Miracle-dz/UniFAR-FTUs huggingface dataset:
Intermediate sequences increase the detection of homology between sequences.

Two homologous sequences, which have diverged beyond the point where their homology can be recognised by a simple direct comparison, can be related through a third sequence that is suitably intermediate between the two. High scores, for a sequence match between the first and third sequences and between the second and the third sequences, imply that the first and second sequences are related even though their own match score is low. We have tested the usefulness of this idea using a database that contains the sequences of 971 protein domains whose structures are known and whose residue identities with each other are some 40% or less (PDB40D). On the basis of sequence and structural information, 2143 pairs of these sequences are known to have an evolutionary relationship. FASTA, in an all-against-all comparison of the sequences in the database, detected 320 (15%) of these relationships as well as three false positive (i.e. 1% error rate). Using intermediate sequences found by FASTA matches of PDB40D sequences to those in the large non-redundant OWL database we could detect 550 evolutionary relationships with an error rate of 1%. This means the intermediate sequence procedure increases the ability to recognise the evolutionary relationships amongst the PDB40D sequences by 70%.
Evolutionary analysis of the antigenic determinant, glycosylation, and sialidase sites of neuraminidase from the human influenza A virus isolated in China from 1995 to 2012

Background: Improve the understanding of evaluative characteristics of the NA gene, NA protease active sites, and NA glycosylation sites in H1N1 virus isolated from China during 1995-2012. Method: A total of 200 NA gene sequences were downloaded from the National Center for Biotechnology Information’s GenBank. Phylogenetic analyses, multiple sequence alignment, glyco-sylation sites analyses, and protein structure prediction were conducted with Mega5.05, ClustalW, NetNGlyc1.0 program, and SWISS-MODEL server, respectively. Results: The NA genes of the Chinese pandemic H1N1 2009 virus were different from those of 1995-2008 seasonal sequences (low similarity of 75.5%-77.1%), but were similar to strains from other countries (high similarity of 99.1%-99.9%). The Chinese resistant strains were close to the wild-type strains but had low similarity from other countries. Six glycosylation sites (44 (NHT), 50 (NQS), 58 (NST), 63 (NHT), 70 (NNT), 434 (NTT), and 455 (NWS)) significantly changed, and four other sites remained stable. A total of 8 and 11 NA sialidase activity and auxiliary sites were conserved, respectively, except for the H275Y substitutions in 11 strains. The most common mutations were R222Q, V234M, D344N, and K254R. H275Y, despite its missing glycosylation sites, can change its 3D structure. Conclusions: Except for sialidase, some of the antigenic determinants and glycosylation sites from Chinese H1N1 influenza NA genes have changed in the past 20 y, which is related to the periodic outbreak in China.
Rituximab maintenance treatment of relapsed/resistant follicular non-Hodgkin's lymphoma: long-term outcome of the EORTC 20981 phase III randomized intergroup study.

PURPOSE In 2006, we published the results of the European Organisation for Research and Treatment of Cancer phase III trial EORTC 20981 on the role of rituximab in remission induction and maintenance treatment of relapsed/resistant follicular lymphoma (FL). At that time, the median follow-up for the maintenance phase was 33 months. Now, we report the long-term outcome of maintenance treatment, with a median follow-up of 6 years. PATIENTS AND METHODS Overall, 465 patients were randomly assigned to induction with either six cycles of cyclophosphamide, doxorubicin, vincristine, prednisone (CHOP) or rituximab plus CHOP (R-CHOP). Those in complete remission or partial remission after induction (n = 334) were randomly assigned to maintenance treatment with rituximab (375 mg/m(2) intravenously once every 3 months) or observation. RESULTS Rituximab maintenance significantly improved progression-free survival (PFS) compared with observation (median, 3.7 years v 1.3 years; P < .001; hazard ratio [HR], 0.55), both after CHOP induction (P < .001; HR, 0.37) and R-CHOP (P = .003; HR, 0.69). The 5-year overall survival (OS) was 74% in the rituximab maintenance arm, and it was 64% in the observation arm (P = .07). After progression, a rituximab-containing salvage therapy was given to 59% of patients treated with CHOP followed by observation, compared with 26% after R-CHOP followed by rituximab maintenance. Rituximab maintenance was associated with a significant increase in grades 3 to 4 infections: 9.7% v 2.4% (P = .01). CONCLUSION With long-term follow-up, we confirm the superior PFS with rituximab maintenance in relapsed/resistant FL. The improvement of OS did not reach statistical significance, possibly because of the unbalanced use of rituximab in post-protocol salvage treatment.
Heat shock-induced axenic growth of Bdellovibrio bacteriovorus

