Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural identification by differential mass spectrometry as a criterion for selecting the best quantum chemical calculation of formation enthalpy for tetrachlorinated biphenyls.

RATIONALE The assignment of correct structures for isomers with similar mass spectra (e.g. polyhalogenated aromatic compounds) is not always successful when spectral libraries alone are employed or, even worse, when the compounds are not present in commercial spectral libraries. METHODS We present a computational method based on differential mass spectrometry (Diff-MS) for the validation of formation enthalpy (Δ(f)H) series calculated using quantum chemistry for the fragments produced in electron ionization (EI)-MS. The method simulates the chemical structure identification (CSI) of isomers with similar mass spectra using differential mass spectra and Δ(f)H series. The best Δ(f)H values were those from which the correct structures could be derived. RESULTS We have used six tetrachlorinated biphenyl isomers (TeCBs 44, 46, 52, 66, 74, 77). Their EI mass spectra were acquired at 70 eV and, for the principal ions, five series of Δ(f) H values were computed by the semi-empirical methods, AM1, MINDO3, MNDO, PM3, and RM1. The generation of differential mass spectra and the correlation with the Δ(f)H series for the calculation of probabilities from the list of structural assignments were carried out with the ordering algorithm (ORD) of the CSI-Diff-MS Data Analysis 3.1. 1 program. CONCLUSIONS Intelligent software, used for structural elucidation based on MS and QCC, was employed to select the best values of the formation enthalpies of TeCBs. The advantages and disadvantages of the semi-empirical methods for the calculation of Δ(f)H values for different TeCB ions are critically presented. The best semi-empirical methods were RM1, AM1 and MINDO3, which can be used to calculate the Δ(f)H database necessary to identify TeCB isomers. This approach allowed the correct assignment of structures for isomers with very similar mass spectra and demonstrated the reliability of the correlation between differential mass spectra and the formation enthalpies of the fragment ions.
Meeting the decision-making preferences of patients with breast cancer in oncology consultations: impact on decision-related outcomes.

PURPOSE To investigate how involvement preferences of patients with breast cancer change during the treatment decision-making process and determine the impact of meeting patients' expectations on decision-making outcomes. PATIENTS AND METHODS Participants were 683 patients with breast cancer from 62 oncologists in five different countries recruited to an International Breast Cancer Study Group (IBCSG 33-03) project. Questionnaires elicited patients' pre- and postconsultation preferences for involvement in treatment decision making and whether these were met or not. Decision-related outcomes were assessed postconsultation. RESULTS Before the consultation, most patients preferred shared or patient-directed treatment decision making. After the consultation, 43% of patients' preferences changed, and most shifted toward patient-directed decisions. The actual postconsultation decision was more likely to be made according to postconsultation rather than preconsultation preferences. Compared with patients who were less involved than they had hoped to be, patients who were as involved as they had hoped to be or were even more involved in decision making had significantly better decision-related outcomes. This was true regardless of whether preference change occurred. CONCLUSION Many patients with early-stage breast cancer have treatment options and approach treatment decisions with a desire for decisional control, which may increase after their consultation. Patients' ultimate involvement preferences were more likely to be consistent with the way the decision was actually made, suggesting that patients need to feel concordance between their preference and the actual decision. Patients who directed decisions, even if more than they hoped for, fared better on all decision-related outcomes. These results emphasize the need for oncologists to endorse and facilitate patient participation in treatment decision making.
The rifampicin‐inducible genes srn6 from F and pnd from R483 are regulated by antisense RNAs and mediate plasmid maintenance by kiiling of plasmid‐free segregants

