Miracle-dz/UniFAR-FTUs huggingface dataset:
Optical identification of radio-loud active galactic nuclei in the ROSAT-Green-Bank sample with SDSS spectroscopy

Results of extended and refined optical identification of 181 radio/X-ray sources in the RASS-Green Bank (RGB) catalog are presented (Brinkmann et al. 1997) which have been spectroscopically observed in the Sloan Digital Sky Survey (SDSS) DR5. The SDSS spectra of the optical counterparts are modeled in a careful and self-consistent way by incorporating the host galaxy's starlight. Optical emission line parameters are presented, which are derived accurately and reliably, along with the radio 1.4–5 GHz spectral indices estimated using (non-simultaneous) archival data. For 72 sources, the identifications are presented for the first time. It is confirmed that the majority of strong radio/X-ray emitters are radio-loud active galactic nuclei (AGNs), particularly blazars. Taking advantage of the high spectral quality and resolution and our refined spectral modeling, we are able to disentangle narrow line radio galaxies (NLRGs), as vaguely termed in most previous identification work, into Seyfert II galaxies and LINERs (low-ionization nuclear emission regions), based on the standard emission line diagnostics. The NLRGs in the RGB sample, mostly belonging to ‘weak line radio galaxies’, are found to have optical spectra consistent predominantly with LINERs, and only a small fraction with Seyfert II galaxies. A small number of LINERs have radio power as high as 1023 – 1026 W Hz−1 at 5 GHz, being among the strongest radio emitting LINERs known so far. Two sources are identified with radio-loud narrow line Seyfert 1 galaxies (NLS1s), a class of rare objects. The presence is also confirmed of flat-spectrum radio quasars whose radio–optical–X-ray effective spectral indices are similar to those of High-energy peaked BL Lacs (HBLs), as suggested by Padovani et al., although it is still a debate as to whether this is the case for their actual spectral energy distributions.
THE UNDERGROUND ECONOMY HOLD BACK FINANCIAL DEEPENING ? E VIDENCE FROM THE I TALIAN CREDIT MARKET

The paper investigates the relationship between underground activities and financial deepening. The access to external finance requires entrepreneurs to disclose credible information through formal documentation. This requirement may be impossible to oblige to for many informal producers who lack a proper book-keeping of their operations. For the same reason irregular workers may find difficult to borrow for financing both consumption and housing purchase. Using panel data on Italian regional credit markets we find a strong negative impact of the share of irregular employment on outstanding credit to the private sector. According to our estimates a shift of 1 per cent of the employees from regular activities to irregular ones corresponds to a decline of about 2 percentage points in the volume of business lending and of 0.3 percentage points in outstanding credit to households, both expressed as ratios to GDP. Conversely, the feedback effects from financial deepening to the size of the informal sector are weak and statistically not significant. Through a difference-in-difference approach exploiting the regularisation program for immigrant workers launched in 2002 we also identify a negative effect of the irregular labour on banks’ entry decisions in the local credit markets, now defined in terms of provinces. JEL classification: G21, O17, R23.
Nutrient and sediment runoff from agricultural landscapes with varying suites of conservation practices in the Mississippi Alluvial Valley

