Miracle-dz/UniFAR-FTUs huggingface dataset:
Corticolous bryophytes in managed Douglas-fir forests: habitat differentiation and responses to thinning and fertilization

Corticolous bryophytes, that is, mosses and liverworts that inhabit tree trunks, represent an important compo - nent of plant diversity in temperate ecosystems, but little is known of their ecology in managed forests. In this study, we quantified community composition and habitat differentiation of corticolous bryophytes in Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco) plantations subjected to experimental thinning and fertilization treatments. Twenty-four bryophyte species were recorded in a sample of 480, 225 cm 2 quadrats on 60 tree trunks. All moss species and obligately epiphytic liverworts (those with a primary habitat preference for tree trunks) showed highest cover values on south and west exposures. In contrast, facultatively epiphytic liverworts occurred only at the tree base, and mainly on north and west exposures. Pairwise correlations among species cover values were nearly always positive, and cover of the most abundant species, Isothecium myosuroides, was also positively correlated with local species richness of other bryophyte taxa. These patterns suggest that competitive interactions among bryophyte species are not strong in this community. There was little evidence for fertilization or thinning effects on total bryophyte cover or species richness. However, analyses of community composition and species-specific responses indicated significant negative effects of thinning on some bryophyte species. Observed patterns of habitat differentiation, interspecific associations, and treat- ment responses suggest that stand hydrology and microclimate are of primary importance in determining the distribu- tion and abundance of corticolous bryophytes in managed forests.
Site of reentry in paroxysmal supraventricular tachycardia in man.

His bundle recordings during spontaneous and induced episodes of paroxysmal supraventricular tachycardia (SVT) demonstrated that the site of reentry responsible for this arrhythmia was in the A-V node. In five patients studied, A-V conduction time and refractory periods were normal, but atrial premature depolarizations (APD) within a portion of the relative refractory period of the A-V node consistently produced atrial reentry—echoes or sustained SVT. In two patients, APDs falling within the A-V effective refractory period failed to excite the His bundle but still reentered within the A-V node and began SVT. It was noted that the various relationships between atrial and ventricular depolarizations on the surface ECG did not reflect different mechanisms for SVT, but only variations in A-V nodal conduction time.
Lowered cerebral glucose utilization in amyotrophic lateral sclerosis

Regional cerebral metabolic rates for glucose (rCMRGlc) were analyzed in 19 studies of 12 patients with amyotrophic lateral sclerosis (ALS) by positron emission tomography (PET) with {18F}2‐fluoro‐2‐deoxy‐D‐glucose. In the 8 ALS patients with upper motor neuron signs, the mean cortical rCMRGlc was significantly lower than in 11 age‐matched control subjects (p < 0.001). The degree of hypometabolism correlated with the duration of the clinical signs and extended throughout the cortex and basal ganglia, but not to the cerebellum. Of the 4 such patients who had repeat PET scans, 3 demonstrated significant subsequent reduction in the rCMRGlc, corresponding to the worsening of the clinical picture. In contrast, 4 ALS patients with disease confined to lower motor neurons and 3 patients with lower motor neuron disease from old paralytic poliomyelitis had normal or near‐normal rCMRGlc throughout the brain. Because histological evidence shows no generalized neuronal cell loss in the cortex of ALS patients, including in some cases the primary motor regions, the demonstration of severe generalized hypometabolism in structurally normal cortex indicates that some cortical neurons exist in a state of neuronal nonfunction, rather than cell death, and that anatomoclinical correlations may be more complex. The data also indicate that ALS with upper motor neuron involvement extends beyond the corticospinal tracts and differs in cortical function from the ALS confined to lower motor neurons or the other lower motor neuron disorders.
Promoter hypermethylation in prostate cancer.

BACKGROUND The prostate gland is the most common site of cancer and the second leading cause of cancer mortality in American men. It is well known that epigenetic alterations such as DNA methylation within the regulatory (promoter) regions of genes are associated with transcriptional silencing in cancer. Promoter hypermethylation of critical pathway genes could be potential biomarkers and therapeutic targets for prostate cancer. METHODS This review discusses current information on methylated genes associated with prostate cancer development and progression. RESULTS Over 30 genes have been investigated for promoter methylation in prostate cancer. These methylated genes are involved in critical pathways, such as DNA repair, metabolism, and invasion/metastasis. The role of hypermethylated genes in regulation of critical pathways in prostate cancer is reviewed. CONCLUSIONS These findings may provide new information of the pathogenesis of prostate cancer. Certain epigenetic alterations in prostate tumors are being translated into clinical practice for therapeutic use.
Evaluation of PSD Components and AAR Parameters as Input Features for a SVM Classifier Applied to a Robotic Wheelchair

