Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrating animal temperament within ecology and evolution

Temperament describes the idea that individual behavioural differences are repeatable over time and across situations. This common phenomenon covers numerous traits, such as aggressiveness, avoidance of novelty, willingness to take risks, exploration, and sociality. The study of temperament is central to animal psychology, behavioural genetics, pharmacology, and animal husbandry, but relatively few studies have examined the ecology and evolution of temperament traits. This situation is surprising, given that temperament is likely to exert an important influence on many aspects of animal ecology and evolution, and that individual variation in temperament appears to be pervasive amongst animal species. Possible explanations for this neglect of temperament include a perceived irrelevance, an insufficient understanding of the link between temperament traits and fitness, and a lack of coherence in terminology with similar traits often given different names, or different traits given the same name. We propose that temperament can and should be studied within an evolutionary ecology framework and provide a terminology that could be used as a working tool for ecological studies of temperament. Our terminology includes five major temperament trait categories: shyness‐boldness, exploration‐avoidance, activity, sociability and aggressiveness. This terminology does not make inferences regarding underlying dispositions or psychological processes, which may have restrained ecologists and evolutionary biologists from working on these traits. We present extensive literature reviews that demonstrate that temperament traits are heritable, and linked to fitness and to several other traits of importance to ecology and evolution. Furthermore, we describe ecologically relevant measurement methods and point to several ecological and evolutionary topics that would benefit from considering temperament, such as phenotypic plasticity, conservation biology, population sampling, and invasion biology.
Induction of Broadly Neutralizing H1N1 Influenza Antibodies by Vaccination

Toward a General Flu Vaccination Current seasonal influenza virus vaccines are targeted against specific viral strains and do not provide broad, durable protection. Seasonal influenza vaccines induce protective antibody responses against regions of viral hemagglutinin (HA) that rapidly mutate so that very soon, the virus becomes resistant to vaccination. Conserved regions of HA also exist, and a major goal of influenza vaccine development is to design a vaccine that elicits antibodies against the conserved regions so that protection against a wide range of viral strains is achieved. Wei et al. (p. 1060, published online 15 July; see the Perspective by Doms) show that a combined HA DNA prime, followed by boosting with a seasonal vaccine, elicits broadly cross-reactive neutralizing antibody responses in mice, ferrets, and nonhuman primates, which were protective in mice and ferrets against heterologous influenza challenge. The neutralizing antibodies were directed against the conserved HA stem region, which indicates the possibility that a more broadly protective vaccine against influenza could be developed. An influenza virus vaccine elicits a broadly neutralizing, cross-protective antibody response in mice, ferrets, and nonhuman primates. The rapid dissemination of the 2009 pandemic influenza virus underscores the need for universal influenza vaccines that elicit protective immunity to diverse viral strains. Here, we show that vaccination with plasmid DNA encoding H1N1 influenza hemagglutinin (HA) and boosting with seasonal vaccine or replication-defective adenovirus 5 vector encoding HA stimulated the production of broadly neutralizing influenza antibodies. This prime/boost combination increased the neutralization of diverse H1N1 strains dating from 1934 to 2007 as compared to either component alone and conferred protection against divergent H1N1 viruses in mice and ferrets. These antibodies were directed to the conserved stem region of HA and were also elicited in nonhuman primates. Cross-neutralization of H1N1 subtypes elicited by this approach provides a basis for the development of a universal influenza vaccine for humans.
Glial and neuronal proteins in serum predict outcome after severe traumatic brain injury

Objective: To study the ability of glial (glial fibrillary acidic protein [GFAP] and S100b) and neuronal (neuron specific enolase [NSE]) protein levels in peripheral blood to predict outcome after severe traumatic brain injury. Methods: Eighty-five patients with severe traumatic brain injury (admission Glasgow Coma Score [GCS] ≤ 8) were included. Blood samples taken at the time of hospital admission were analyzed for S100b, GFAP, and NSE. Data collected included demographic and clinical variables. Outcome was assessed using the Glasgow Outcome Scale (GOS) at 6 months post injury. Results: The median serum levels of S100b, GFAP, and NSE were raised 18.3 fold (S100b), 4.6 fold (GFAP), and twofold (NSE) compared to normal reference values. S100b, GFAP, and NSE serum levels correlated significantly with the injury severity score and CT findings but not with age, sex, or GCS. S100b, GFAP, and NSE levels were significantly higher in patients who died or had a poor outcome 6 months post injury than in those who were alive or had good outcome. S100b level >1.13 μg/L was the strongest predictor of death with 100% discrimination, but GFAP (>1.5 μg/L) and NSE (>21.7 μg/L) levels also strongly predicted death (adjusted odds ratios 5.82 [for GFAP] and 3.91 [for NSE]). S100b, GFAP, and NSE all strongly predicted poor outcome (adjusted odds ratios 5.12 [S100b], 8.82 [GFAP], and 3.95 [NSE]). Conclusions: These results suggest that determination of serum levels of glial and neuronal proteins may add to the clinical assessment of the primary damage and prediction of outcome after severe traumatic brain injury.
Response characteristics and receptive field widths of on‐bipolar cells in the mouse retina

