Miracle-dz/UniFAR-FTUs huggingface dataset:
Correction to Efficient Calculation of Electronic Absorption Spectra by Means of Intensity-Selected Time-Dependent Density Functional Tight Binding.

During the last two decades density functional based linear response approaches have become the de facto standard for the calculation of optical properties of small- and medium-sized molecules. At the heart of these methods is the solution of an eigenvalue equation in the space of single-orbital transitions, whose quickly increasing number makes such calculations costly if not infeasible for larger molecules. This is especially true for time-dependent density functional tight binding (TD-DFTB), where the evaluation of the matrix elements is inexpensive. For the relatively large systems that can be studied the solution of the eigenvalue equation therefore determines the cost of the calculation. We propose to do an oscillator strength based truncation of the single-orbital transition space to reduce the computational effort of TD-DFTB based absorption spectra calculations. We show that even a sizable truncation does not destroy the principal features of the absorption spectrum, while naturally avoiding the unnecessary calculation of excitations with small oscillator strengths. We argue that the reduced computational cost of intensity-selected TD-DFTB together with its ease of use compared to other methods lowers the barrier of performing optical property calculations of large molecules and can serve to make such calculations possible in a wider array of applications.
Individual migration patterns of Eurasian golden plovers Pluvialis apricaria breeding in Swedish Lapland: Examples of cold spell-induced winter movements

Tracking studies normally focus on long-distance migrants, meaning that our understanding about short-distance migration remains limited. In this study, we present the first individual tracks of the Eurasian golden plover Pluvialis apricaria, a short-distance migrant, which were tracked from a Scandinavian breeding population using geolocators. In addition, golden plovers are known for their cold spell-induced winter movements, and this study provides some first individual tracking data on this type of movements. In three cases the plovers spent the winter in NW Europe and in four cases they departed during winter from NW Europe to spend the rest of the winter in Iberia or Morocco (one bird that was tracked during two subsequent migration cycles moved to Iberia in the first winter but remained in NW Europe during the second winter). The four winter departures were associated with a cold spell in NW Europe during which maximum temperatures dropped to freezing. Cold spell-induced winter movements were notably long and fast. The birds that remained at their NW European wintering site did not experience such cold spell. However, the plovers did not always move in response to freezing temperatures, as demonstrated by the individual that was tracked for a second season, when it experienced four cold spells at its wintering site in NW France without leaving. Little information was obtained about spring migration, but one bird had a prominent counter-clockwise loop migration pattern through E Europe. Due to their cold spell winter movements, golden plovers exhibit great flexibility in migration patterns, resulting in a notably large spread in final wintering areas.
Word mover's distance for affect detection

Emotion detection from text has been an important task in Natural language processing (NLP) for many years. Many approaches were based on the emotional words or lexicon in order to detect emotions. While the word embedding vectors like Word2Vec were successfully employed in many NLP approaches. Also, word mover's distance (WMD) is a method introduced recently to calculate the distance between two documents based on the embedded words. However, this paper is investigating the ability to detect or classify emotions in sentences using word vectorization and distance measures. Our results confirm the novelty of using Word2Vec and WMD in predicting the emotions in text.
Multiple sclerosis: relationships between cytokines, MRI lesion burden, visual evoked potentials and disability scores

Aim: The aim of this study was to investigate the relationships between the disability (EDSS) scores, magnetic resonance imaging (MRI) lesion burden, the visual evoked potential (VEP) latencies and the cytokine levels in patients with multiple sclerosis (MS) that previously not studied. Method: Study group consisted of 40 MS patients with either relapsing-remitting (RR) (n=29) or secondary progressive course (n=11) and control group comprised 35 matched healthy subjects. Student’s t test, Mann-Whitney U, Chi-squared and correlation analyses were used for statistical analyses. Result: In patient group EDSS scores varied from 1.5 to 8.5, all had abnormal MRI T2 plaque burden and 65.0% had abnormal VEP latencies. Serum levels of tumor necrosis factor-alpha (TNF-а) and interleukin-2 receptor (IL-2R) were significantly higher in patients compared to controls (P 0.05). The total EDSS scores significantly correlated with the T2 plaque counts (r=0.637, P 0.05). Conclusion: Our data indicate that despite clinical stability, immunological activity is not interrrupted in MS and the production of different cytokines were not uniformly affected by the immunomodulator medication. New therapeutic strategies correcting cytokine balance may be useful in MS.
Forecasting Pollen Concentration by a Two‐Step Functional Model

