Miracle-dz/UniFAR-FTUs huggingface dataset:
A new use for a familiar fold: the X-ray crystal structure of GTP-bound GTP cyclohydrolase III from Methanocaldococcus jannaschii reveals a two metal ion catalytic mechanism.

GTP cyclohydrolase (GCH) III from Methanocaldococcus jannaschii, which catalyzes the conversion of GTP to 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (FAPy), has been shown to require Mg2+ for catalytic activity and is activated by monovalent cations such as K+ and ammonium [Graham, D. E. , Xu, H. , and White, R. H. (2002) Biochemistry 41, 15074-15084]. The reaction is formally identical to that catalyzed by a GCH II ortholog (SCO 6655) from Streptomyces coelicolor; however, SCO 6655, like other GCH II proteins, is a zinc-containing protein. The structure of GCH III complexed with GTP solved at 2 A resolution clearly shows that GCH III adopts a distinct fold that is closely related to the palm domains of phosphodiesterases, such as DNA polymerase I. GCH III is a tetramer of identical subunits; each monomer is composed of an N- and a C-terminal domain that adopt nearly superimposible structures, suggesting that the protein has arisen by gene duplication. Three metal ions were located in the active site, two of which occupy positions that are analogous to those occupied by divalent metal ions in the structures of a number of palm domain containing proteins, such as DNA polymerase I. Two conserved Asp residues that coordinate the metal ions, which are also found in palm domain containing proteins, are observed in GCH III. Site-directed variants (Asp-->Asn) of these residues in GCH III are less active than wild-type. The third metal ion, most likely a potassium ion, is involved in substrate recognition through coordination of O6 of GTP. The arrangement of the metal ions in the active site suggests that GCH III utilizes two metal ion catalysis. The structure of GCH III extends the repertoire of possible reactions with a palm fold to include cyclohydrolase chemistry.
The Fama-French Three Factor Model and the Capital Asset Pricing Model : Evidence from the Indian Stock Market

The study aimed to provide empirical evidence on the validity of various asset pricing models for India. Specifically, it examined the behaviour of stock returns in relation to market beta, firm size (market equity), and book-to-market equity factors. I tested for the capital asset pricing model (CAPM), introduced by Sharpe (1964), Lintner (1965), Mossin (1966), and Black (1972) and then for a well-known extension to CAPM provided by Fama and French (1992), that is, the three factor model which moves away from the oversimplified relation between excess portfolio returns and excess market returns as prophesized by CAPM. I differed from the previous studies on this topic, in the Indian market, in three significant ways. First, I constructed a higher number of portfolios to minimize variability within a portfolio. Second, I considered post-2008 stock market data, so as to exclude any impact of the economic crisis. Third, I also carried out a joint test on the constant term in the portfolio regressions using the GRS test statistic. Given the time period in consideration, the empirical tests conducted support the Fama-French three-factor model in explaining the variation of stock returns better than the single factor CAPM for the Indian stock market.
Exfiltrations using polymorphic blending techniques: Analysis and countermeasures

Cyber espionage campaigns and cyber attacks make use of data exfiltration on a regular basis causing damages for billions of dollars. Nowadays, they represent one of the primary threats, and they are performed by criminals, companies and states. Normally, data exfiltration uses classic application-layer protocols (e.g. FTP or HTTP) in combination with very basic obfuscation mechanisms. Even though in most cases these techniques are effective enough, this paper describes how instead they can be detected using properly configured IDSs. Moreover, we introduce a novel approach named polymorphic blending exfiltration that serves to avoid detection from signature-based as well as anomaly-based IDSs. This technique permits to blend the exfiltrated data in the normal and legitimate traffic. We show how IDSs can be easily improved in order to be able to detect such exfiltration. Finally, we conclude presenting different evasion techniques that can be included in the polymorphic blending exfiltration to keep providing a safe undetectable exfiltration.
Investment-Related Pressure and Audit Risk

SUMMARY: This study examines whether auditors regard market pressure on client management as contributing to audit risk. The literature suggests that when management jobs are threatened by negative market reaction to poor mergers and acquisitions investment, managers are more likely to misstate financial statements in the post-investment period due to pressure on their job security (Bens, Goodman, and Neamtiu 2012). We find that firms under such investment-related pressure experience larger increases in audit fees and audit lags in the post-investment period. Our findings suggest that auditors perceive market pressure on client management as a risk factor, as recommended by Statement on Auditing Standards (SAS) No. 99.
Effects of subchronic exposure to Spartakus (prochloraz) on common carp Cyprinus carpio.