The bdellovibrios are obligately predatory bacteria that attack other gram-negative bacteria. They grow only in the periplasmic space of prey unless they mutate to forms that can grow axenically. A culture medium that promoted enhanced growth of prey-independent bdellovibrios was developed. The ability of this medium to support the growth of prey-dependent bdellovibrios was tested under transcription-altering conditions. This approach tested the hypothesis that the inability to grow prey-dependent bdellovibrios in artificial media was rooted in both nutritional and transcriptional signal deficiencies. It was assumed that nutritional deficiencies had been resolved and that empirically applied artificial signals may evoke the expression of genes required for axenic growth of bdellovibrios. Prey-dependent bdellovibrios could be grown in PPYE medium (0.1% proteose peptone 3 and 0.03% Bacto yeast extract adjusted to pH 7.0 and supplemented with 3 mM MgCl2 and 2 mM CaCl2 after autoclaving) after heat shock, and subsequent rounds of growth occurred after additional heat shocks. Heat shock may have generated or simulated signals normally derived from prey.
Humanistic Inquiry in Marketing Research: Philosophy, Method, and Criteria

As the conception of what marketing is has evolved, so must the methods of inquiry also evolve. Marketing now is viewed as a socially constructed enterprise. Thus, what is needed are inputs from the humanistic modes of inquiry developed specifically to address socially constructed phenomena. The author discusses three central aspects of humanistic inquiry, (1) the philosophy and metaphysic of humanism, (2) the methodology of humanistic research, and (3) the criteria appropriate for evaluating studies conducted in the humanistic mode. Humanistic inquiry is compared specifically with the positivist approach currently used by most marketing researchers. Guidelines are provided to assist researchers who may wish to implement the humanistic approach in their own research programs.
Regional administration of irinotecan in combination with 5-fluorouracil and leucovorin in patients with colorectal cancer liver metastases--a pilot experience.

BACKGROUND/AIMS Regional chemotherapy represents an effective approach for the control of isolated liver metastases of colorectal cancer. Fluoropyrimidines have been the basis of systemic and regional chemotherapy of this disease for several decades, but recent studies have demonstrated that the addition of irinotecan (CPT-11) ameliorates the results of systemic treatment. METHODOLOGY Fifteen patients with isolated liver metastases of colorectal carcinoma were treated with regional administration of CPT-11 in combination with 5-fluorouracil/folinic acid (5-FU/FA). CPT-11 (100-200 mg, mean: 93 +/- 25, range: 51-125 mg/m2) was administered weekly in combination with 5-FU (1000-2000 mg, 857 +/- 182, range: 538-1301 mg/m2) and FA (100-350 mg). Peripheral blood leukocyte phenotype was examined during the treatment in selected patients. RESULTS One patient achieved complete response, 4 patients had partial response, 7 patients had stable disease, 1 patient progressed and 2 patients were not evaluable. The response rate was 38% in evaluable patients, and a more than 50% decrease in serum carcinoembryonic antigen levels was observed in 12 out of 14 patients. The treatment was generally well tolerated. All patients, except one, are currently alive at mean follow-up of 11 +/- 6 (median: 10, range: 5-24) months. The therapy is still being continued in 8 patients. CONCLUSIONS Weekly CPT-11/5-FU/FA is highly effective in the treatment of patients with metastatic colorectal cancer limited to the liver, even after failure of previous 5-FU/FA. The present regimen should be tested as a first line treatment in phase III trial.
Factors to consider in using [U-C]palmitate for analysis of sphingolipid biosynthesis by tandem mass spectrometry[S]