The gene systems srnB of plasmid F and pnd of plasmid R483 were discovered because of their induction by rifampicin. Induction caused membrane damage, RNase I influx, degradation of stable RNA and, consequently, cell killing. We show here that the srnB and pnd systems mediate efficient stabilization of a mini‐R1 test‐plasmid. We also show that the killer genes srnB′ and pndA are regulated by antisense RNAs, and that the srnC‐ and pndB‐encoded antisense RNAs, denoted SrnC‐ and PndB‐RNAs, are unstable molecules of approximately 60 nucleotides. The srnB and pndA mRNAs were found to be very stable. The differential decay rates of the inhibitory antisense RNAs and the killer‐gene‐encoding mRNAs explain the induction of these gene systems by rifampicin. Furthermore, the observed plasmid‐stabilization phenotype associated with the srnB and pnd systems is a consequence of this differential RNA decay: the newborn plasmid‐free cells inherit the stable mRNAs, which, after decay of the unstable antisense RNAs, are translated Into killer proteins, thus leading to selective killing of the plasmid‐free segregants. Thus our observations lead us to conclude that the F srnB and R483 pnd systems are phenotypically indistinguishable from the R1 hok/sok system, despite a 50% dissimilarity at the level of DNA sequence.
Deformation of polycrystalline MgO at pressures of the lower mantle

[1] Room temperature investigations on the shear strength, elastic moduli, elastic anisotropy, and deformation mechanisms of MgO (periclase) are performed in situ up to pressures of 47 GPa using radial X-ray diffraction and the diamond anvil cell. The calculated elastic moduli are in agreement with previous Brillouin spectroscopy studies. The uniaxial stress component in the polycrystalline MgO sample is found to increase rapidly to 8.5(+/-1) GPa at a pressure of 10(+/-1) GPa in all experiments. Under axial compression, a strong cube texture develops which was recorded in situ. It is probable that the preferred orientation of MgO is due to deformation by slip. A comparison between the experimental textures and results from polycrystal plasticity suggest that the {110} [1 (1) over bar0] is the only significantly active slip system under very high confining pressure at room temperature. These data demonstrate the feasibility of analyzing elastic moduli, shear strength, and deformation mechanisms under pressures relevant for the Earth's lower mantle. Implications for the anisotropy and rheology of the lower mantle are discussed.
Responses of Soil Fungal Populations and Communities to the Thinning of Cryptomeria Japonica Forests

Forest management activities, such as tree thinning, alter forest ecology, including key components of forest ecosystems, including fungal communities. In the present study, we investigate the effects of forest thinning intensity on the populations and structures of fungal soil communities in the Cryptomeria japonica forests of central Taiwan as well as the dynamics of soil fungi communities in these forests after a thinning disturbance. Although the populations of soil fungi significantly increased in the first 6 months after thinning, these increases had subsided by 9 months. This pulse was attributed to a transient increase in the populations of rapid colonizers. A multiple regression analysis positively correlated fungal populations with organic matter content and cellulase activity. Thinning initially provided large amounts of fresh leaves and roots as nutrient-rich substrates for soil fungi. Denaturing gradient gel electrophoresis (DGGE) profiles indicated that soil fungal communities significantly differed among plots with 0% (control), 25%, and 50% tree thinning in the first 21 months post-thinning, with no significant differences being observed after 21 months. The fungal communities of these forest soils also changed with the seasons, and an interactive relationship was detected between seasons and treatments. Seasonal variations in fungal communities were the most pronounced after 50% tree thinning. The results of the present study demonstrate that the soil fungi of Taiwanese C. japonica forests are very sensitive to thinning disturbances, but recover stability after a relatively short period of time.
Differential Responses to a Visual Self-Motion Signal in Human Medial Cortical Regions Revealed by Wide-View Stimulation