OBJECTIVES The aim of the study was to investigate effects of the fungicide formulation Spartakus (prochloraz 450 g.L-1) on common carp Cyprinus carpio through biometric, biochemical, haematological and antioxidant indices, induction of xenobiotic metabolizing enzymes and histological examination of selected tissues. DESIGN The test was performed on juvenile fish, which was exposed to Spartakus (concentrations of prochloraz: 0.05; 0.15 and 0.38 mg.L-1) for 28 days. Haematological indices were assessed using unified methods of haematological examination in fish. Plasma biochemical indices were determined by biochemical analyzer. Concentration of total cytochrome P450 (CYP), glutathione (GSH) content and glutathione-S-transferase (GST) activity were determined spectrophotometrically in hepatopancreas. Activity of liver ethoxyresorufin-O-deethylase (EROD) activity was measured spectrofluorimetrically. Ferric reducing ability of plasma (FRAP) and ceruloplasmin activity were assessed spectrophotometrically. Histological changes in samples of hepatopancreas, skin, gills, spleen, head kidney and caudal kidney were examined by light microscopy. RESULTS There was a significant rise in hepatosomatic index (HSI) (p<0.01), CYP and EROD (p<0.05) of fish exposed to prochloraz of 0.15 and 0.38 mg.L-1 whereas GST was induced by all concentrations tested and GSH by 0.38 mg.L-1 (p<0.05). Red blood cell count decreased significantly (p<0.05) in prochloraz of 0.05 and 0.15 mg.L-1. Plasma potassium increased (p<0.01) in all Spartakus treated groups, a decline in total protein (p<0.05), ALT, Na+ and Ca (p<0.01) was found in fish exposed to prochloraz of 0.38 mg.L-1. Ceruloplasmin activity was elevated (p<0.05) in the highest concentration tested, FRAP declined (p<0.05) in the same group. Histopathological changes in gills were demonstrated in all pesticide treated groups, with a decreased activity of skin mucous cells in prochloraz of 0.38 mg.L-1. CONCLUSION The subchronic exposure to Spartakus influenced HSI, induced xenobitic metabolizing enzymes, initiated a disorder of selected plasma indices and a decline in red blood cell count, caused minor histological impairment, and affected antioxidant activities of the test fish.
Anti-GM1 antibodies are not associated with cerebral atrophy in patients with multiple sclerosis

Objectives The aim of this study was to correlate the brain atrophy with serum levels of anti-GM1 antibodies in patients with relapsing–remitting multiple sclerosis (RRMS). Methods Plasma sample from 52 patients with RRMS and 65 healthy controls were examined for anti-GM1 antibodies. Patients with RRMS underwent to MRI study with automated method called SIENAX that calculated an estimate of gray matter (GMV) and white matter (WMV) volumes. Results The percentage of RRMS patients with increased anti-GM1 was 37.8%. Elevated levels of anti-GM1 antibodies did not correlate with brain atrophy. Conclusions Anti-GM1 antibodies do not represent a marker of axonal damage in patients with RRMS.
Tissue‐specific and light‐regulated expression of a pea nuclear gene encoding the small subunit of ribulose‐1,5‐bisphosphate carboxylase.