This study describes the use of a stable-isotope labeled precursor ([U-13C]palmitate) to analyze de novo sphingolipid biosynthesis by tandem mass spectrometry. It also describes factors to consider in interpreting the data, including the isotope's location (13C appears in three isotopomers and isotopologues: [M + 16] for the sphingoid base or N-acyl fatty acid, and [M + 32] for both); the isotopic enrichment of palmitoyl-CoA; and its elongation, desaturation, and incorporation into N-acyl-sphingolipids. For HEK293 cells incubated with 0.1 mM [U-13C]palmitic acid, ∼60% of the total palmitoyl-CoA was 13C-labeled by 3 h (which was near isotopic equilibrium); with this correction, the rates of de novo biosynthesis of C16:0-ceramide, C16:0-monohexosylceramide, and C16:0-sphingomyelins were 62 ± 3, 13 ± 2, and 60 ± 11 pmol/h per mg protein, respectively, which are consistent with an estimated rate of appearance of C16:0-ceramide using exponential growth modeling (119 ± 11 pmol/h per mg protein). Including estimates for the very long-chain fatty acyl-CoAs, the overall rate of sphingolipid biosynthesis can be estimated to be at least ∼1.6-fold higher. Thus, consideration of these factors gives a more accurate picture of de novo sphingolipid biosynthesis than has been possible to-date, while acknowledging that there are inherent limitations to such approximations.
Maintenance of body temperature in elderly patients who have joint replacement surgery A comparison between the heat and moisture exchanger and heated humidifier

The effect of a heat and moisture exchanger on intra‐operative aural canal (core) and mean skin temperatures was investigated in elderly patients who had elective total hip arthroplasty under general anaesthesia with artificial ventilation of the lungs. Group 1 (n = 20) did not receive any form of artificial humidification while in group 2 (n = 20) a heat and moisture exchanger was inserted in the breathing system and in group 3 (n = 20) the inspired gases were humidified and warmed at 40°C by means of a heated humidifier. Time of surgery, intravenous fluid administration and operating theatre temperature were standardised. Mean (SD) aural canal (core) temperature decreased significantly in groups 1 and 2 (p < 0.001), while there was a fall of 0.3°C(0.6) in group 3, which was not significant. Mean skin temperature decreased during anaesthesia and surgery in both groups 1 and 2 (p < 0.05), while it increased in group 3. There was a significantly greater loss of body heat in groups 1 and 2 compared with group 3 intra‐operatively (p < 0.001). We conclude that a heat and moisture exchanger did not prevent the decrease in intra‐operative body temperature in elderly patients.
A novel sleeve monopole with broad bandwidth

Owing to simplicity, polarization purity, power capacity, good match, and low cost, the use of a coaxially fed monopole in a parallel plate waveguide is an attractive option as an adapter or a feed and has been extensively investigated for years. However, a simple coaxially fed linear monopole particularly offers a narrow impedance bandwidth. So some modified monopoles have been often applied to wireless communication antennas in the past decades. The input impedance performance has been significantly improved by means of the various loading techniques, such as dielectric coatings, attached dielectric resonator structures, and disc-ended or top-hat structures. Previously, an alternative is a leaky-mode aperture-coupled dielectric resonator, which has been successfully used as a feed of a class of omnidirectional antennas suitable for wireless communication systems. In this article, a novel sleeve monopole type is proposed to further improve the impedance performance of a monopole. This structure simply consists of a second sleeve and a sleeve monopole vertically put between a parallel plate waveguide. Compared to traditional structures used in a parallel plate waveguide, this modified sleeve monopole has the merit of noticeably broad impedance bandwidth and still maintains the feature of simple structure, low cost, and pure polarization. Because of simple manufacture, broad bandwidth, and good match, this novel structure has shown a promising potential application in various microwave applications and wireless/satellite communications.
Compact fractal patch microstrip antenna fed by coplanar waveguide for long term evolution communications