Summary A functional regression model to forecast the cypress pollen concentration during a given time interval, considering the air temperature in a previous interval as the input, is derived by means of a two‐step procedure. This estimation is carried out by functional principal component (FPC) analysis and the residual noise is also modeled by FPC regression, taking as the explicative process the pollen concentration during the earlier interval. The prediction performance is then tested on pollen data series recorded in Granada (Spain) over a period of 10 years.
Normotensive Diabetic BB/W Rats Show Enhanced Reflex Tachycardia

Spontaneously diabetic BB/W rats were compared with age-matched regular Wistar and nondiabetic BB/W rats to determine whether the presence of diabetes would alter cardiovascular regulation appreciably. Systolic and mean blood pressures measured with the tail-cuff method from 12 to 26 wk of age tended to be slightly higher in diabetic than nondiabetic BB/W rats, but the differences were not significant. Mean pressures recorded from indwelling catheters in the same rats at 28 wk of age also did not differ significantly, thereby verifying that the diabetic rats were not hypertensive. To measure baroreflex sensitivity, heart-rate responses were elicited reflexly by elevating blood pressure with phenylephrine or lowering it with sodium nitroprusside. Although reflex bradycardia elicited with phenylephrine was the same, reflex tachycardia elicited with sodium nitroprusside was more pronounced in diabetic BB/W than other rats. Underlying autonomic mechanisms were then assessed by repeating the baroreflex tests after either cholinergic blockade with methylatropine or β-adrenergic blockade with propranolol. Magnitude of reflex bradycardia after inhibition by either cholinergic or β-adrenergic blockade still did not differ between rat groups but that of reflex tachycardia remained significantly stronger in diabetic BB/W than other rats. These results collectively show that, although diabetic BB/W rats remained normotensive, they had enhanced reflex tachycardia that persisted even after efferent autonomic blockade. The failure to develop higher pressures with time further indicates that without additional manipulation, these rats cannot be used experimentally to simulate the simultaneous presence of hypertension in diabetic patients.
Mathematical techniques for shape modelling in computer graphics : a distance-based approach

This research is concerned with shape modelling in computer graphics. The dissertation provides a review of the main research topics and developments in shape modelling and discusses current visualisation techniques required for the display of the models produced. In computer graphics surfaces are normally defined using analytic functions. Geometry however, supplies many shapes without providing their analytic descriptions. These are defined implicitly through fundamental relationships between primitive geometrical objects. Transferring this approach in computer graphics, opens new directions in shape modelling by enabling the definition of new objects or supplying a rigorous alternative to analytical definitions of objects with complex analytical descriptions. We review, in this dissertation, relevant works in the area of implicit modelling. Based on our observations on the shortcomings of these works, we develop an implicit modelling approach which draws on a seminal technique in this area: the distance based object definition. We investigate the principles, potential and applications of this technique both in conceptual terms (modelling aspects) and on technical merit (visualisation issues). This is the context of this PhD research. The conceptual and technological frameworks developed are presented in terms of a comprehensive investigation of an object's constituent primitives and modelling constraints on the one hand, and software visualisation platforms on the other. Finally, we adopt a critical perspective of our work to discuss possible directions for further improvements and exploitation for the modelling approach we have developed.
Sequential extractions of selenium soils from Stewart Lake: total selenium and speciation measurements with ICP-MS detection.

