Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing the isotopic composition of atmospheric ammonia emission sources using passive samplers and a combined oxidation-bacterial denitrifier approach.

RATIONALE Ammonia (NH3) emissions are a substantial source of nitrogen pollution to sensitive terrestrial, aquatic, and marine ecosystems and dependable quantification of NH3 sources is of growing importance due to recently observed increases in ammonium (NH4(+)) deposition rates. While determination of the nitrogen isotopic composition of NH3 (δ(15)N-NH3) can aid in the quantification of NH3 emission sources, existing methods have precluded a comprehensive assessment of δ(15)N-NH3 values from major emission sources. METHODS We report an approach for the δ(15)N-NH4(+) analysis of low concentration NH4(+) samples that couples the bromate oxidation of NH4(+) to NO2(-) and the microbial denitrifier method for δ(15)N-NO2(-) analysis. This approach reduces the required sample mass by 50-fold relative to standard elemental analysis (EA) procedures, is capable of high throughput, and eliminates toxic chemicals used in a prior method for the analysis of low concentration samples. Using this approach, we report a comprehensive inventory of δ(15)N-NH3 values from major emission sources (including livestock operations, marine sources, vehicles, fertilized cornfields) collected using passive sampling devices. RESULTS The δ(15)N-NH4(+) analysis approach developed has a standard deviation of ±0.7‰ and was used to analyze passively collected NH3 emissions with a wide range of ambient NH3 concentrations (0.2 to 165.6 µg/m(3)). The δ(15)N-NH3 values reveal that the NH3 emitted from volatilized livestock waste and fertilizer has relatively low δ(15)N values (-56 to -23‰), allowing it to be differentiated from NH3 emitted from fossil fuel sources that are characterized by relatively high δ(15)N values (-15 to +2‰). CONCLUSIONS The isotopic source signatures presented in this emission inventory can be used as an additional tool in identifying NH3 emission sources and tracing their transport across localized landscapes and regions. The insight into the transport of NH3 emissions provided by isotopic investigation is an important step in devising strategies to reduce future NH3 emissions, a mounting concern for air quality scientists, epidemiologists, and policy-makers.
Transcriptional Interference and Repression Modulate the Conjugative Ability of the Symbiotic Plasmid of Rhizobium etli

ABSTRACT Bacteria of the order Rhizobiales are able to establish nitrogen-fixing symbioses with legumes. Commonly, genes for symbiosis are harbored on large symbiotic plasmids. Although the transfer of symbiotic plasmids is commonly detected in nature, there are few experimentally characterized examples. In Rhizobium etli, the product of rctA inhibits the conjugation of the symbiotic plasmid by reducing the transcription of the virB operon. rctA is transcribed divergently from this operon, and its product is predicted to have a DNA binding domain. In the present study, using DNase I footprinting and binding assays, we demonstrated the specific binding of RctA to the virB operon promoter. A 9-bp motif in the spacer region of this promoter (the rctA binding motif box) and the presence of a functional −10 region were critical elements for RctA binding. Transcriptional fusion analyses revealed that the elimination of either element provoked a relief of RctA-mediated repression. These data support a model in which RctA inhibits the access of the RNA polymerase to the virB promoter. Interestingly, rctA expression levels were modulated by transcriptional interference from transcripts emanating from the virB promoter. This phenomenon adds another level of regulation for this system, thus revealing a novel mechanism of plasmid transfer regulation in the Rhizobiales.
Evolution of hard proteins in the sauropsid integument in relation to the cornification of skin derivatives in amniotes