This paper proposes a new design of compact fractal patch microstrip antenna fed by coplanar waveguide to reduce the antenna dimension and to increase its bandwidth for Long Term Evolution application purposes. The results shown return loss of −23.45 dB and VSWR 1.144 can be achieved by controlling the height and the width of the fractal patch dimension. Bandwidth of the proposed antenna is 375 MHz which is equal to an increase of 200% compared to the conventional rectangular patch antenna and also the dimension of fractal patch antenna can be reduced until 66%.
Intellectual decline predicts the parietal perfusion deficit in Alzheimer's disease.

UNLABELLED The pathophysiology of Alzheimer's disease may be reflected more in an individual's decline from premorbid levels of functioning than in current measures of absolute severity. To test this hypothesis, we computed an index of intellectual decline for individual patients and examined its relationship to Alzheimer's disease-related functional brain abnormalities. METHODS We studied 27 patients with Alzheimer's disease diagnosed by ADRDA-NINCDS criteria. We used patient demographics and published formulas to construct estimates of premorbid Wechsler Adult Intelligence Scale (WAIS-R) IQs for each subject in the sample and used a current IQ assessment to estimate the decline in IQ that occurred during the disease for each subject. Cortical perfusion was quantified by the planar 133Xe regional cerebral blood flow (rCBF) technique. The characteristic abnormality in parietal cortex was expressed by the parietal index (PI). RESULTS Over the estimated disease duration of 3.8 +/- 2.2 yr, the full-scaled IQ declined by an estimated 28.0 +/- 15.5 points. The current PI was in turn well correlated with the IQ decline (r = 0.66; p < 0.001). This association was linear and stronger than those with other, more common measures of current severity. A multiple stepwise regression analysis suggested that IQ decline alone accounted for the variance in PI related to clinical deterioration. Actual images showed a mild blood flow deficit in patients with the smallest estimated IQ declines but deep and extensive lesions in patients with large declines. CONCLUSION These results suggest that the decline from the premorbid baseline, rather than current level of functioning, best predicts the extent of brain damage reflected in the rCBF abnormality, a finding independent of demographic variance.
Image Blob Detection : A Machine Learning Approach

The field of computer vision has developed several methods of detecting contiguous circular pixel areas, or blobs. While both blob detection and computer vision are both still in their infancy, they are already being used in a variety of applications with significant successes. This study examined the effectiveness of classification-based machine learning algorithims on blobs and compared several models with a baseline to measure their performance. The system’s objective was to take an image of a golf course as input and output the location of a golf ball in the image, if one is detected. The system took a raw image file as input, scanned it for blobs using image processing software, and then classified each blob as positive or negative as output. Results showed that several classification models, especially tree-based models such as Random Forest, could be used to classify blobs with statistically significant success.
Localization and Quantum Percolation

Electronic wave functions are studied on dilute lattices, at dimensionalities $1l~dl~8$. Generalized average inverse participation ratios are expanded in powers of the bond concentration, $p$. $Dlog$ Pad\'e approximants indicate that these ratios diverge as ${({p}_{q}\ensuremath{-}p)}^{{\ensuremath{\gamma}}_{q}}$, signaling the appearance of extended states for $pg{p}_{q}$. These Anderson transitions occur above classical percolation. No divergence is detected at $d=2$. These results are consistent with the existence of localized states at the center of the band.
Cardiac remodelling and myocardial recovery: lost in translation?