Different techniques have been employed in order to evaluate the most efficient procedure for the extraction of selenium from soil as required for speciation. Selenium contaminated sediments from Stewart Lake Wetland, California were used. A strong acid mineralization of the samples gives quantitative total selenium, which is then used to estimate recoveries for the milder extraction methods. The different extraction methodologies involve the sequential use of water, buffer (phosphate, pH 7) and either acid solution (e.g. HNO3 or HCl) or basic solutions (e.g. ammonium acetate, NaOH or TMAH). Pyrophosphate extraction was also evaluated and showed that selenium was not associated with humic acids. The extractants were subsequently analyzed by size exclusion chromatography (SEC) with UV (254 and 400 nm) and on-line ICP-MS detection; anion exchange chromatography, and ion-pair reversed phase chromatography with ICP-MS detection. For sequential extractions the extraction efficiencies showed that the basic extractions were more efficient than the acidic. The difference between the acidic and the basic extraction efficiency is carried to the sulfite extraction, suggesting that whatever is not extracted by the acid is subsequently extracted by the sulfite. The species identified with the different chromatographies were selenate, selenite, elemental selenium and some organic selenium.
Molecular Diagnostics—An Emerging Frontier in Dermatopathology

Advances made within the field of genomics and proteomics have facilitated the emergence of a new era of molecular diagnostics. However, ongoing rapid developments in molecular methodology ensure that this remains a complex field, accessible primarily to scientists who routinely utilize these techniques. For this reason, in this article we provide a concise overview of established and emerging molecular methods and discuss their role as diagnostic adjuncts in Dermatopathology. Important nonmolecular techniques that are used in conjunction with molecular methods are also highlighted.
An efficient blind calibration method for nonlinearity mis-matches in M-channel TIADCs

As gain, offset, and timing mismatches, nonlinearity mismatches also contribute to spurious components which deteriorate TIADC’s performance. This paper proposes an efficient blind calibration method for nonlinearity mismatches in M-channel TIADCs. A modified model for nonlinearity mismatches is established by exploiting binary Hadamard transform (BHT) and differentiator. The calibration is composed of two stages— mismatches compensation and coefficients identification. The principle of mismatches compensation is to reconstruct estimations of the mismatchesinduced spurious components and subtract them from the original TIADC’s output. The coefficients identification is performed based on filtered-x least mean square (FxLMS) algorithm. By using improved model and calibration algorithm, the proposed method consumes less computational resource according to the complexity comparison. To tackle the 4-order nonlinearity mismatches in an 16-channel TIADC, the proposed method consumes 23% fewer multipliers than the previous work. Simulation results reveal that both effective resolution and dynamic range improve a lot after calibration.
ABO blood group-incompatible living donor kidney transplantation: a prospective, single-centre analysis including serial protocol biopsies.

BACKGROUND ABO incompatible kidney transplantation using antigen-specific immunoadsorption is increasingly performed but data on outcome, complications and protocol biopsies are still scarce. The present prospective single-centre study was aimed at these issues. METHODS This was a prospective single-centre cohort study of 10 successive ABO incompatible living donor kidney transplantations at the University Hospital Basel from September 2005 to October 2007. The following parameters were closely monitored during the whole follow-up: graft function, albuminuria, blood group antibody titres, CD19+ cell count, total IgG and IgG subclasses, CMV antigenaemia, decoy cells in the urine, EBV and polyoma BK virus PCR in the blood. Protocol biopsies were performed on Days 0 and 7 after 3, 6, 12 and 18 months. RESULTS Patient and graft survival is 100% after a median follow-up of 489 days (range 183-916 days). Median serum creatinine is 137 micromol/l (range 70-215 micromol/l), and median urine albumin-creatinine ratio (UACR) is 3.1 mg/ mmol (range 0.6-7.8 mg/mmol) at the time of the last follow-up. All patients had sustained diminished CD19+ cell count and/or total IgG concentrations. Neither CMV antigenaemia nor EBV replication in the blood was observed. Seven patients had positive polyoma BK virus replication in the blood but none developed polyoma virus-associated nephropathy (PVAN). Protocol biopsies revealed rejection Banff IIa in three patients on Day 7, and in one patient after 3 and 6 months. Banff Ia rejection was found in five patients. All rejection episodes resolved. Mild signs of chronic antibody-mediated rejection were observed in five patients. CONCLUSIONS ABO-incompatible kidney transplantation seems to be successful and safe. Modifications of the current protocol may be possible and may further reduce potential side effects and costs.
Pediatric Lymphoma: A 10-year Experience at a Tertiary Care Hospital in Pakistan