Hard skin appendages in amniotes comprise scales, feathers and hairs. The cell organization of these appendages probably derived from the localization of specialized areas of dermal–epidermal interaction in the integument. The horny scales and the other derivatives were formed from large areas of dermal–epidermal interaction. The evolution of these skin appendages was characterized by the production of specific coiled‐coil keratins and associated proteins in the inter‐filament matrix. Unlike mammalian keratin‐associated proteins, those of sauropsids contain a double beta‐folded sequence of about 20 amino acids, known as the core‐box. The core‐box shows 60%–95% sequence identity with known reptilian and avian proteins. The core‐box determines the polymerization of these proteins into filaments indicated as beta‐keratin filaments. The nucleotide and derived amino acid sequences for these sauropsid keratin‐associated proteins are presented in conjunction with a hypothesis about their evolution in reptiles‐birds compared to mammalian keratin‐associated proteins. It is suggested that genes coding for ancestral glycine‐serine‐rich sequences of alpha‐keratins produced a new class of small matrix proteins. In sauropsids, matrix proteins may have originated after mutation and enrichment in proline, probably in a central region of the ancestral protein. This mutation gave rise to the core‐box, and other regions of the original protein evolved differently in the various reptilians orders. In lepidosaurians, two main groups, the high glycine proline and the high cysteine proline proteins, were formed. In archosaurians and chelonians two main groups later diversified into the high glycine proline tyrosine, non‐feather proteins, and into the glycine‐tyrosine‐poor group of feather proteins, which evolved in birds. The latter proteins were particularly suited for making the elongated barb/barbule cells of feathers. In therapsids‐mammals, mutations of the ancestral proteins formed the high glycine‐tyrosine or the high cysteine proteins but no core‐box was produced in the matrix proteins of the hard corneous material of mammalian derivatives.
Norms and usage in language history, 1600-1900 : a sociolinguistic and comparative perspective

1. Acknowledgements 2. The interplay of language norms and usage patterns. Comparing the history of Dutch, English, French and German (by Rutten, Gijsbert) 3. Dutch 4. Language norms and language use in seventeenth-century Dutch: Negation and the genitive (by Nobels, Judith) 5. Language norms and language use in eighteenth-century Dutch: Final n and the genitive (by Simons, Tanja) 6. Norms and usage in nineteenth-century Southern Dutch (by Vosters, Rik) 7. English 8. Norms and usage in seventeenth-century English (by Nevalainen, Terttu) 9. Eighteenth-century English normative grammars and their readers (by Tieken-Boon van Ostade, Ingrid) 10. Nineteenth-century English: Norms and usage (by Auer, Anita) 11. French 12. From l'usage to le bon usage and back: Norms and usage in seventeenth-century France (by Ayres-Bennett, Wendy) 13. Jacques-Louis Menetra and his experience of the langue d'oc (by Lodge, R. Anthony) 14. From local to supra-local: Hybridity in French written documents from the nineteenth century (by Martineau, France) 15. German 16. Language description, prescription and usage in seventeenth-century German (by McLelland, Nicola) 17. Standard German in the eighteenth century: Norms and use (by Langer, Nils) 18. Prescriptive norms and norms of usage in nineteenth-century German (by Elspass, Stephan) 19. Index
Haemopoietic defect and decreased expansion potential of bone marrow autografts from patients with acute myeloid leukaemia in first remission

Autologous bone marrow (BM) transplantation for acute myeloid leukaemia (AML) in complete remission (CR) is frequently followed by a slow haemopoietic recovery. We assessed the haemopoietic capacity of purified BM stem cell (CD34+DR−) and progenitor cell (CD34+DR+) populations from patients with AML in CR, and compared these data with those of normal BM. The feasibility of ex vivo expansion in stroma‐conditioned medium supplemented with cytokines was also investigated.
Uncovering Business Benefits From Regulatory Compliance Systems

Information Technology (IT) has become one of the critical components that facilitates any banking institutions’ ability to meet regulatory requirements, in an efficient and a cost-effective way. In many instances, dedicated regulatory IT systems have been established, and comparable to most implementations, they are often considered a significant investment. Viewed from the longstanding debate on the value of IT investments to organisations, empirical research within the IS domain seems to have placed less emphasis on the possible business contribution of regulatory IT implementations. This paper has attempted to fill this gap by investigating the implementation of anti-money laundering and counter terrorism financing (AML/CFT) systems within banking institutions. Arising from this study, important new insights into the variety of business benefits, that might arise from the implementation of a regulatory system, has been identified.
Dynamic forward prediction for prosthetic hand control by integration of EMG, MMG and kinematic signals