1 Voltage‐clamp and current‐clamp recordings were made from bipolar cells in dark‐adapted mouse retinal slices. Light‐evoked responses fell into three groups corresponding to the rod bipolar cells, on‐cone bipolar cells and off‐cone bipolar cells. The morphology of the recorded cells confirmed this classification. 2 Intensity‐response relations were well fitted by a Michaelis saturation function with Hill coefficients of 1.15 ± 0.11 (n= 6) for rod bipolar cells and 2.33 ± 0.06 (n= 4) for cone inputs onto on‐cone bipolar cells. 3 In the absence of antagonists for GABA or glycine receptors, light‐evoked synaptic currents for all cells displayed linear current‐voltage relations that reversed near 0 mV, indicating that very little inhibition was activated under dark‐adapted recording conditions. Saturating light stimuli evoked conductances of 0.81 ± 0.56 nS (n= 4) in rod bipolar cells and 1.1 ± 0.8 nS (n= 4) in on‐cone bipolar cells. 4 Receptive field widths were estimated by flashing a vertical light bar at various locations along the slice. Rod and on‐cone bipolar cells had receptive field widths of 67 ± 16 μm (n= 6) and 43 ± 7 μm (n= 5), respectively. The maximum spatial resolution of an array of such cone bipolar cells was estimated to be 0.3 cycles deg−1, compared with a maximum resolution of 0.5 cycles deg−1 obtained from behavioural studies in mice. Our results suggest that this limit to spatial resolution could be imposed early in the visual system by the size of the bipolar cell receptive fields.
The differentiation and survival of murine neurons in vitro is promoted by soluble factors produced by an astrocytic cell line

The influence of accessory cells on the generation of neurons and neuronal survival has been studied in vitro using an immortalised, cloned cell line, Ast‐1, which has many of the functional and phenotypic characteristics of cells of the astrocytic lineage. It was found that monolayers of Ast‐1 cells were equivalent to monolayers of primary astrocytes in their ability to promote the generation of neurofilament positive neurons from neuroepithelial cells obtained from embryonic day 10 (E10) mice; and both were superior to NIH 3T3 cells. Ast‐1 cell monolayers were also found to provide a suitable substrate for the prolonged survival (at least 3 days in vitro) of neurofilament positive neurons obtained from E17 mice, whereas neurons plated onto NIH 3T3 cells were all dead after 2 days. Medium conditioned by Ast‐1 cells displayed similar biological activities to that of the monolayers: It increased the number of neurons generated from the E10 neuroepithelial cells, whether they were plated directly onto glass coverslips or onto monolayers of NIH 3T3 cells; and it increased the survival of E17 neurons plated directly onto glass coverslips. In addition, the Ast‐1 conditioned medium was shown to promote the survival of the neuroepithelial cells. These results confirm that one of the mechanisms by which astrocytes or their precursors may regulate neuronal development is by secreting soluble growth factors, as has been previously documented in the case of fibroblast growth factor (FGF) (Hatten et al., 1988; Drago et al., 1991a). However, it appears in this system that FGF is not responsible for the demonstrated biological activities, and the Ast‐1 action appears to be mediated by putatively novel factor(s). © 1993 Wiley‐Liss, Inc.
Subunit compositions and catalytic properties of proteasomes from developmental temperature- sensitive mutants of Drosophila melanogaster.