We have examined the expression of a member of the multigene family encoding the small subunit (rbcS) of ribulose‐1,5‐bisphosphate carboxylase in various tissues of pea. The rbcS gene, pPS‐2.4, was characterized by DNA sequence analysis and 5′ and 3′ end mapping of its mRNA transcript. rbcS polypeptides were shown to be differentially present in various tissues of light‐ and dark‐grown plants. Northern analysis shows that compared with green leaves, the level of rbcS mRNA is reduced to approximately 50% in pericarps, 8% in petals and seeds, and 1‐3% in etiolated leaves, stems, and roots. 5′ S1 nuclease mapping of total rbcS mRNA was used to quantitate the relative amount of pPS‐2.4 gene‐specific transcripts in each tissue. pPS‐2.4 mRNA accounts for approximately 30‐35% of total rbcS transcripts in green leaves, but only 5‐10% in pericarps, 15‐20% in seeds, and is below detection in petals and etiolated leaves. We conclude that the pPS‐2.4 gene is expressed in a tissue‐specific, light‐regulated fashion and that transcriptional controls of individual rbcS genes vary.
Economic Development and Trade Liberalization: the Indonesian Experience

From 1950 to 1965, Indonesia followed an import substitution industrialization development strategy . From 1966 to the present, Indonesia has moved toward an export oriented development strategy. This paper tests the predictions of the Heckscher-Ohlin-Samuelson (HOS) model of international trade by comparing Indonesia's economic performance under two contrasting development strategies. The paper concludes that Indonesia's economic performance under the opposing development strategies supports the predictions of the HOS model. Furthermore, the Indonesian experience under the two development strategies supports the "trade as an engine of growth" hypothesis.
Quantitative microwave imaging in Lp Banach spaces: A numerical assessment

A numerical assessment concerning the reconstruction capabilities of a recently proposed imaging measurement method working at microwave frequencies is proposed. The approach is based on the electric field integral equations of the inverse scattering problem, which are solved by using an iterative inexact-Newton method developed in Lp Banach spaces. Quantitative errors on the reconstruction of a canonical configuration are evaluated in different conditions. Accordingly, the effects of the choice of several parameters of the imaging configuration and operating conditions are discussed.
Immunochemical relationship of the major outer membrane protein of Rhodopseudomonas sphaeroides 2.4.1 to proteins of other photosynthetic bacteria

Immunoblots of sodium dodecyl sulfate-polyacrylamide gels derived from outer membrane preparations of various strains of Rhodopseudomonas sphaeroides revealed polypeptides which cross-reacted with antibody directed against the major outer membrane protein of R. sphaeroides 2.4. 1. Immunochemical quantitation of the major outer membrane protein of strain 2.4. 1 showed approximately 5.5 x 10(4) molecules per cell whether cells were grown chemoheterotrophically or photoheterotrophically. Rhodospirillum rubrum outer membranes contained a cross-reactive protein, whereas the outer membranes derived from Rhodopseudomonas capsulata and Paracoccus denitrificans showed no cross-reaction with the antibody prepared against the major outer membrane protein from R. sphaeroides 2.4. 1.
Stability analysis of power amplifiers

The paper presents recent advances on stability-analysis methods, applied to power amplifiers, which often exhibit undesired behavior. Techniques will be provided to detect the most common types of bifurcations, or qualitative changes of the solution stability when a parameter is varied continuously. The bifurcation analysis techniques are combined with pole-zero identification in order to detect an undesired coexistence of stable solutions. Bifurcation loci provide instability contours versus practical design parameters and can be used to evaluate the impact of the instability on the overall amplifier performance and to stabilize the amplifier. Various examples of usual instability phenomena in power amplifiers will be presented.
4D phase contrast MRI at 3 T: Effect of standard and blood‐pool contrast agents on SNR, PC‐MRA, and blood flow visualization

Time‐resolved phase contrast (PC) MRI with velocity encoding in three directions (flow‐sensitive four‐dimensional MRI) can be employed to assess three‐dimensional blood flow in the entire aortic lumen within a single measurement. These data can be used not only for the visualization of blood flow but also to derive additional information on vascular geometry with three‐dimensional PC MR angiography (MRA). As PC‐MRA is sensitive to available signal‐to‐noise ratio, standard and novel blood pool contrast agents may help to enhance PC‐MRA image quality. In a group of 30 healthy volunteers, the influence of different contrast agents on vascular signal‐to‐noise ratio, PC‐MRA quality, and subsequent three‐dimensional stream‐line visualization in the thoracic aorta was determined. Flow‐sensitive four‐dimensional MRI data acquired with contrast agent provided significantly improved signal‐to‐noise ratio in magnitude data and noise reduction in velocity data compared to measurements without contrast media. The agreement of three‐dimensional PC‐MRA with reference standard contrast‐enhanced MRA was good for both contrast agents, with improved PC‐MRA performance for blood pool contrast agent, particularly for the smaller supra‐aortic branches. For three‐dimensional flow visualization, a trend toward improved results for the data with contrast agent was observed. Magn Reson Med, 2010. © 2009 Wiley‐Liss, Inc.
Effect of dimethyl sulfoxide on human carcinoma cells, inhibition of plasminogen activator synthesis, change in cell morphology, and alteration of response to cholera toxin