We propose a new framework for extracting information from extrinsic muscles in the forearm that will allow a continuous, natural and intuitive control of a neuroprosthetic devices and robotic hands. This is achieved through a continuous mapping between muscle activity and joint angles rather than prior discretisation of hand gestures. We instructed 6 able-bodied subjects, to perform everyday object manipulation tasks. We recorded the Electromyographic (EMG) and Mechanomyographic (MMG) activities of 5 extrinsic muscles of the hand in their forearm, while simultaneously monitoring 11 joints of hand and fingers using a sensorised glove. We used these signals to train a Gaussian Process (GP) and a Vector AutoRegressive Moving Average model with Exogenous inputs (VARMAX) to learn the mapping from current muscle activity and current joint state to predict future hand configurations. We investigated the performances of both models across tasks, subjects and different joints for varying time-lags, finding that both models have good generalisation properties and high correlation even for time-lags in the order of hundreds of milliseconds. Our results suggest that regression is a very appealing tool for natural, intuitive and continuous control of robotic devices, with particular focus on prosthetic replacements where high dexterity is required for complex movements.
Platelet-derived growth factor induces phosphorylation of multiple JAK family kinases and STAT proteins

Receptors for interferons and other cytokines signal through the action of associated protein tyrosine kinases of the JAK family and latent cytoplasmic transcription factors of the STAT family. Genetic and biochemical analysis of interferon signaling indicates that activation of STATs by interferons requires two distinct JAK family kinases. Loss of either of the required JAKs prevents activation of the other JAK and extinguishes STAT activation. These observations suggest that JAKs provide interferon receptors with a critical catalytic signaling function and that at least two JAKs must be incorporated into an active receptor complex. JAK and STAT proteins are also activated by ligands such as platelet-derived growth factor (PDGF), which act through receptors that possess intrinsic protein tyrosine kinase activity, raising questions about the role of JAKs in signal transduction by this class of receptors. Here, we show that all three of the ubiquitously expressed JAKs--JAK1, JAK2, and Tyk2--become phosphorylated on tyrosine in both mouse BALB/c 3T3 cells and human fibroblasts engineered to express the PDGF-beta receptor. All three proteins are also associated with the activated receptor. Through the use of cell lines each lacking an individual JAK, we find that in contrast to interferon signaling, PDGF-induced JAK phosphorylation and activation of STAT1 and STAT3 is independent of the presence of any other single JAK but does require receptor tyrosine kinase activity. These results suggests that the mechanism of JAK activation and JAK function in signaling differs between receptor tyrosine kinases and interferon receptors.
On hierarchical brain tumor segmentation in MRI using fully convolutional neural networks: A preliminary study

Magnetic Resonance Imaging is the preferred imaging modality for assessing brain tumors, and segmentation is necessary for diagnosis and treatment planning. Thus, robust automatic segmentation methods are required. Machine learning proposals where the model is learned from data are quite successful. Hierarchical segmentation approaches firstly segment the whole tumor, followed by intra-tumor tissue identification. However, results comparing it with single stages approaches are needed, as state of the art results are also achieved by all-at-once strategies. Currently, fully convolutional networks approaches for segmentation are very efficient. In this paper, a hierarchical approach for brain tumor segmentation using a fully convolutional network is studied. The evaluation is performed on the Brain Tumor Segmentation Challenge 2013 dataset, and we report the metrics Dice Score Coefficient, Positive Predictive Value, and Sensitivity. Results show benefits from segmenting the complete tumor first, over all tissues in one stage. Moreover, the tumor core also benefits from such approach. This behavior may be justified by the high data imbalance observed between tumor and normal tissues, which is mitigated by considering the tumor as a whole.
Virus-Specific Cellular Immune Correlates of Survival in Vaccinated Monkeys after Simian Immunodeficiency Virus Challenge