Vision is important for estimating self-motion, which is thought to involve optic-flow processing. Here, we investigated the fMRI response profiles in visual area V6, the precuneus motion area (PcM), and the cingulate sulcus visual area (CSv)—three medial brain regions recently shown to be sensitive to optic-flow. We used wide-view stereoscopic stimulation to induce robust self-motion processing. Stimuli included static, randomly moving, and coherently moving dots (simulating forward self-motion). We varied the stimulus size and the presence of stereoscopic information. A combination of univariate and multi-voxel pattern analyses (MVPA) revealed that fMRI responses in the three regions differed from each other. The univariate analysis identified optic-flow selectivity and an effect of stimulus size in V6, PcM, and CSv, among which only CSv showed a significantly lower response to random motion stimuli compared with static conditions. Furthermore, MVPA revealed an optic-flow specific multi-voxel pattern in the PcM and CSv, where the discrimination of coherent motion from both random motion and static conditions showed above-chance prediction accuracy, but that of random motion from static conditions did not. Additionally, while area V6 successfully classified different stimulus sizes regardless of motion pattern, this classification was only partial in PcM and was absent in CSv. This may reflect the known retinotopic representation in V6 and the absence of such clear visuospatial representation in CSv. We also found significant correlations between the strength of subjective self-motion and univariate activation in all examined regions except for primary visual cortex (V1). This neuro-perceptual correlation was significantly higher for V6, PcM, and CSv when compared with V1, and higher for CSv when compared with the visual motion area hMT+. Our convergent results suggest the significant involvement of CSv in self-motion processing, which may give rise to its percept.
Functional mastery of percussive technology in nut-cracking and stone-flaking actions: experimental comparison and implications for the evolution of the human brain

Various authors have suggested behavioural similarities between tool use in early hominins and chimpanzee nut cracking, where nut cracking might be interpreted as a precursor of more complex stone flaking. In this paper, we bring together and review two separate strands of research on chimpanzee and human tool use and cognitive abilities. Firstly, and in the greatest detail, we review our recent experimental work on behavioural organization and skill acquisition in nut-cracking and stone-knapping tasks, highlighting similarities and differences between the two tasks that may be informative for the interpretation of stone tools in the early archaeological record. Secondly, and more briefly, we outline a model of the comparative neuropsychology of primate tool use and discuss recent descriptive anatomical and statistical analyses of anthropoid primate brain evolution, focusing on cortico-cerebellar systems. By juxtaposing these two strands of research, we are able to identify unsolved problems that can usefully be addressed by future research in each of these two research areas.
Measuring Turnover Intention: A Study of IT Professionals in Pakistan

IT firms in Pakistan have witnessed high turnover during the past years, but no serious efforts have been made to find out the factors causing this. The focus of this study was on three independent variables namely job satisfaction, organizational commitment and perceived alternative job opportunities, that are thought to be associated with turnover intentions. The findings revealed that job satisfaction and organizational commitment had negative effect on turnover intentions, whereas perceived alternative job opportunities had significant positive correlation with turnover intentions and is the major factor associated with turnover intention among IT Professionals in Pakistan. Implications for managers are also discussed.
Genetic variability and heritability of grain yield components and grain mineral concentration in India's pearl millet (Pennisetum glaucum (L) R. Br.) accessions

Pearl millet ( Pennisetum glaucum (L.) R. Br. ) is an important cereal in semi-arid tropics in Africa and India. Conventionally, millet has good amounts of grain minerals compared to other cereals. Estimation of genetic parameters would be useful in developing appropriate breeding and selection strategies. The present study was conducted to evaluate the local pearl millet accessions to assess the magnitude of variability and to understand the heritable component of variation present in the yield and nutritional characters. A field trial was laid under the complete randomized block design (RCBD) with three replications; observation were recorded on eight morphological and seven nutritional characters (as detailed in material and methods) including anti-nutritional properties such as phytate content among 61 genotypes collected from millet collection. The phenotypic co-efficient of variation (PCV) was greater than genotypic co-efficient of variation (GCV) for all the characters studied; this shows the influence of environmental factors on the characters. The phosphorus content had expressed the highest phenotypic and genotypic variances (845.30 and 772.08, respectively). The magnitudes of phenotypic and genotypic variances were low for the 100 grain weight (0.001 for both phenotypic and genotypic variance). High estimates of genetic co-efficient of variation, heritability and genetic advance were exhibited by iron and crude fat content. Heritability is a measure of possible genetic advancement under selection. High heritability was observed for all the traits under study except seed weight which had moderate heritability. High value of heritability coupled with high genetic advance as per cent of mean were recorded for number of productive tillers, crude protein, crude fat, phytate, phosphorus, calcium, iron and zinc content, indicating the important role of additive gene action for the expression of these characters. Therefore, selection based on these characters could bring about desired improvement in yield as well as nutritional quality of pearl millet cultivars. Key words: Genetic-advance, Heritability, Variability, Micronutrients, Malnutrition
IL-17 Is a Critical Component of Vaccine-Induced Protection against Lung Infection by Lipopolysaccharide-Heterologous Strains of Pseudomonas aeruginosa1