Two dominant temperature-sensitive (DTS) Drosophila mutants are missense mutations of proteasome genes encoding beta-type subunits beta6/C5 (DTS5) and beta2/Z (DTS7). At nonpermissive temperature (29 degrees C), heterozygotes (DTS5/+ and DTS7/+) develop normally until metamorphosis; pupae fail to mature and die before eclosion. Proteasomes were purified from wild-type (WT) and heterozygous adult flies raised at permissive temperature (25 degrees C). Two-dimensional gel electrophoresis separated at least 28 proteins, 13 of which were identified with monospecific antibodies to alpha6/C2 (five species), alpha2/C3 (three species), alpha7/C8 (three species), alpha5/zeta, and beta1/Y subunits. Both quantitative and qualitative differences were observed between WT and DTS/+ proteasomes, with DTS5/+ deviating more from WT than DTS7/+ proteasomes. In DTS5/+ there was a shift to more acidic species of C2 and C3 and a shift to less acidic species of 32-kDa subunits (#3-#7) recognized by an anti-alpha subunit monoclonal antibody (MCP222) and were losses of two 32-kDa subunits (#2 and #3), decreases in Y (25 kDa; 2-fold) and 31-kDa (#9; 2-fold) subunits, and increases in 52-kDa (#1; 1.9-fold) and 24-kDa (#13; 2.3-fold) subunits. In DTS7/+ there was a less pronounced shift to acidic species of C3 and no pI shift in C2 species and subunits #3-#7 and were decreases in #9 (2.5-fold) and #14 (3-fold) and a loss of #2. The three C8 species were similar between WT, DTS5/+, and DTS7/+ proteasomes. Qualitatively, the most dramatic difference was the appearance of a new 24-kDa subunit (#16) in DTS/+ preparations, with about a 14-fold greater amount of #16 in DTS7/+ than in DTS5/+ proteasomes. Catalytically, WT and DTS/+ proteasomes had similar peptidase activities, although the DTS/+ proteasomes were slightly more sensitive to SDS and elevated temperatures in vitro. The incorporation of DTS subunits apparently altered proteasome assembly and/or processing at permissive temperature with little effect on catalytic activities. These data suggest that at nonpermissive temperature, assembly/processing is more severely affected, producing DTS-containing complexes that lack functions essential for cellular proliferation and differentiation at metamorphosis.
Synergy between Auraptene, Ionizing Radiation, and Anticancer Drugs in Colon Adenocarcinoma Cells

Colorectal cancer is a growing health concern with increasing mortality rates, and resistance to anticancer drugs and radiotherapy is a serious drawback in its treatment. Auraptene is a natural prenyloxycoumarin with valuable anticancer effects. The aim of current study was to determine the synergy between auraptene, ionizing radiation, and chemotherapeutic drugs in colon adenocarcinoma cells for the first time. To do so, HT29 cells were treated with combination of auraptene + cisplatin, + doxorubicin, or + vincristine. Furthermore, cells were pretreated with nontoxic auraptene and then exposed to various doses of X‐radiation. Assessment of cell viability not only indicated significant (p < 0.05) synergic effects of auraptene and anticancer agents, also revealed more significant (p < 0.01) increase in the toxicity of applied radiations in auraptene pretreated cells. Interesting synergy between auraptene and radiotherapy was then confirmed by morphological alterations, DAPI staining, and flow cytometric analysis of the cell cycle. Moreover, real‐time reverse transcription polymerase chain reaction analysis indicated significant (p < 0.01) overexpression of p21, but not GATA6, in auraptene pretreated cells after radiotherapy, and also significant (p < 0.01) down regulation of CD44 and ALDH1 by auraptene. According to present results, auraptene could be considered as an effective natural coumarin to improve the outcome of current chemoradiotherapy options. Copyright © 2017 John Wiley & Sons, Ltd.
Learning to Teach Science through Inquiry: Experiences of Preservice Teachers.

This investigation explored the experiences of a cohort of preservice science teachers learning to teach science in their student teaching placements. Participants included seven preservice biology teachers enrolled in a one-year Master of Arts in Teaching program. One part of this program was to learn different ways to teach science, with one aspect focusing on inquiry instruction. Data sources included three open-ended surveys and two semi-structured interviews. A constant comparative approach was used for data analysis to understand the experiences of the preservice teachers during their student teaching placements. Results indicate that at the start of their student teaching placements, participants held favorable views of inquiry instruction and anticipated its use in the classrooms. However, opportunities to observe these methods in their mentor teacher’s classrooms were limited. This investigation reveals that while reform documents, as well as the majority of science educators, emphasize inquiry instruction, preservice teachers do not have the opportunities to practice this type of instruction during their student teaching placements. The successes and limitations of inquiry that did occur during their student teaching placements, as well as reasons preventing the use of inquiry, are explored.
Das kolorektale Karzinom (KRK) beim jungen Patienten – ist das Alter ein prognostischer Faktor?