ABSTRACT Understanding the characteristics of the virus-specific T-lymphocyte response that will confer optimal protection against the clinical progression of AIDS will inform the development of an effective cellular immunity-based human immunodeficiency virus vaccine. We have recently shown that survival in plasmid DNA-primed/recombinant adenovirus-boosted rhesus monkeys that are challenged with the simian immunodeficiency virus SIVmac251 is associated with the preservation postchallenge of central memory CD4+ T lymphocytes and robust gamma interferon (IFN-γ)-producing SIV-specific CD8+ and CD4+ T-lymphocyte responses. The present studies were initiated to extend these observations to determine which virus-specific T-lymphocyte subpopulations play a primary role in controlling disease progression and to characterize the functional repertoire of these cells. We show that the preservation of the SIV-specific central memory CD8+ T-lymphocyte population and a linked SIV-specific CD4+ T-lymphocyte response are associated with prolonged survival in vaccinated monkeys following challenge. Furthermore, we demonstrate that SIV-specific IFN-γ-, tumor necrosis factor alpha-, and interleukin-2-producing T lymphocytes are all comparably associated with protection against disease progression. These findings underscore the contribution of virus-specific central memory T lymphocytes to controlling clinical progression in vaccinated individuals following a primate immunodeficiency virus infection.
Blind deconvolution using maximum a posteriori estimates with dictionary learning

Blind deconvolution aims to obtain the original sharp image from the observed blurred image due to various distortion factors such as noise, out-of-focus, camera shake, etc. The solution to this imaging inverse problem is severely ill-posed and various heuristics in the form of some prior is required to approximate the solution. In this paper, we propose an novel deblurring algorithm using maximum a posteriori (MAP) estimation combined with sparse priors from a previously trained dictionary along with edge prior. The proposed numerical optimization methods can produce results, far better when compared to similar existing state-of-the-art methods.
Phoenix date palm injuries: a review of injuries from the Phoenix date palm treated at the Starship Children's Hospital.

BACKGROUND The purpose of this study was to review patients treated for penetrating Phoenix date palm injuries. Documentation of the clinical behaviour of these injuries was sought as they have different clinical outcomes to other foreign body injuries. METHODS Data was collected via a retrospective review of patient files and imaging studies of all patients with foreign body injury admitted to the Orthopaedic Service of Starship Children's Hospital between 1992 and 1997. RESULTS Of 250 patients admitted with foreign body injuries, 21 cases were identified as caused by the Phoenix date palm. The age range was 5 to 12 years. There was a median delay of 43 days between the time of injury and presentation to hospital. An average of 1.3 operations were performed on each patient. Ultrasound was used in 12 cases, foreign body was identified in 10 patients--a sensitivity of 83%. Intraoperative ultrasound was also found to be beneficial in three of these cases. CONCLUSIONS Phoenix date palm injuries often have a protracted course. The initial diagnosis and treatment of such injuries is often delayed. Fracturing and fragmentation of the barbs may occur and multiple surgical procedures may be required to remove all of the foreign material. The Phoenix date palm barbs may cause a severe tissue reaction with sterile granulomatous synovitis and bony pseudotumour formation. A high level of suspicion on history taking and surgical exploration is needed. Total synovectomy for delayed joint or tendon sheath involvement may be required when fragmentation has occurred. Ultrasound has higher sensitivity for detection of thorn foreign bodies than magnetic resonance imaging.
Simultaneous Recordings from the Primary Visual Cortex and Lateral Geniculate Nucleus Reveal Rhythmic Interactions and a Cortical Source for Gamma-Band Oscillations