In a murine model of acute fatal pneumonia, we previously showed that nasal immunization with a live-attenuated aroA deletant of Pseudomonas aeruginosa strain PAO1 elicited LPS serogroup-specific protection, indicating that opsonic Ab to the LPS O Ag was the most important immune effector. Because P. aeruginosa strain PA14 possesses additional virulence factors, we hypothesized that a live-attenuated vaccine based on PA14 might elicit a broader array of immune effectors. Thus, an aroA deletant of PA14, denoted PA14ΔaroA, was constructed. PA14ΔaroA-immunized mice were protected against lethal pneumonia caused not only by the parental strain but also by cytotoxic variants of the O Ag-heterologous P. aeruginosa strains PAO1 and PAO6a,d. Remarkably, serum from PA14ΔaroA-immunized mice had very low levels of opsonic activity against strain PAO1 and could not passively transfer protection, suggesting that an antibody-independent mechanism was needed for the observed cross-serogroup protection. Compared with control mice, PA14ΔaroA-immunized mice had more rapid recruitment of neutrophils to the airways early after challenge. T cells isolated from P. aeruginosa ΔaroA-immunized mice proliferated and produced IL-17 in high quantities after coculture with gentamicin-killed P. aeruginosa. Six hours following challenge, PA14ΔaroA-immunized mice had significantly higher levels of IL-17 in bronchoalveolar lavage fluid compared with unimmunized, Escherichia coli-immunized, or PAO1ΔaroA-immunized mice. Antibody-mediated depletion of IL-17 before challenge or absence of the IL-17 receptor abrogated the PA14ΔaroA vaccine’s protection against lethal pneumonia. These data show that IL-17 plays a critical role in antibody-independent vaccine-induced protection against LPS-heterologous strains of P. aeruginosa in the lung.
Early (E12) cortical progenitors can change their fate upon heterotopic transplantation

To help understand how the cortical map is set up during the early stages of corticogenesis, we have examined the developmental fate of embryonic day (E) 12 cortical progenitors in the rat. We have analysed the pattern of thalamic connections and cytoarchitectonic organization developed by progenitor cells removed at E12 from the presumptive parietal or occipital cortex and grafted into the parietal cortex of newborn hosts. Occipital progenitors grafted into the parietal cortex differentiated into neurons that developed reciprocal connections with the ventrobasal complex of the host thalamus. They could also form barrel‐like structures, within which axons of the ventrobasal complex were distributed in dense patches. Some of these barrel‐like structures were arranged in rows. Moreover, these progenitors failed to develop characteristic traits of occipital cortex cells as they did not establish connections with the dorsal lateral geniculate nucleus. We propose that cortical progenitors are not committed at E12 and, upon heterotopic transplantation, have the capacity to respond to local cues and to subsequently differentiate and maintain major phenotypic characteristics of neurons in their new environment. Only early progenitors are multipotent. By E13/E14, indeed, most cortical cells become irreversibly committed and upon heterotopic transplantation differentiate neurons with phenotypic characteristics of their cortical site of origin (Pinaudeau et al., 2000, Eur. J. Neurosci., 12, 2486–2496).
Genetic Structures of Copy Number Variants Revealed by Genotyping Single Sperm

