Miracle-dz/UniFAR-FTUs huggingface dataset:
Practicality of detection of genetically modified organisms (GMOs) in food

increase in new GMOs (genetically modified organisms) has led to specific legislation world-wide to regulate the presence and/or the amount of GMOs in food, food ingredients, feeds and agriculture commodities. Regulatory demands of labelling and traceability of GMOs in the food chain need suitable sampling protocols and analytical methods. At present, two main techniques, the DNA-based polymerase chain reaction (PCR) and the protein-based enzyme-linked immunosorbent assay (ELISA) are most widely used, although new technologies, such as microarrays, have been also developed. The highly specific and sensitive real-time PCR (RT-PCR) is the method of choice for GMO quantitative estimatation. The potential and the limits of PCR and the practicality of RT-PCR for GMO detection are discussed in the light of actual legislation and of the constraints imposed by the food production chain.
Tamoxifen-Induced Venothromboembolic Events: Exploring Validation of Putative Genetic Association

Objective A pilot study to examine accrual rates, efficiency of data capture approaches, study design and genotyping capacity for a future genetic validation study was undertaken. Design The process pilot evaluated feasibility of applying a matched case-control design to validate association of two candidate estrogen receptor (ER) single nucleotide polymorphisms (SNPs) with incidence of venothromboembolic events (VTE) in breast cancer patients treated with tamoxifen where criteria included frequency matching by age, number of years diagnosed with breast cancer within 4-year intervals, and geographic residency. Setting The study was conducted at Marshfield Clinic, in central Wisconsin. Participants Study-eligible cases with a breast cancer diagnosis between 1994 and 2006 who experienced a VTE within 5 years of last tamoxifen exposure were matched at a ratio of 1:4 to controls with a breast cancer diagnosed between 1994 and 2006 with no VTE history following tamoxifen exposure for ≥2 years. Methods Feasibility of enrolling, phenotyping, and genotyping 20% of the total number of validated eligible cases and controls was tested in order to project enrollment rates and assess probability of enrolling the projected sample size for the prospective validation study and adequacy of planned data capture. Conditional logistic regression analysis was conducted for the matched case-control study design. Results Enrollment accruals included 19 of 24 targeted cases (79%), and 74 of 96 (77%) targeted controls. Electronic data capture for most variables was nearly 100%. No unexpected statistically significant differences were observed between cases and controls. Capacity to conduct in-house screening for rs2234689 (ER1 PvuII), rs9340799 (ER1 XbaI), rs13146272 (CYP4V2), rs2227589 (SERPINC 1) and rs1613662 (GP6) was successfully established. Association of GP6 with VTE was further validated (P=0.0403; OR, 0.19). Conclusion Accrual rates to the larger prospective study will require a multi-center design to ensure enrollment of adequate numbers of cases and controls for achieving the projected sample size required to validate association of the ER SNPs. To prevent study failure due to poor accrual, the importance of conducting feasibility studies before launching large scale validation studies of genetic association and adverse drug events, is discussed.
A Human Activity Recognition System Based On Sensory Data Related to Object Usage

— Sensor-based Activity Recognition systems usually accounts which sensors have been activated to perform an activity. The system then combines the conditional probabilities of those sensors to represent different activities and takes the decision based on that. However, the information about the sensors which are not activated may also be of great help in deciding which activity has been performed. This paper proposes an approach where the sensory data related to both usage and non-usage of objects are utilized to make the classification of activities. Experimental results also show the promising performance of the proposed method.
Lapped transform-based image denoising with the generalised Gaussian prior

We introduce a new image denoising method based on the statistical modelling of dyadic rearranged lapped transform LT coefficients. Based on Kolomogrov-Smirnov KS goodness of fit test, we have shown that the statistical distribution of the dyadic rearranged LT coefficients in a subband is best approximated by the generalised Gaussian distribution. A Bayesian minimum mean square error MMSE estimator is used to obtain the estimate of noise free coefficients, which is based on modelling the global distribution of the dyadic rearranged LT coefficients using generalised Gaussian distribution. The LT-based image denoising method with generalised Gaussian prior shows highly encouraging both objective and subjective results when compared to several well-known image denoising methods.
Study of relationship between heart rate variability and autonomic function using cold pressor test for Malaysian population