Zusammenfassung Hintergrund: Die Prognose der Patienten, die in jungen Jahren an einem kolorektalen Karzinom (KRK) erkranken, wird in der Literatur kontrovers diskutiert. Ziel der vorliegenden Arbeit war es, mögliche Unterschiede zwischen jüngeren (< 40 Jahre) und älteren (≥ 40 Jahre) Patienten mit KRK zu identifizieren. Patienten und Methoden: Die Daten von 51 jüngeren (< 40 Jahren) und 2122 älteren Patienten (≥ 40 Jahren) wurden prospektiv gesammelt und retrospektiv im Hinblick auf klinische Parameter, Therapie und Prognose verglichen. Patienten mit KRK aufgrund einer familiären adenomatösen Polyposis, Colitis ulcerosa oder Morbus Crohn wurden ausgeschlossen. Ergebnisse: Bei den jüngeren Patienten lagen signifikant häufiger muzinöse Adenokarzinome vor (p = 0,033). Bei der Verteilung der Geschlechter, der Lokalisation und dem Vorliegen eines Notfall- bzw. Elektiveingriffs fanden sich keine Unterschiede zwischen den Altersgruppen. Auch bezüglich der UICC-Stadienverteilung (UICC: Union internationale contre le cancer) und der Residualtumorklassifikation konnten keine signifikanten Unterschiede identifiziert werden. Eine postoperative (adjuvante/therapeutische oder palliative) Therapie wurde bei den jüngeren Patienten vor allem mit Kolonkarzinom signifikant häufiger durchgeführt (p = 0,001). Bei den jüngeren kurativ resezierten Patienten mit Kolonkarzinom fanden sich ein signifikant besseres beobachtetes (5-Jahres-Rate: 94 versus 76 %; p = 0,024) und krankheitsfreies Überleben (88 vs. 69 %; p = 0,013). Diese Tendenz führte sich bei den Patienten mit Rektumkarzinom fort (84 vs. 75 % und 72 vs. 65 %), ohne das Signifikanzniveau zu erreichen (p = 0,155 und 0,269). Unter Berücksichtigung der unterschiedlichen Lebenserwartung zeigte die Analyse des relativen Überlebens allenfalls geringe Unterschiede (Kolonkarzinom 5-Jahres-Rate: 94 vs. 89 %; Rektumkarzinom 84 vs. 84 %). Schlussfolgerung: Die generelle Annahme einer schlechteren Prognose jüngerer Patienten mit KRK konnte nicht bestätigt werden. Jüngere Patienten haben, pathohistologisch begründet, eine schlechtere Ausgangssituation. Aber diese wird durch den besseren Allgemeinzustand, weniger Vorerkrankungen, eine schnellere postoperative Rekonvaleszenz und eine zeitnah zur Operation in vollem Umfang erfolgte postoperative (adjuvante, therapeutische oder palliative) Therapie ausgeglichen. Daraus resultiert schließlich für jüngere Patienten ein besseres beobachtetes Überleben aber – unter Berücksichtigung der unterschiedlichen Lebenserwartung – kein Unterschied bezüglich des relativen Überlebens.
Aging of Tetrahedral Structure in a Lennard-Jones Glass 1

We study the aging of a glassy Lennard-Jones binary mixture with molecular dynamics simulations. We follow the evolution of the packing as a function of the system’s age tw, the time passed since the system is quenched to below its glass transition temperature. We focus on simple properties of all tetrahedra formed by the majority of particles. We find that both the averages and the distributions of the edge length of tetrahedra and of their standard deviation monotonically evolve over time: they age. Specifically the aging process decreases the irregularity of tetrahedra while loosening them up. This is in stark contrast with previous experiments on slightly charged hard-sphere colloidal suspension where tetrahedral geometry was found to be a poor indicator of age. Furthermore, we confirm that tetrahedral packings sample microscopic structure in a non-trivial way.
Pollution Characteristics of PM2.5 during a Typical Haze Episode in Xiamen, China