Increasing concern regarding environmental degradation in coastal areas that experience annual hypoxic zones has led to the need for mitigation of nutrient laden runoff from inland landscapes. An annual occurrence of a hypoxic zone in the Gulf of Mexico has led to the development and implementation of nutrient reduction strategies throughout the Mississippi River Basin (MRB). With federal, state, and private financial and technical assistance, landowners have implemented best management practices (BMPs) to combat nutrient and sediment nonpoint source pollution; however, the effectiveness of these BMPs alone or utilized together has not been quantified. This study uses a field-scale, paired watershed approach in two watersheds in the Mississippi Alluvial Valley to test for differences in sediment and nutrient runoff concentrations between four management systems. A total of 774 samples (415 baseflow samples and 359 stormflow samples) were collected from 2011 to 2015. Median baseflow concentrations across all sites within this study were 52 mg L−1 for total suspended solids (TSS), 0.38 mg L−1 for total phosphorus (TP), 0.09 mg L−1 for nitrate-nitrite (NO3−-NO2−), and 0.81 mg L−1 for ammonium (NH4+). Median sediment and nutrient concentrations from stormflow samples across all sites within the study were greater than baseflow concentrations. Median stormflow concentrations across all sites were 985 mg L−1 for TSS, 1.21 mg L−1 for TP, 0.32 mg L−1 for NO3−-NO2−, and 1.04 mg L−1 for NH4+. Results showed no strong improvements in water quality from agricultural landscapes where suites of BMPs had been implemented, rather the data showed variability in runoff concentrations indicative of strong influences from environmental and management variables. Study outcomes highlight opportunities to better capture nutrient dynamics at the field scale through adaptive management of BMPs for increased effectiveness of nonpoint source pollution reduction and monitoring.
Wrapped progressive sampling search for optimizing learning algorithm parameters

We present a heuristic meta-learning search method for finding a set of optimized algorithmic parameters for a range of machine learning algo- rithms. The method, wrapped progressive sampling, is a combination of classifier wrapping and progressive sampling of training data. A series of experiments on UCI benchmark data sets with nominal features, and five machine learning algorithms to which simple wrapping and wrapped progres- sive sampling is applied, yields results that show little improvement for the algorithm which offers few parameter variations, but marked improvements for the algorithms offering many possible testable parameter combinations, yielding up to 32.2% error reduction with the winnow learning algorithm
When Positive Stereotypes Threaten Intellectual Performance: The Psychological Hazards of “Model Minority” Status

Asian-American women's performance on a test of quantitative skill was studied as a function of whether their Asian, female, or individual identity was salient at the time of testing. In previous research, ethnicity salience was found to result in enhanced math performance among Asian women. However, the investigators relied on a subtle manipulation of ethnicity salience that likely did not invoke concerns about group reputation nor make salient the common cultural stereotypes concerning Asians' mathematical prowess. We induced a focus on ethnic identity in a manner that was likely to make other people's high performance expectations more salient. Under these conditions, ethnicity salience resulted in diminished ability to concentrate, which in turn led to significantly impaired math performance. Thus, although people commonly hold positive stereotypes about Asians' mathematical skills, making these stereotypes salient prior to performance can create the potential for “choking” under the pressure of high expectations.
Measuring situation awareness of surgeons in laparoscopic training

The study of surgeons' eye movements is an innovative way of assessing skill and situation awareness, in that a comparison of eye movement strategies between expert surgeons and novices may show differences that can be used in training. Our preliminary study compared eye movements of 4 experts and 4 novices performing a simulated gall bladder removal task on a dummy patient with an audible heartbeat and simulated vital signs displayed on a secondary monitor. We used a head-mounted Locarna PT-Mini eyetracker to record fixation locations during the operation. The results showed that novices concentrated so hard on the surgical display that they were hardly able to look at the patient's vital signs, even when heart rate audibly changed during the procedure. In comparison, experts glanced occasionally at the vitals monitor, thus being able to observe the patient condition.
Are southern South American Rivers linked to the solar variability?