Two distinct signal features suitable to be used as input to a Support-Vector Machine (SVM) classifier in an application involving hands motor imagery and the correspondent EEG signal are evaluated in this paper. Such features are the Power Spectral Density (PSD) components and the Adaptive Autoregressive (AAR) parameters. Different classification times (CT) and time intervals are evaluated, for the AAR-based and the PSD-based features, respectively. The best result (an accuracy of 97.1%) is obtained when using PSD components, while the AAR parameters generated an accuracy of 94.3%. The results also demonstrate that it is possible to use only two EEG channels (bipolar configuration around C3 andC4), discarding the bipolar configuration aroundCz. The algorithms were tested with a proprietary EEG data set involving 4 individuals and with a data set provided by the University of Graz (Austria) as well. The resulting classification system is now being implemented in a Brain-Computer Interface (BCI) used to guide a robotic wheelchair.
Pilot study of collective decision-making in the code review process

Political arguments and voting requirements often follow a simple majority method which is a decision rule that selects various alternatives that have a majority, that is, more than half the votes. On the other hand, Q&A services such as StackExchange and Yahoo! Answers use the simple majority method only as a reference point. In other words, even if an answer receives a majority vote (which represents a preferred answer for followers), the questioner might not accept the answer. In this case, the voting is used only as a reference. Open Source Software (OSS) projects might also use the voting approach only as a reference on the code review process, because a core reviewer (who makes the final decision) might not integrate a patch which was approved by reviewers into the version control system. Likewise, the votes from other reviewers might also only be used as a reference. This study identifies how many patch sets for code review follow the simple majority method in collective decision-making among reviewers. As a case study, we have analysed the criteria needed to integrate patch sets using Qt project data. From the results, we have found that only 59.5% patch sets followed the simple majority method. Patch sets with more negative votes than positive votes were likely to be rejected. Furthermore, the last vote in the first review also impacted the final decision in the first review.
Identification of protein partners of the human immunodeficiency virus 1 tat/rev exon 3 leads to the discovery of a new HIV-1 splicing regulator, protein hnRNP K

HIV-1 pre-mRNA splicing depends upon 4 donor and 8 acceptor sites, which are used in combination to produce more than 40 different mRNAs. The acceptor site A7 plays an essential role for tat and rev mRNA production. The SLS2-A7 stem-loop structure containing site A7 was also proposed to modulate HIV-1 RNA export by the Rev protein. To further characterize nuclear factors involved in these processes, we purified RNP complexes formed by incubation of SLS2-A7 RNA transcripts in HeLa cell nuclear extracts by affinity chromatography and identified 33 associated proteins by nanoLC-MS/MS. By UV cross-linking, immunoselection and EMSA, we showed that, in addition to the well-known hnRNP A1 inhibitor of site A7, nucleolin, hnRNP H and hnRNP K interact directly with SLS2-A7 RNA. Nucleolin binds to a cluster of successive canonical NRE motifs in SLS2-A7 RNA, which is unique in HIV-1 RNA. Proteins hnRNP A1 and hnRNP K bind synergistically to SLS2-A7 RNA and both have a negative effect on site A7 activity. By the use of a plasmid expressing a truncated version of HIV-1 RNA, we showed a strong effect of the overexpression of hnRNP K in HeLa cells on HIV-1 alternative splicing. As a consequence, production of the Nef protein was strongly reduced. Interestingly also, many proteins identified in our proteomic analysis are known to modulate either the Rev activity or other mechanisms required for HIV-1 multiplication and several of them seem to be recruited by hnRNP K, suggesting that hnRNP K plays an important role for HIV-1 biology.
The role of CYP26 enzymes in retinoic acid clearance

Retinoic acid (RA) is a critical signaling molecule that regulates gene transcription and the cell cycle. Understanding of RA signaling has increased dramatically over the past decades, but the connection between whole body RA homeostasis and gene regulation in individual cells is still unclear. It has been proposed that cytochrome P450 family 26 (CYP26) enzymes have a role in determining the cellular exposure to RA by inactivating RA in cells that do not need RA. The CYP26 enzymes have been shown to metabolize RA efficiently and they are also inducible by RA in selected systems. However, their expression patterns in different cell types and a mechanistic understanding of their function is still lacking. Based on preliminary kinetic data and protein expression levels, one may predict that if CYP26A1 is expressed in the liver at even very low levels, it will be the major RA hydroxylase in this tissue. As such, it is an attractive pharmacological target for drug development when one aims to increase circulating or cellular RA concentrations. To further the understanding of how CYP26 enzymes contribute to the regulation of RA homeostasis, structural information of the CYP26s, commercially available recombinant enzymes and good specific and sensitive antibodies are needed.
Accurate Queuing Analysis of IEEE 802.11 MAC Layer