Human carcinoma HEp-3 lost its tumorigenic and metastatic potential upon prolonged culture in vitro. This change was accompanied by a reduced production of plasminogen activator (PA) of the urokinase type (uPA), which is secreted by HEp-3 cells, a change in response to effectors that modulate uPA production, and an alteration of cell morphology. Similar but more rapid changes occurred when malignant HEp-3 cells were exposed to dimethyl sulfoxide (DMSO). uPA activity in the culture medium dropped below 50% of the control level within 6 h after the addition of DMSO and became undetectable after 24 h of treatment. This drop in uPA activity was not caused by an increased production of PA inhibitors. The cell-associated uPA decreased to 25 to 30% of the control level within 6 h of DMSO treatment and remained at this level for at least 96 h; the reduced uPA production was partially accounted for by a rapid decrease in the functional and chemical concentration of uPA mRNA. In contrast, the concentrations of most of the abundant mRNA species did not appear to be significantly affected, and cell growth was only slightly inhibited in the presence of DMSO. Malignant HEp-3 cells treated with DMSO responded to cholera toxin with an enhanced production of uPA, and their morphology became indistinguishable from that of nonmalignant HEp-3 cells grown in vitro for prolonged periods of time. All of the above changes were fully and rapidly reversible. The inhibitory effect of DMSO on PA production appears to be specific for uPA of human cell lines.
Confidence limits for hazardous concentrations based on logistically distributed NOEC toxicity data.

This paper deals with the calculation of Hazardous Concentrations of toxic substances from small sets of laboratory toxicity data, e.g., NOECs. A procedure due to Van Straalen and Denneman, as adapted from Kooijman (case n = 1), in which one seeks a concentration that protects 95% of the biological species is modified to account for the uncertainty in the estimates. New constants are obtained by simulation. These allow the calculation of the one-sided 95% left confidence limit of the Hazardous Concentration, from the mean and standard deviation of a sample of (laboratory) toxicity data. This 95% confidence limit is always lower than the 95% certainty value calculated with the Kooijman (n = 1)/Van Straalen method. The authors also derive constants to calculate a one-sided 50% confidence value, that overpredicts as often as it underpredicts. This value may be used as a median guess of the Hazardous Concentration. It will always be higher than the 95% certainty value of the Kooijman (n = 1)/Van Straalen method. However, by using the 50% value, one runs the risk of protecting substantially less than 95% of the biological species.
Regulatory T cell subtypes and TGF-β1 gene expression in chronic allograft dysfunction.

BACKGROUND Regulatory T cells have been suggested to have a protective role against acute rejection in allograft recipients. However, there is little information available about their contribution to chronic rejection process. The role of transforming growth factor-beta 1 (TGF-β1) as a profibrogenic and/or immunoregulatory cytokine in renal allografts is also controversial. OBJECTIVES To evaluate the frequency of CD4+CD25+CD127- and CD3+CD8+CD28- regulatory T cells in chronic allograft dysfunction (CAD) and to investigate the expression of TGF-β1 in renal allografts. METHODS Thirty biopsy-proven CAD patients were pair-matched with 30 stable graft function patients and a third group of healthy volunteers. Flowcytometry was performed on PBMCs to determine the frequency of CD3+CD8+CD28- and CD4+CD25+CD127- regulatory T cells in lymphocyt population. TGF-β1 gene expression was assessed by Real Time PCR. RESULTS The percentages of CD3+CD8+CD28- Tregs among renal allograft recipients was higher than healthy controls (p<0.001) since stable graft patients showed the most rates. The frequency of CD4+CD25+CD127- Tregs was lower in CAD patients than stable recipients (p=0.024) and healthy group (p=0.015). TGF-β1 gene expression was greater in CAD patients compared to healthy group (p=0.03) but there was no significant difference between gene expression of stable graft patients and healthy volunteers. CONCLUSION The negative association between the frequency of regulatory T cell subtypes and chronic allograft dysfunction proposes these cells as probable candidates for promoting allograft survival. Moreover, despite the immunoregulatory capacity of TGF-β1, it is likely to be implicated in chronic damages of allograft tissue.
[Clinical comparison of GC regimen (gemcitabine and cisplatin) versus FEC regimen (fluorouracil, epirubicin, and cyclophosphamide) as neoadjuvant chemotherapy for breast cancer].