This article explores the Sun's influence on the hydrological cycle in southern South America (SSA) at the range of interannual‐to‐multidecadal scales from the early 1900s to 2011. The solar variability is described by the sunspot number (SSN) index. The hydrological cycle is examined by using annual mean discharges of the Paraná River (PAR) and the Atuel River (ATU) that represents the behaviour of the subtropical Argentinean Andean hydrological system. Wavelet‐based methods are used in order to describe relationships in the entire time‐frequency domain. The SSN–PAR connection is statistically weak in oscillations with period about 11 years (the Schwabe's solar cycle). Therefore, the solar forcing at this scale must be considered with great caution. The periodicity about 30 years is highly significant throughout the analysed period. Two potential physical mechanisms affecting the Paraná discharge could be involved: one is the solar irradiance influence on the Inter Tropical Convergence Zone (ITCZ), and the other is the solar influence on the Pacific long‐term variability. The SSN–ATU connection shows by far the most striking, robust and convincing result for the Schwabe cycle. A large amplitude and statistically significant cycle with a period about 11 years is observed not only in the Morlet‐based global and local wavelet spectra of the Atuel discharges and SSN but also in the global and local spectra of Cross and Coherent wavelets in most of the analysed period. High (low) discharges occur following maxima (minima) of the Schwabe cycles with time lags of up to ∼2 years. Previous studies have shown a close relationship between the subtropical Argentinean Andean Rivers and the El Niño/Southern Oscillation (ENSO), as well as a solar influence on the ENSO variability. We suggest that El Niño events occurring a few years after solar maxima could explain the connection. Periodicities longer than 30 years are suggested.
Fine-Tuning of FACT by the Ubiquitin Proteasome System in Regulation of Transcriptional Elongation

ABSTRACT FACT (facilitates chromatin transcription), an evolutionarily conserved histone chaperone involved in transcription and other DNA transactions, is upregulated in cancers, and its downregulation is associated with cellular death. However, it is not clearly understood how FACT is fine-tuned for normal cellular functions. Here, we show that the FACT subunit Spt16 is ubiquitylated by San1 (an E3 ubiquitin ligase) and degraded by the 26S proteasome. Enhanced abundance of Spt16 in the absence of San1 impairs transcriptional elongation. Likewise, decreased abundance of Spt16 also reduces transcription. Thus, an optimal level of Spt16 is required for efficient transcriptional elongation, which is maintained by San1 via ubiquitylation and proteasomal degradation. Consistently, San1 associates with the coding sequences of active genes to regulate Spt16's abundance. Further, we found that enhanced abundance of Spt16 in the absence of San1 impairs chromatin reassembly at the coding sequence, similarly to the results seen following inactivation of Spt16. Efficient chromatin reassembly enhances the fidelity of transcriptional elongation. Taken together, our results demonstrate for the first time a fine-tuning of FACT by a ubiquitin proteasome system in promoting chromatin reassembly in the wake of elongating RNA polymerase II and transcriptional elongation, thus revealing novel regulatory mechanisms of gene expression.
Influences of response position and hand posture on the orthogonal Simon effect

When lateralized responses are made to the locations of vertically arrayed stimuli, two types of mapping effect have been reported: an overall up–right/down–left advantage and mapping preferences that vary with response position. According to Cho and Proctor's (2003) multiple asymmetric codes account, these orthogonal stimulus–response compatibility effects are due to the correspondence of stimulus polarity and response polarity, as determined by the positions relative to multiple frames of reference. The present study examined these two types of orthogonal compatibility for situations in which participants made left–right responses to the colours of a vertically arrayed stimulus set, and stimulus location was irrelevant. Although a significant orthogonal Simon effect was not evident when responding at a centred, neutral response position, the effect was modulated by response eccentricity (Experiment 2) and hand posture (Experiment 3). These effects are qualitatively similar to those obtained when stimulus location is task relevant. The results imply that, as Proctor and Cho's (2006) polarity correspondence principle suggests, the stimulus polarity code activates the response code of corresponding polarity even when stimulus location is irrelevant to the task.
Regulation and use of the extracellular matrix by Trypanosoma cruzi during early infection