Oscillatory synchronization of neuronal activity has been proposed as a mechanism to modulate effective connectivity between interacting neuronal populations. In the visual system, oscillations in the gamma-frequency range (30–100 Hz) are thought to subserve corticocortical communication. To test whether a similar mechanism might influence subcortical-cortical communication, we recorded local field potential activity from retinotopically aligned regions in the lateral geniculate nucleus (LGN) and primary visual cortex (V1) of alert macaque monkeys viewing stimuli known to produce strong cortical gamma-band oscillations. As predicted, we found robust gamma-band power in V1. In contrast, visual stimulation did not evoke gamma-band activity in the LGN. Interestingly, an analysis of oscillatory phase synchronization of LGN and V1 activity identified synchronization in the alpha (8–14 Hz) and beta (15–30 Hz) frequency bands. Further analysis of directed connectivity revealed that alpha-band interactions mediated corticogeniculate feedback processing, whereas beta-band interactions mediated geniculocortical feedforward processing. These results demonstrate that although the LGN and V1 display functional interactions in the lower frequency bands, gamma-band activity in the alert monkey is largely an emergent property of cortex.
Laboratory simulated dissipation of metsulfuron methyl and chlorimuron ethyl in soils and their residual fate in rice, wheat and soybean at harvest

Two sulfonylurea herbicides, metsulfuron methyl (Ally 20 WP) and chlorimuron ethyl (Classic 25 WP) were evaluated for their dissipation behaviour in alluvial, coastal saline and laterite soils under laboratory incubated condition at 60% water holding capacity of soils and 30 °C temperature was maintained. In field study herbicides were applied twice for the control of grasses, annual and perennials broad leaves weeds and sedges in rice, wheat and soybean to find out the residual fate of both the herbicides on different matrices of respective crops after harvest. Extraction and clean up methodologies for the herbicides were standardized and subsequently analyzed by HPLC. The study revealed that the half-lives of metsulfuron methyl and chlorimuron ethyl ranged from 10.75 to 13.94 d irrespective of soils and doses applied. Field trials with rice, wheat and soybean also revealed that these two herbicides could safely be recommended for application as no residues were detected in the harvest samples.
Concomitant Radiotherapy and Carboplatin in Locally Advanced Bladder Cancer

Objective: The aim of the study was to assess the efficacy and safety of concomitant radiotherapy (CRT) and carboplatin. Patients and Methods: From 1992 until 1997, 67 patients with T3 invasive bladder cancer (IBC) were treated using CRT and carboplatin. X-Ray radiotherapy (10 MeV) was applied using LINAC in a locoregional technique, with a total tumor dose of 65 Gy in 32 fractions. Carboplatin was administered as a bolus infusion once a week, on day 5, up to a total dose of 900 mg. Results: The most frequent toxicity was hematological. Of the 67 treated patients, 92.5% achieved a clinically complete response, and 7.5% developed progressive disease during therapy. The 5-year overall survival was 55% and disease-free survival was 35%. Conclusion: CRT and carboplatin appear to be safe and extremely active in the treatment of T3 IBC, but the results should be confirmed in a randomized study.
Symptom-Based Outcome Measures for Dyspepsia and GERD Trials: A Systematic Review

BACKGROUND:Symptom assessment using questionnaires has been recommended as the primary outcome measure in clinical gastroesophageal reflux and dyspepsia trials. Questionnaires should have proven reliability, validity, and responsiveness, and may assess the frequency and/or severity of dyspepsia symptoms. Although a number of measures have been developed, it remains unclear which of these should be used in new trials.OBJECTIVE:To describe existing questionnaire outcome measures that assess symptoms of gastroesophageal reflux dyspepsia for use in clinical trials.METHODS:Studies were identified from Medline, Embase, the Cochrane library, and reference lists. The inclusion criterion was that the study assessed a questionnaire, which measured the frequency or severity of dyspepsia or gastroesophageal reflux symptoms, in a sample of patients.RESULTS:No direct comparison between questionnaires was possible due to methodological heterogeneity. Thirty-seven studies describing 26 questionnaires met the inclusion criteria. Twelve were unidimensional (assessed symptoms only) and 14 were multidimensional (also assessed quality of life). Eleven questionnaires assessed both frequency and severity of dyspepsia, and 10 had proven reliability, validity, and responsiveness. No studies compared different questionnaires.CONCLUSIONS:Future gastroesophageal reflux and dyspepsia clinical trials should use unidimensional or multidimensional outcome measures that assess both the frequency and severity of symptoms, and have proven reliability, validity, and responsiveness. Further research is necessary to compare existing outcome measures to determine which are the most reliable, valid, and responsive instruments.