In this paper, we develop an analytical model for IEEE 802.11 MAC protocol with arbitrary buffer size in unsaturated conditions. The model comprises of a generalized Markov chain model and an M/G/1/K queuing model. We give the thorough and accurate queuing analysis of IEEE 802.11 MAC layer. It's shown that for practical 802.11 WLAN (i.e., buffer size larger than one and number of stations comparatively large) under the optimal offered load, the total throughput is maximized, the packet blocking probability (due to limited buffer size) and the average queuing delay tends to zero, the average MAC service delay as well as its standard deviation is much lower than that in saturated conditions. The simulations show the analytical model is highly accurate.
Susceptibility testing of Mycobacterium avium complex isolates

Mycobacterium avium complex (MAC) includes M. avium and M. intracellulare (MAI), and they are the most frequent isolates among the nontuberculous mycobacteria found in specimens taken from patients. It is ubiquitous in the environment (22, 31, 103, 104), and water aerosols have been suggested as the most likely transmission route (22, 31, 32, 87). As identified by their serovars, the proportion ofM. avium andM. intracellulare isolates in patients reflects the distribution of these species in the environments of different geographic areas (22, 25, 85, 87, 107). Infections caused by these organisms are not transmissible from person to person (53, 62). Prior to the emergence of the AIDS epidemic, MAC infections most often manifested in humans as a localized pulmonary disease which in the United States occurred in 2,000 to 3,000 patients annually (27, 62, 86, 103, 109, 111). Most noticeable among other localized manifestations was cervical lymphadenopathy in children (29, 76, 86, 89, 96, 99). Clinical features of pulmonary MAC disease were described in a number of reports emphasizing that in most of the patients this disease developed on the background of an underlying chronic pulmonary disease, silicosis, diabetes mellitus, cancer, treatment with corticosteroids, or other conditions that might have affected their immunity (13, 75, 114). The most recent reports suggested that MAC pulmonary disease can occur in persons without identifiable predisposing conditions (61, 90). MAC pulmonary disease appears most often in either multinodular bronchiectasis or cavitary forms (61, 67, 91, 98). The diagnosis in patients with minimal lung damage may represent a challenge since it requires differentiation between invasive disease and simply colonization of mycobacteria in the bronchi, and especially in patients with bronchiectasis, cysts, and posttuberculosis cavities. Therefore, the diagnosis requires repeated isolation of a substantial number of bacteria from sputum along with clinical and radiologic data. Disseminated MAC infections were reported in up to 24% of AIDS patients (54, 56), but its probability can be especially high in those with advanced AIDS, when the CD4 lymphocyte count is less than 100/mm (8, 50, 52, 57, 85). This new MAC epidemic is growing with the increasing number of AIDS patients and their increasing period of survival, most noticeable in industrialized countries. The diagnosis of disseminated MAC infections is based on isolation of mycobacteria from blood or tissue biopsy specimens, along with symptoms attributed to this disease (3, 30, 34, 68, 115, 117). ANTIMICROBIAL THERAPY OF MAC INFECTIONS
A Flexible System for Cultivation of Methanococcus and Other Formate-Utilizing Methanogens

Many hydrogenotrophic methanogens use either H2 or formate as the major electron donor to reduce CO2 for methane production. The conventional cultivation of these organisms uses H2 and CO2 as the substrate with frequent replenishment of gas during growth. H2 is explosive and requires an expensive gassing system to handle safely. Formate is as an ideal alternative substrate from the standpoints of both economy and safety but leads to large changes in the culture pH during growth. Here, we report that glycylglycine is an inexpensive and nontoxic buffer suitable for growth of Methanococcus maripaludis and Methanothermococcus okinawensis. This cultivation system is suitable for growth on liquid as well as solid medium in serum bottles. Moreover, it allows cultivation of liter scale cultures without expensive fermentation equipment. This formate cultivation system provides an inexpensive and flexible alternative for the growth of formate-utilizing, hydrogenotrophic methanogens.
Epstein–Barr virus persistence and infection of autoreactive plasma cells in synovial lymphoid structures in rheumatoid arthritis

