy has left deep divides between classes and races in the country. The research asks if formal volunteering serves to enhance social cohesion or reinforces such social divides. Logistic analysis is applied to the 2001 South African World Values Survey, to measure the strength of the relationship between the likelihood to volunteer, and selected human, social and cultural capital variables. The analysis shows that volunteering tends to align with existing social divides. Individuals are more likely to volunteer if they are educated and affluent, supporting the dominant status theory. Prejudice and not valuing sharing are also associated with a higher proclivity for volunteering. Broadly, we find that the available evidence suggests that volunteering is associated with bonding, rather than bridging, social capital. Although hardly uncontentious, broad-based support for and involvement in religious volunteering suggest that religious communities and congregations could in the future provide a bridge to help heal the rifts if links between such communities are strengthened.
Welfare States in Transition

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Destabilizing loop swaps in the CDRs of an immunoglobulin VL domain

It is generally believed that loop regions in globular proteins, and particularly hypervariable loops in immunoglobulins, can accommodate a wide variety of sequence changes without jeopardizing protein structure or stability. We show here, however, that novel sequences introduced within complementarity determining regions (CDRs) 1 and 3 of the immunoglobulin variable domain REI VL can significantly diminish the stability of the native state of this protein. Besides their implications for the general role of loops in the stability of globular proteins, these results suggest previously unrecognized stability constraints on the variability of CDRs that may impact efforts to engineer new and improved activities into antibodies.
Small-bowel neoplasms: prospective evaluation of MR enteroclysis.

PURPOSE To prospectively evaluate the accuracy of magnetic resonance (MR) enteroclysis in the detection of small-bowel neoplasms in symptomatic patients, with conventional endoscopy, tissue specimen, capsule endoscopy, conventional enteroclysis, and follow-up findings as reference standards. MATERIALS AND METHODS The study protocol was approved by the human research committee, and all patients gave written informed consent. One hundred fifty patients (83 male, 67 female; mean age, 42.6 years; age range, 17-84 years) who were clinically suspected of having small-bowel neoplasm and whose previous upper and lower gastrointestinal endoscopy findings were normal underwent MR enteroclysis. The MR enteroclysis findings were prospectively evaluated for the presence of focal bowel wall thickening, small-bowel masses, and small-bowel stenosis. Positive MR enteroclysis findings were compared with histopathologic examination results obtained after surgical (n = 19) or endoscopic (n = 2) procedures. Negative MR enteroclysis results were compared with the results of enteroscopy (n = 5), capsule endoscopy (n = 53), or conventional enteroclysis with subsequent clinical follow-up (n = 71). The diagnostic performance of MR enteroclysis was analyzed on a per-patient basis. RESULTS MR enteroclysis was successfully completed in all 150 patients and enabled correct detection of 19 small-bowel neoplasms, which were confirmed at histopathologic examination: three carcinoid neoplasms, two adenocarcinomas, two stromal tumors, five lymphomas, one angiomatous mass, three small-bowel metastases, one leiomyoma, one adenoma, and one lipoma. Overall sensitivity, specificity, and accuracy in identifying patients with small-bowel lesions were 86% (19 of 22), 98% (126 of 128), and 97% (145 of 150), respectively. Two MR enteroclysis examinations yielded false-positive findings, and three yielded false-negative findings. CONCLUSION MR enteroclysis is an accurate modality for detecting small-bowel neoplasms in symptomatic patients.
Technology Orientation , Dynamic Capabilities and SMEs Performance

To deal with these fast changing business environments that characterise emerging economies and to seize the opportunities that these environments opens up, any size firms and especially SMEs, must develop their dynamic capabilities to achieve sustained competitive advantages. This study investigates the role of a technology orientation on firm performance, by exploring the relationship between technology orientation [TO], different dynamic capabilities and performance. This study uses survey data from a random sample of 154 small to medium-sized enterprises (SMEs) located in Science Parks in Iran. The findings support the hypothesis that a firm’s technology orientation associates with performance and also a firm’s dynamic capabilities positively mediate the relationship between technology orientation and firm performance. The results show that among three different types of dynamic capabilities, learning capability most effectively mediates the impact of technology orientation on performance.
ExsB Is Required for Correct Assembly of the Pseudomonas aeruginosa Type III Secretion Apparatus in the Bacterial Membrane and Full Virulence In Vivo

ABSTRACT Pseudomonas aeruginosa is responsible for high-morbidity infections of cystic fibrosis patients and is a major agent of nosocomial infections. One of its most potent virulence factors is a type III secretion system (T3SS) that injects toxins directly into the host cell cytoplasm. ExsB, a lipoprotein localized in the bacterial outer membrane, is one of the components of this machinery, of which the function remained elusive until now. The localization of the exsB gene within the exsCEBA regulatory gene operon suggested an implication in the T3SS regulation, while its similarity with yscW from Yersinia spp. argued in favor of a role in machinery assembly. The present work shows that ExsB is necessary for full in vivo virulence of P. aeruginosa. Furthermore, the requirement of ExsB for optimal T3SS assembly and activity is demonstrated using eukaryotic cell infection and in vitro assays. In particular, ExsB promotes the assembly of the T3SS secretin in the bacterial outer membrane, highlighting the molecular role of ExsB as a pilotin. This involvement in the regulation of the T3S apparatus assembly may explain the localization of the ExsB-encoding gene within the regulatory gene operon.
Lactobacillus plantarum 299v reduces colonisation of Clostridium difficile in critically ill patients treated with antibiotics

Background: The incidence of Clostridium difficile‐associated disease (CDAD) in hospitalised patients is increasing. Critically ill patients are often treated with antibiotics and are at a high risk of developing CDAD. Lactobacillus plantarum 299v (Lp299v) has been found to reduce recurrence of CDAD. We investigated intensive care unit (ICU) patients with respect to the impact of Lp299v on C. difficile colonisation and on gut permeability and parameters of inflammation and infection in that context.
Early mortality among adults accessing a community-based antiretroviral service in South Africa: implications for programme design

Objectives:To determine rates, risk factors and causes of death among patients accessing a community-based antiretroviral treatment (ART) programme both prior to and following initiation of treatment. Methods:All in-programme deaths were ascertained between September 2002 and March 2005 among treatment-naive patients enrolled into a prospective community-based ART cohort in Cape Town, South Africa. Results:Of 712 patients (median CD4 cell count, 94 cells/μl), 578 (81%) started triple ART a median of 29 days after enrolment. 68 (9.5%) patients died during 563 person-years of observation. The high pretreatment mortality rate of 35.6 deaths/100 person-years [95% confidence interval (CI), 23.0–55.1) decreased to 2.5/100 person-years (95% CI, 0.9–6.6) at 1 year among those who received ART. However, within the first 90 days from enrolment, 29 of 44 (66%) deaths occurred among patients awaiting ART; these would not be identified by an on-treatment analysis. Multivariate analysis showed that risk of death (both pre-treatment and on-treatment) was independently associated with baseline CD4 cell count and World Health Organization (WHO) clinical stage; stage 4 disease was the strongest risk factor. Major attributed causes of death were wasting syndrome, tuberculosis, acute bacterial infections, malignancy and immune reconstitution disease. Conclusions:Most early in-programme deaths occurred among patients with advanced immunodeficiency but who had not yet started ART. Programme evaluation using on-treatment analyses greatly underestimated early mortality. This mortality would be reduced by minimizing unnecessary in-programme delays in treatment initiation and by starting ART before development of WHO stage 4 disease.