Lymphoma is the third most common childhood malignancy. Less information is available on this disease and its outcome from our country. We present here a single institute experience. A retrospective study was carried out at Aga Khan University Hospital, Karachi on children (<15 y) diagnosed with lymphoma from 1998 to 2007. Sixty-eight patients were identified. Fifty-one children were diagnosed as non-Hodgkin lymphoma (NHL). Mean age of presentation was 8.4 years with male-to-female ratio of 5.8 : 1. Most common histopathologic subtype of NHL was Burkitt lymphoma (55%). Abdominal mass was the main presenting feature of Burkitt and diffuse large B cell lymphoma. T-lymphoblastic lymphoma presented mainly as mediastinal mass. Ten children died, 4 secondary to tumor lysis syndrome, 5 because of disease progression, and 1 with chemotherapy-induced toxicity. One-third of the patients left without treatment. Seventeen children were diagnosed as Hodgkin lymphoma with mixed cellularity as the commonest subtype (65%). Overall survival of children with NHL and Hodgkin lymphoma was 62% and 94%, respectively. A greater proportion of NHL, advanced stage, and profound male preponderance were observed. Improvement in survival can only be achieved with increasing awareness, identifying and tackling causes of abandonment, early referral, and better supportive care.
Localization of Phosphatidylinositol (3,4,5)-Trisphosphate to Phagosomes in Entamoeba histolytica Achieved Using Glutathione S-Transferase- and Green Fluorescent Protein-Tagged Lipid Biosensors

ABSTRACT Entamoeba histolytica is an intestinal protozoan parasite that causes amoebic dysentery and liver abscess. Phagocytosis by the parasite is a critical virulence process, since it is a prerequisite for tissue invasion and establishment of chronic infection. While the roles of many of the proteins that regulate phagocytosis-related signaling events in E. histolytica have been characterized, the functions of lipids in this cellular process remain largely unknown in this parasite. In other systems, phosphatidylinositol (3,4,5)-trisphosphate (PIP3), a major product of phosphoinositide 3 kinase (PI3-kinase) activity, is essential for phagocytosis. Pleckstrin homology (PH) domains are protein domains that specifically bind to PIP3. In this study, we utilized glutathione S-transferase (GST)- and green fluorescent protein (GFP)-labeled PH domains as lipid biosensors to characterize the spatiotemporal aspects of PIP3 distribution during various endocytic processes in E. histolytica. PIP3-specific biosensors accumulated at extending pseudopodia and in phagosomal cups in trophozoites exposed to erythrocytes but did not localize to pinocytic compartments during the uptake of a fluid-phase marker, dextran. Our results suggest that PIP3 is involved in the early stages of phagosome formation in E. histolytica. In addition, we demonstrated that PIP3 exists at high steady-state levels in the plasma membrane of E. histolytica and that these levels, unlike those in mammalian cells, are not abolished by serum withdrawal. Finally, expression of a PH domain in trophozoites inhibited erythrophagocytosis and enhanced motility, providing genetic evidence supporting the role of PI3-kinase signaling in these processes in E. histolytica.
Active cytomegalovirus infection is not a risk factor for Epstein–Barr virus DNAemia in the allogeneic stem cell transplantation setting