Background Copy number variants (CNVs) occupy a significant portion of the human genome and may have important roles in meiotic recombination, human genome evolution and gene expression. Many genetic diseases may be underlain by CNVs. However, because of the presence of their multiple copies, variability in copy numbers and the diploidy of the human genome, detailed genetic structure of CNVs cannot be readily studied by available techniques. Methodology/Principal Findings Single sperm samples were used as the primary subjects for the study so that CNV haplotypes in the sperm donors could be studied individually. Forty-eight CNVs characterized in a previous study were analyzed using a microarray-based high-throughput genotyping method after multiplex amplification. Seventeen single nucleotide polymorphisms (SNPs) were also included as controls. Two single-base variants, either allelic or paralogous, could be discriminated for all markers. Microarray data were used to resolve SNP alleles and CNV haplotypes, to quantitatively assess the numbers and compositions of the paralogous segments in each CNV haplotype. Conclusions/Significance This is the first study of the genetic structure of CNVs on a large scale. Resulting information may help understand evolution of the human genome, gain insight into many genetic processes, and discriminate between CNVs and SNPs. The highly sensitive high-throughput experimental system with haploid sperm samples as subjects may be used to facilitate detailed large-scale CNV analysis.
Eribulin in heavily pretreated metastatic breast cancer: A tertiary care center experience from India.

INTRODUCTION Heavily pretreated metastatic breast cancer (MBC) remains a major therapeutic challenge with limited treatment options this. Eribulin, an anti-microtubule agent, has been recently approved for this indication. There are sparse data from the Asian region for eribulin and merits exploration. MATERIALS AND METHODS This was a single institution retrospective analysis of MBC patients treated with eribulin from 2013 to 2014. These patients had received at least 2 lines of prior therapy for metastatic disease. Patients received standard doses of eribulin and were monitored for toxicity and responses. RESULTS Eighteen patients were included in this analysis. They had received a median of 6 lines of therapy previously (including adjuvant treatment) and had significant visceral involvement (median 3 organs). A median of 4 cycles of eribulin was delivered. There were no complete responses; partial responses were seen in 33% (6/18), stable disease status in 28% (5/18) patients, and progressive disease on eribulin in 39% (7/18) patients. The median progression-free survival was 15 weeks (3.5 months), and median overall survival was 27 weeks (6.2 months). Significant Grade 3/4 toxicities seen included peripheral neuropathy in 28% (5/18) and neutropenia in 28% (5/18) of patients while dose reductions were required in 22% (4/18) of patients. CONCLUSION Eribulin offers a viable, well-tolerated regimen that provides meaningful clinical benefit in Indian patients with MBC.
Using red light for in situ observations of deep-sea fishes

Observations of animals in the deep ocean typically require the use of bright lights that can damage eyes and disrupt normal behaviors. Although the use of infrared light is an effective means of unobtrusive observation on land, it is far less effective in the ocean where long wavelength light is rapidly attenuated by seawater. Here we describe in situ observations of the behavior of the sablefish, Anoplopoma fimbria, around a baited site under different lighting conditions. Fish were observed with low-light-level imaging that had adequate sensitivity to compensate for the attenuation losses associated with the use of long wavelength light in water. ROV-based experiments compared the number of sablefish seen around bait, illuminated alternately with red vs. white light. Significantly more fish were seen under red light than white light with the average number of sablefish observed per 10min viewing interval under red light being 38.9 (718.5 SD) compared to 7.5 (77.1 SD) under white light. Under both red and white light sablefish spent only brief periods in the illumination field (10.5 s [78.7 SD] under red light and 6.6 s [78.7 SD] under white light). It appeared that sablefish were responding to competing drives of attraction to the bait and avoidance of the lights and that the avoidance was greater for white light than for red light. Observations were also made with the newly developed deep-sea observatory, Eye-in-the-Sea, using long wavelength LED illumination. The onset of LED illumination did not generally produce a startle response from fish around the bait, and in some cases invoked no response at all. However, in the majority of cases the fish moved out of the circle of red-light illumination during the 7.5 s recording period, indicating that the light was detectable and aversive to these fish. This was true with both 660 and 680 nm LED illuminators. We conclude that while a sharper short-wavelength cutoff of the illumination source is required to achieve truly unobtrusive observation, red light is nonetheless significantly less disruptive than white light for observing deepsea fish behavior, and can provide adequate illumination when used in combination with image-intensified cameras. r 2005 Elsevier Ltd. All rights reserved.