In this study, mass concentrations and chemical compositions of fine particles, mass concentrations of coarse particles, light extinction, and meteorological parameters in the atmosphere ofXiamenwere presented and analyzed to study the chemical and optical characteristics of a typical haze episode from Dec 25, 2010 to Jan 1, 2011. The major chemical compositions of PM2.5, such as water soluble inorganic ions (WSIIs), carbonaceous fractions (mainly composed of organic carbon (OC) and elemental carbon (EC)), and elements were determined. The results showed that with the typical haze episode process, the concentrations of PM2.5 mass, WSIIs, OC, EC, and TE first increased and then decreased. The average concentrations of PM2.5 mass in the stages of Before Haze, During Haze, and After Haze were (88.80 ± 19.97), (135.41 ± 36.20), and (96.35 ± 36.26) μg/m3, respectively. The corresponding average concentrations of secondary organic carbon (SOC) were 6.72, 8.18, and 10.39 μg/m3, accounting for 46.5%, 27.0%, and 61.0% of OC, respectively. S42- , NO3-, and NH4+ were three major WSIIs species, accounting for 31.4%, 26.0%, and 12.1% of total WSIIs. The major elements in PM2.5 were S, K, Fe, Zn, Pb, Ti, and Mn, covering 97.9% of the total elements, while the percentage of the other ten elements was only 2.1%. The average value of light extinction coefficients (bext) was 371.0 ±147.1 Mm-1 during the typical haze episode. The average percentage contributions to bext were 39.3% for organic mass, 19.9% for elemental carbon, 16.0% for ammonium sulfate, 13.0% for coarse mass, and 11.8% for ammonium nitrate.
Optical Fiber Ring Cavity Sensor for Label-Free DNA Detection

An outcladding sensitized label-free DNA biosensor is developed based on tilted fiber Bragg gratings. The biosensor, functionalized with peptide nucleic acid (PNA) probes, is based on a double tilted fiber Bragg grating that forms a modified Fabry-Perot core-cladding closed-loop cavity. Interference is set up between an injected guided mode and the reflected core mode and cladding modes created by the light scattered by the tilted gratings, leading to the generation of interference fringes within both these spectral notches. When the DNA binds to the PNA probes attached onto the fiber cladding, a refractive index change occurs at the cladding-PNA interface and the fringe visibility changes accordingly. Real-time spectral measurement results are reported, showing that a 10-nM DNA solution induces a 10% modulation of the corresponding fringes visibility. Cycling tests are performed for measuring and checking the repeatability of the sensor.
MODELING INDIVIDUAL DIFFERENCES AMONG WRITERS USING READERBENCH

The current study builds upon a previous study, which examined the degree to which the lexical properties of students’ essays could predict their vocabulary scores. We expand on this previous research by incorporating new natural language processing indices related to both the surface- and discourse-levels of students’ essays. Additionally, we investigate the degree to which these NLP indices can be used to account for variance in students’ reading comprehension skills. We calculated linguistic essay features using our framework, ReaderBench, which is an automated text analysis tools that calculates indices related to linguistic and rhetorical features of text. University students (n = 108) produced timed (25 minutes), argumentative essays, which were then analyzed by ReaderBench. Additionally, they completed the Gates-MacGinitie Vocabulary and Reading comprehension tests. The results of this study indicated that two indices were able to account for 32.4% of the variance in vocabulary scores and 31.6% of the variance in reading comprehension scores. Follow-up analyses revealed that these models further improved when only considering essays that contained multiple paragraph (R2 values = .61 and .49, respectively). Overall, the results of the current study suggest that natural language processing techniques can help to inform models of individual differences among student writers.
Microscale Distribution of Nitrification Activity in Sediment Determined with a Shielded Microsensor for Nitrate

Microprofiles of O2 and NO3- were measured simultaneously in freshwater sediment with microsensors which were completely free from electrical interference because of coaxial designs. Depth profiles of nitrification (NO3- production) and denitrification (NO3- consumption) were subsequently determined by computer simulation of the measured microprofiles. The nitrifying bacterial community responded very quickly to changes in environmental conditions, and new steady-state microprofiles of O2 and NO3- were usually approached within a few hours after perturbation. Nitrification started quickly after introduction of O2 in previously anoxic layers, suggesting prolonged survival of the nitrifiers during anaerobiosis. Changes in the availability of O2 and NH4+ greatly affected the nitrification profile, and there was a high rate of coupled nitrification-denitrification under conditions in which nitrification occurred right above the oxic-anoxic interface. Addition of C2H2 rapidly removed the NO3- peaks, indicating that NO3- production was due mainly to autotrophic nitrification.