Chagas disease, which was once thought to be confined to endemic regions of Latin America, has now gone global becoming a new worldwide challenge. For more than a century since its discovery, it has remained neglected with no effective drugs or vaccines. The mechanisms by which Trypanosoma cruzi regulates and uses the extracellular matrix (ECM) to invade cells and cause disease are just beginning to be understood. Here we critically review and discuss the regulation of the ECM interactome by T. cruzi, the use of the ECM by T. cruzi and analyze the molecular ECM/T. cruzi interphase during the early process of infection. It has been shown that invasive trypomastigote forms of T. cruzi use and modulate components of the ECM during the initial process of infection. Infective trypomastigotes up-regulate the expression of laminin γ-1 (LAMC1) and thrombospondin (THBS1) to facilitate the recruitment of trypomastigotes to enhance cellular infection. Silencing the expression of LAMC1 and THBS1 by stable RNAi dramatically reduces trypanosome infection. T. cruzi gp83, a ligand that mediates the attachment of trypanosomes to cells to initiate infection, up-regulates LAMC1 expression to enhance cellular infection. Infective trypomastigotes use Tc85 to interact with laminin, p45 mucin to interact with LAMC1 through galectin-3 (LGALS3), a human lectin, and calreticulin (TcCRT) to interact with TSB1 to enhance cellular infection. Silencing the expression of LGALS3 also reduces cellular infection. Despite the role of the ECM in T. cruzi infection, almost nothing is known about the ECM interactome networks operating in the process of T. cruzi infection and its ligands. Here, we present the first elucidation of the human ECM interactome network regulated by T. cruzi and its gp83 ligand that facilitates cellular infection. The elucidation of the human ECM interactome regulated by T. cruzi and the dissection of the molecular ECM/T. cruzi interphase using systems biology approaches are not only critically important for the understanding of the molecular pathogenesis of T. cruzi infection but also for developing novel approaches of intervention in Chagas disease.
Identification of rcnA (yohM), a Nickel and Cobalt Resistance Gene in Escherichia coli

ABSTRACT We report here on the isolation and primary characterization of the yohM gene of Escherichia coli. We show that yohM encodes a membrane-bound polypeptide conferring increased nickel and cobalt resistance in E. coli. yohM was specifically induced by nickel or cobalt but not by cadmium, zinc, or copper. Mutation of yohM increased the accumulation of nickel inside the cell, whereas cells harboring yohM in multicopy displayed reduced intracellular nickel content. Our data support the hypothesis that YohM is the first described efflux system for nickel and cobalt in E. coli. We propose rcnA (resistance to cobalt and nickel) as the new denomination of yohM.
18F-FDG Uptake in Reactive Neck Lymph Nodes of Oral Cancer: Relationship to Lymphoid Follicles

PET using 18F-FDG is acceptable as a preoperative diagnostic tool for head and neck cancer. PET combined with CT provides precise localization of neck lymph nodes. Reactive lymphadenopathy is well known as a principal cause of false-positive findings on PET/CT for nodal staging. We investigated the reactive lymph nodes of oral cancer to elucidate the 18F-FDG–avid area in these nodes. Methods: Surgically dissected neck lymph nodes of oral cancer were retrospectively reviewed. Of the patients without pathologic nodal metastasis who underwent preoperative PET/CT, 11 patients with 31 enlarged lymph nodes at 20 levels were enrolled. The maximum standardized uptake value (SUVmax) of each lymph node was recorded. The diameters of the long and short axes were measured by pathologic sectioning, and the sectional surface area was calculated in square millimeters. Besides being stained with hematoxylin and eosin, the sections were immunohistochemically stained by CD79a for B cells, CD3 for T cells, CD68 for macrophages, CD21 for follicular dendritic cells (FDCs), and ubiquitous glucose transporter type 1 (GLUT1). The expression of GLUT1 was compared with staining of lymphoid cells. The numbers of total lymphoid follicles and hyperplastic secondary follicles were counted on CD21 and hematoxylin and eosin sections, respectively. The follicular reactivity index was determined as the ratio of secondary follicles relative to total follicles on the corresponding section. These parameters of reactive lymph nodes were analyzed on a level basis. Results: GLUT1 was expressed exclusively in lymphoid follicles, whose staining pattern was identical to that of FDCs. The calculated sectional area correlated significantly with the number of total follicles (r = 0.560; P = 0.0101). SUVmax did not correlate with the number of total follicles (P = 0.8947) but correlated significantly with the number of secondary follicles (r = 0.535; P = 0.0152). In addition, a strong positive correlation between SUVmax and the follicular reactivity index was demonstrated (r = 0.829; P < 0.0001). Conclusion: GLUT1 was expressed on cytoplasmic protrusions of FDCs in lymphoid follicles. The 18F-FDG accumulation in reactive lymphadenopathy depended on secondary follicles. FDCs in germinal centers of secondary follicles are suggested to be avid for 18F-FDG and the principal cause of false-positive findings for nodal staging.
Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication

MOTIVATION The costs of head-on versus codirectional collisions between the replication complex and the much slower transcription complex on the circular bacterial chromosomes are much debated. Although it is established that the number of genes on the leading strand is higher than on the lagging strand of replication, the consequences of collisions on the length of transcription units are unknown. RESULTS Here, we show that transcription units are generally longer on the leading strand, in rough proportion to the bias in number of units between the two strands. We propose a statistical physics model, based on the assumption that the proportion of interrupted transcripts for each unit is the major factor contributing to these biases. Its main prediction is that a large replication/transcription speed ratio implies a low leading/lagging bias for transcription unit length and number. This model is validated by an analysis of proven and predicted units in Escherichia coli and Bacillus subtilis. The results are consistent with an equal cost of head-on versus codirectional collisions.
Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors

With the increasing number of eukaryotic genomes available, high-throughput automated tools for identification of regulatory DNA sequences are becoming increasingly feasible. Several computational approaches for the prediction of regulatory elements were recently developed. Here we combine the prediction of clusters of binding sites for transcription factors with context information taken from genome annotations. Target Explorer automates the entire process from the creation of a customized library of binding sites for known transcription factors through the prediction and annotation of putative target genes that are potentially regulated by these factors. It was specifically designed for the well-annotated Drosophila melanogaster genome, but most options can be used for sequences from other genomes as well. Target Explorer is available at http://trantor.bioc. columbia.edu/Target_Explorer/
Temporal versus first-order logic to query temporal databases

A database history can be modeled as a (finite) sequence of instances discretely ordered by time. Similarly, the behavior of a system such as an operating system or a reactive system can be modeled by an infinite such sequence. One can view the sequence as one single database where each relation has an additional column holding the time instant of validity of each tuple. The temporal database can then be queried using standard relational calculus (first-order logic) on this "timestamp" representation. One may alternatively use an implicit access to time and express queries in temporal logic. It is known that these two approaches yield the same expressive power in the propositional case. Their comparison in the predicate/database context remained open. We prove here that there are first-order logic queries on the timestamp representation that are not expressible in (extended) temporal logic. The proof technique is novel and is based on communication complexity. On leave from INRIA-Rocquencourt y Work performed while on leave at INRIA-Rocquencourt. Post-doctoral research fellow of the Belgian National Fund for Scientific Research. Contact address: Jan Van den Bussche, Informatica , UIA, Universiteitsplein 1, B-2610 Antwerpen, Belgium. E-mail: vdbuss@uia.ua. ac.be.
Three recognition events at the branch‐site adenine.

An adenosine at the branch site, the nucleophile for the first transesterification step of splicing, is nearly invariant in mammalian pre‐mRNA introns. The chemical groups on the adenine base were varied systematically and assayed for formation of early spliceosome complexes and execution of the first and second steps of splicing. Recognition of constituents of the adenine is critical in formation of a U2 snRNP‐containing complex on a minimal branch‐site oligonucleotide. Furthermore, the efficiencies of the first and second chemical steps have different dependencies on the functional groups of the adenine. In total, the chemical groups on the adenine base at the branch site are differentially recognized during at least three different processes in the splicing of pre‐mRNA. Moreover, a protein, p14, interacts with the adenine in a base‐specific fashion and may mediate early recognition of this base.