The insight that decreases in left ventricular (LV) volume and mass occur secondary to the recovery of the myocardium at the cellular and molecular level has engendered a wider appreciation of the importance of LV remodelling as a mechanism for worsening heart failure. Despite these recent insights into the recognition of the importance of LV reverse remodelling in heart failure, many clinicians do not consider simple measurements of LV structure (i.e. LV volume) in their routine clinical decision‐making process, preferring instead to rely on measurements of LV function [e.g. ejection fraction (EF)] when making decisions about medical and surgical treatment options. Although there are probably multiple reasons of why the use of LV volumes has not gained wider acceptance in day‐to‐day clinical management of heart failure patients, the most likely reason is that clinicians remain extremely comfortable using the LVEF to assess their heart failure patients. Importantly, LV volumes predict outcome more reliably than does the EF. Moreover, knowledge regarding LV volumes is extremely useful in optimizing patient selection for surgical and device therapies. Based on the foregoing arguments, we suggest that it is time to begin developing individualized clinical strategies based upon a consideration of the important role that LV remodelling plays in the pathogenesis of heart failure, and that we begin to incorporate measurements of LV volume and mass into the clinical decision‐making process.
A Matched‐Cohort Study of Utilization Outcomes for an Adult Medicaid Population Enrolled in an Asthma Disease Management Program

Few studies have examined the clinical and utilization impact of asthma disease management programs for Medicaid beneficiaries. This study examines utilization and clinical outcomes for an adult group of low- to moderate-risk patients with asthma. Propensity scores are used to construct matched samples of treated-control pairs in order to establish equivalent comparison groups and evaluate the effects of program participation. During the program period, the participants experienced 33.3% fewer hospitalizations, 42% fewer bed days, 87% fewer asthma-related admissions, fewer ED visits, and higher rates of medication usage than those for matched controls, suggesting the beneficial impact of participation for Medicaid program participants.
The Seller's Sense: Buying–Selling Perspective Affects the Sensitivity to Expected Value Differences

Previous work comparing pricing decisions by buyers and sellers has primarily focused on the endowment effect, the phenomenon that selling prices exceed buying prices. Here, we examine whether pricing decisions by buyers and sellers also vary in sensitivity to differences between objects' expected values (EVs). Both a loss-aversion account (which posits that losses are weighted more heavily than gains) and a loss-attention account (which posits increased attention to a task when it involves possible losses) predict that pricing decisions by sellers should exhibit higher sensitivity. The latter, however, additionally predicts that this pattern should only emerge under certain conditions. In studies 1 and 2, we reanalyzed two published datasets in which participants priced monetary lotteries as sellers or buyers. It emerged that sellers showed greater EV sensitivity (defined as the rank correlation between the set price for each lottery and its EV) except in a condition with an extended deliberation time of 15 seconds. In study 3, the buyer–seller difference in EV sensitivity was replicated even when the pricing task was presented repeatedly, while in study 4, it was eliminated when buying and selling trials were randomly mixed. The reduction of the “seller's sense” in long deliberation and mixed trials settings supports an attentional resource-based account of the differences between sellers and buyers in their EV sensitivity. Copyright © 2016 John Wiley & Sons, Ltd.
A Novel Planar Printed Dual-Band Magneto-Electric Dipole Antenna

In this paper, a novel planar printed dual-band magneto-electric dipole antenna is proposed. The proposed antenna is composed of a conventional bow-tie patch as an electric dipole, a semi-circular loop that operates as a magnetic dipole, a coplanar ground plane, and a wideband microstrip-to-coplanar-stripline transition balun. By etching a pair of complementary capacitively loaded loop slots on the bow-tie radiation patch, a notched band is introduced to form the dual-band antenna. And a coplanar ground is adopted to make the entire antenna become a planar printed structure. Additionally, the proposed antenna loads the periodical interdigital capacitance structure on the semi-circular loop for the purpose of making the current flowing along the loop maintain the same phase and improving the performances of the magnetic dipole. The proposed antenna was fabricated and measured. The measured results keep in good accordance with the simulated ones. Consequently, the proposed antenna achieves a dual-band operation at 2.37~2.82 GHz (17.3%) and 3.14~4.10 GHz (26.5%) with the Voltage Standing Wave Ratio (VSWR) less than 2, so it can be applied for WLAN (2.4–2.484 GHz) and WiMAX (2.5–2.69 GHz/3.4–3.69 GHz). Meanwhile, the stable gain, symmetrical, and stable unidirectional radiation patterns, low cross polarization, and low back lobe are also obtained at the dual bands.