Objectives Rheumatoid arthritis (RA) is associated with an increased Epstein–Barr virus (EBV) blood DNA load, a robust immune response to EBV and cross-reactive circulating antibodies to viral and self-antigens. However, the role of EBV in RA pathogenesis remains elusive. Here, we investigated the relationship between synovial EBV infection, ectopic lymphoid structures (ELS) and immunity to citrullinated self and EBV proteins. Methods Latent and lytic EBV infection was investigated in 43 RA synovial tissues characterised for presence/absence of ELS and in 11 control osteoarthritis synovia using RT-PCR, in situ hybridisation and immunohistochemistry. Synovial production of anti-citrullinated protein (ACPA) and anti-citrullinated EBV peptide (VCP1/VCP2) antibodies was investigated in situ and in vivo in the severe combined immunodeficiency (SCID)/RA chimeric model. Results EBV dysregulation was observed exclusively in ELS+ RA but not osteoarthritis (OA) synovia, as revealed by presence of EBV latent (LMP2A, EBV-encoded small RNA (EBER)) transcripts, EBER+ cells and immunoreactivity for EBV latent (LMP1, LMP2A) and lytic (BFRF1) antigens in ELS-associated B cells and plasma cells, respectively. Importantly, a large proportion of ACPA-producing plasma cells surrounding synovial germinal centres were infected with EBV. Furthermore, ELS-containing RA synovia transplanted into SCID mice supported production of ACPA and anti-VCP1/VCP2 antibodies. Analysis of CD4+ and CD8+ T-cell localisation and granzyme B expression suggests that EBV persistence in ELS-containing synovia may be favoured by exclusion of CD8+ T cells from B-cell follicles and impaired CD8-mediated cytotoxicity. Conclusions We demonstrated active EBV infection within ELS in the RA synovium in association with local differentiation of ACPA-reactive B cells.
Transitory Cognitive Impairment in Epileptic Children during a CPT Task

EEGs and behavioral responses were studied in two sex matched groups of 58 epileptic and 20 healthy children between 8 and 12 years of age, during the execution of a go-no go CPT (X; A-X) task to determine transitory cognitive impairment (TCI) incidence. Paroxysmal discharges were found on 87.9% and 5% of the EEGs in the epileptic and control groups respectively, with no differences related to sex. The predominant EEG findings with respect to paroxysmal discharges were the association of two or more types of paroxysms with frequency higher than 5/minute, an average duration less than 0.5 second and topographical distribution over temporal-parietal-occipital areas without significant interhemispheric differences. TCI was detected in 36.2% of epileptic children. The epileptic group showed significantly higher numbers of behavioral errors and longer reaction times (RTs) in relation to the control group. Analyzing RTs on the two blocks of the task, linear discriminant analysis showed an acceptable classification of TCI incidence between groups.
Validation of a similarity measurement method for clustering cardiac signals

Development of personalized cardiovascular management systems involves automatic identification of the current data as normal or pathological; considering cardiac data as time-series, the illness identification may be performed by seeking similarity between the current patient's time-series data and a reference signal and then proceeding to illness stratification (clustering). Seven of the most common methods of time-series similarity measurement were assessed by imposing 6 types of distortions to the reference signal, considering for each distortion 20 possible variations. This study employed 10 seconds length records of arterial blood pressure signals of healthy subjects, collected from a public database. Then clustering using Partitioning Around Medoids was performed among pathological and non-pathological data considering 3 different clusters. Clustering results confirm usage of the reduced basis Discrete Wavelet Transform resulting from the combination of Haar wavelet decomposition with the Karhunen-Loève transforms, presenting an accuracy ranging from 76% to 85% when partitioning around Medoids clustering is used.
Optimizing differentiated discretization for audio circuits beyond driving point transfer functions

One goal of Virtual Analog modeling of audio circuits is to produce digital models whose behavior matches analog prototypes as closely as possible. Discretization methods provide a systematic approach to generate such models but they introduce frequency response error, such as frequency warping for the trapezoidal method. Recent work showed how using different discretization methods for each reactive element could reduce such error for driving point transfer functions. It further provided a procedure to optimize that error according to a chosen metric through joint selection of the discretization parameters. Here, we extend that approach to the general case of transfer functions with one input and an arbitrary number of outputs expressed as linear combinations of the network variables, and we consider error metrics based on the L2 and the L1 norms. To demonstrate the validity of our approach, we apply the optimization procedure for the response of a Hammond organ vibrato/chorus ladder filter, a 19-output, 36th order filter, where each output frequency response presents many features spread across its passband.
Evaluating named entity recognition and disambiguation in news and tweets

Named entity recognition and disambiguation are important for information extraction and populating knowledge bases. Detecting and classifying named entities has traditionally been taken on by the natural language processing community, whilst linking of entities to external resources, such as DBpedia and GeoNames, has been the domain of the Semantic Web community. As these tasks are treated in different communities, it is difficult to assess the performance of these tasks combined. We conduct a thorough evaluation of the NERD-ML approach [2], an approach that combines named entity recognition (NER) from the NLP community and named entity linking (NEL) from the SW community. We present experiments and results on the CoNLL 2003 English 2003 dataset for NER and the AIDA CoNLL-YAGO2 dataset for NEL in the newswire domain and on the MSM’13 corpus for NER and the Dercynski et al. [1] dataset for NEL in the twitter domain. Our results indicate that combining approaches from the NLP and SW communities improves the performance for NER. As the NEL task is more recent, there is as yet no common agreement on the annotation level to adopt, which makes it difficult to assess the performance of different systems.