BACKGROUND & OBJECTIVE Neoadjuvant chemotherapy plays a crucial role in treating breast cancer, but there is no standard regimen. Recently, FEC regimen [5-fluorouracil (5-FU), epirubicin (EPI), plus cyclophosphamide (CTX)] is the most commonly used; gemcitabine (GEM) is also a new active antimetabolite for breast cancer, however, the experience with neoadjuvant gemcitabine is limited. This study was to compare the efficacy of GC regimen and FEC regimen on breast cancer, and observe the adverse events. METHODS From Mar. 2003 to Sep. 2005, 62 patients with stage II-III breast cancer were treated with 2 cycles of either GC regimen or FEC regimen before operation. The 22 patients in GC group received GEM (1000 mg/m(2)) by intravenous injection on Day 1 and Day 8, and DDP (75 mg/m(2)) by intravenous injection on Day 2. The 40 patients in FEC group received EPI (50 mg/m(2)) by intravenous injection on Day 1, CTX (500 mg/m(2)) by intravenous injection on Day 1 and Day 8, and 5-FU (500 mg/m(2)) by 4-hour continuous infusion on Day 1 and Day 8. Clinical response and adverse events were assessed after neoadjuvant chemotherapy. RESULTS The overall response rate (RR) was 63.6% in GC group and 72.5% in FEC group. After GC therapy, 4 patients showed clinical complete remission (cCR), 2 pathologic complete remission (pCR), 10 partial remission (PR), 8 stable disease (SD)û while after FEC therapy, 9 patients showed cCR, 5 pCR, 20 PR, 10 SD. The most common adverse events were anemia, leukopenia, and nausea/vomiting. More cases of leukopenia were observed in GC group (18/22, P<0.05), and more cases of anemia in FEC group (29/40, P<0.05); the occurrence rates of gastroenteric reaction were similar in both groups. Only 1 patient in GC group suffered from oral mucositis; no renal toxicity and neurotoxicity were observed. CONCLUSIONS GC and FEC regimens are both effective for breast cancer with tolerable adverse events. The efficacy of FEC regimen is better than that of GT regimen.
Performance evaluation of ZigBee in indoor and outdoor environment

Wireless Sensor Network (WSN) comprises of many distributed independent tiny sensors that used to monitor statistical data of specific environmental conditions such as temperature, humidity, rain, pressure and many other. WSN use unlicensed 2.4 GHz Industrial, Scientific and Medical (ISM) radio frequency band for data transmission. WSN applications are being used in many industries and civilian areas, for various purposes such as environmental monitoring, habitat monitoring, traffic monitoring, precision agriculture monitoring, security monitoring, facility automation and traceability systems. Deployment of WSN in an outdoor or indoor environment always raised issue of signal loses and signal interference. In WSN, data is transmitted over wireless medium which is easily affected by external aspect such as walls, trees, heavy bushes, multiple signal interference and others. Currently, IEEE standard 802.15. 4 MAC protocol and ZigBee are the most famous protocols which are been used in WSN industry. In this paper, we have performed several experiments under various conditions such as indoor, outdoor, co-existence of Bluetooth to observe the ZigBee performance and interference effects. The experiments were performed physically in real environments which showed ZigBee signal degradation under various indoor and outdoor conditions.