Dear Editor, We read with interest the article by Zallio et al. (1) reporting a statistically significant association between the occurrence of cytomegalovirus (CMV) pp65 antigenemia (AG) and the development of Epstein–Barr (EBV) DNAemia, as determined by real-time PCR (QRT-PCR) in whole blood. These authors suggested that EBV DNAemia monitoring should be intensified in patients with active CMV infection, a strategy that would likely be clinically relevant in standard-risk patients for EBV-associated lymphoproliferative disease (EBV-LPD), who are not routinely monitored at most centers until clinical symptom arise. In a previous study, nevertheless, Carpenter et al. (2), employing QRTPCR assays for measuring both CMV DNA load in plasma and EBV DNA load in PBMCs failed to prove such an association. In the current study, we employed two highly sensitive QRT-PCRs (3–5) to further investigate this issue. Our study cohort consisted of 82 nonconsecutive T-cell replete allo-SCT recipients attended at our center between March 2009 and February 2013 (Table 1). The study period comprised the first 100 d after transplant, time at which both CMV and EBV DNAemia occur at a high rate (6), and CMV and EBV DNAemia monitoring is performed weekly at our center. All patients were EBV seropositive. The patients were treated preemptively with rituximab when EBV DNAemia was >1000 copies/mL. CMV DNAemia was treated preemptively with antivirals as previously reported CMV DNAemia occurred in 67 of 82 patients (7) (81.0%) at a median of 27.5 d after transplant. EBV DNAemia was detected in 27 patients (32.8%) at a median of 49.5 d after transplant. As shown in Table 2, 24 patients experienced both CMV and EBV DNAemia; in 16 of these cases, CMV DNAemia preceded EBV DNAemia. We found no association between the occurrence of CMV DNAemia and the subsequent development of active EBV infection (Table 2). Furthermore, the occurrence of EBV DNAemia was not significantly related to the level of CMV replication, as judged by the need of inception of
The tempo and mode of gopher mound production in a tallgrass prairie remnant

Klaas, B. A. , Moloney, K. A. and Danielson, B. J. 2000. The tempo and mode ofgopher mound production in a tallgrass prairie remnant. – Ecography 23: 246–256.To gain better insight into how small-scale disturbances might affect ecologicalprocesses, such as the maintenance of plant species diversity, we conducted atwo-year study characterizing spatio-temporal patterns of gopher mound productionon a tallgrass prairie remnant located at Anderson Prairie, Iowa, USA. The locationsof all newly produced gopher mounds were mapped on two 80˛80 m permanentplots. We used these data to characterize spatio-temporal patterns of mound produc-tion across a range of scales. We found that mound production was highly clusteredat scales of B8 m over short periods of time (B2 weeks), but shifted in locationover a 3–4 weeks time period, resulting in a clustered pattern at scales of B20 mover longer time periods (up to the 2 yr of the study). We also found that patternsof mound production at intermediate spatial scales (\20 m) remained fairly staticover time, although they differed signiﬁcantly from site to site. The results of thisstudy suggest that small-scale patterns of variability in mound production mayincrease habitat variability over very short spatial scales, possibly providing amechanism that can enhance the development and maintenance of species diversity.
Penicillinase from Klebsiella aerogenes. A comparison with penicillinases from gram-positive species.

Conchie, J. & Levvy, G. A. (1957). Biochem. J. 65, 389. Leaback, D. H. (1960). J. chem. Soc. p. 3166. Levvy, G. A. & McAllan, A. (1961). Biochem. J. 80, 433. Levvy, G. A. , McAllan, A. & Hay, A. J. (1962). Biochem. J. 82, 225. Lineweaver, H. & Burk, D. (1934). J. Amer. chem. Soc. 56, 568. McIlvaine, T. C. (1921). J. biol. Chem. 49, 183. Raymond, A. L. & Schroeder, E. F. (1948). J. Amer. chem. Soc. 70, 2785. Schmid, H. & Karrer, P. (1949). Helv. chim. acta, 32, 1371. Seidman, M. & Link, K. P. (1950). J. Amer. chem. Soc. 72, 4324. Wallenfels, K. & Malhotra, 0. P. (1960). In The Enzymes, 2nd ed., vol. 4, p. 409. Ed. by Boyer, P. D. , Lardy, H. & Myrback, K. New York: Academic Press Inc. Watkins, W. M. (1959). Biochem. J. 71, 261.
Application of N-step-ahead NeuroControl on articulated manipulators

The N-step-ahead control method, called chain-back-propagation, is applied to articulated manipulators. The method is based on a pair of neural networks—the neural controller and the neural emulator—and focuses mainly in the appropriate design of the various global and chain-local penalty functions and the convergence control limitations, needed for the on-line training of the controller. No reference models or paths are needed for the implementation of the method, only set-points. The results, Ž . compared to conventional proportional-derivative PD control and to traditional one-step-ahead neural control, are quite satisfactory, indicating improved accuracy, faster response, and greater overall efficiency. Q 2000 John Wiley & Sons, Inc.