This paper investigates HRV response of healthy subject during cold pressor test using AR spectral analysis with Burg estimation. Cold pressor test is one of the autonomic function tests performed by immersing the hand into cold water. In this study, ECG was recorded from 26 young adults; 9 males and 17 females with age ranging from 20–40. Autoregressive estimated by Burg is used to compute the power spectral density of the R-R interval. From the ongoing results, 22 subjects show an increase of LFnu and a decrease of HFnu during cold pressor while four subjects show opposite response. For LF/HF ratio, nine subjects show values greater than one which indicates a parasympathetic predominance during the CP while 17 from them indicate less than one, reflecting sympathetic predominance.
Severe Acute Respiratory Syndrome Coronavirus Protein nsp1 Is a Novel Eukaryotic Translation Inhibitor That Represses Multiple Steps of Translation Initiation

ABSTRACT Severe acute respiratory syndrome (SARS) coronavirus nonstructural protein 1 (nsp1) binds to the 40S ribosomal subunit and inhibits translation, and it also induces a template-dependent endonucleolytic cleavage of host mRNAs. nsp1 inhibits the translation of cap-dependent and internal ribosome entry site (IRES)-driven mRNAs, including SARS coronavirus mRNAs, hepatitis C virus (HCV), and cricket paralysis virus (CrPV) IRES-driven mRNAs that are resistant to nsp1-induced RNA cleavage. We used an nsp1 mutant, nsp1-CD, lacking the RNA cleavage function, to delineate the mechanism of nsp1-mediated translation inhibition and identify the translation step(s) targeted by nsp1. nsp1 and nsp1-CD had identical inhibitory effects on mRNA templates that are resistant to nsp1-induced RNA cleavage, implying the validity of using nsp1-CD to dissect the translation inhibition function of nsp1. We provide evidence for a novel mode of action of nsp1. nsp1 inhibited the translation initiation step by targeting at least two separate stages: 48S initiation complex formation and the steps involved in the formation of the 80S initiation complex from the 48S complex. nsp1 had a differential, mRNA template-dependent, inhibitory effect on 48S and 80S initiation complex formation. nsp1 inhibited different steps of translation initiation on CrPV and HCV IRES, both of which initiate translation via an IRES-40S binary complex intermediate; nsp1 inhibited binary complex formation on CrPV IRES and 48S complex formation on HCV IRES. Collectively, the data revealed that nsp1 inhibited translation by exerting its effect on multiple stages of translation initiation, depending on the mechanism of initiation operating on the mRNA template.
Predicting chaotic time series.

We present a forecasting technique for chaotic data. After embedding a time series in a state space using delay coordinates, we ''learn'' the induced nonlinear mapping using local approximation. This allows us to make short-term predictions of the future behavior of a time series, using information based only on past values. We present an error estimate for this technique, and demonstrate its effectiveness by applying it to several examples, including data from the Mackey-Glass delay differential equation, Rayleigh-Benard convection, and Taylor-Couette flow.
Challenges in the Knowledge Base Population Slot Filling Task

The Knowledge Based Population (KBP) evaluation track of the Text Analysis Conferences (TAC) has been held for the past 3 years. One of the two tasks of KBP is slot filling: finding within a large corpus the values of a set of attributes of given people and organizations. This task has proven very challenging, with top systems rarely exceeding 30% F-measure. In this paper, we present an error analysis and classification for those answers which could be found by a manual corpus search but were not found by any of the systems participating in the 2010 evaluation. The most common sources of failure were limitations on inference, errors in coreference (particularly with nominal anaphors), and errors in named entity recognition. We relate the types of errors to the characteristics of the task and show the wide diversity of problems that must be addressed to improve overall performance.
Nicotinic ACH receptor subtypes on gastrointestinally projecting neurones in the dorsal motor vagal nucleus of the rat

To determine the predominant nicotinic ACh receptor (nAChR) located on neurones in the dorsal motor nucleus of the vagus (DMV) that project to the gastrointestinal tract, we used the rat brainstem slice preparation and whole‐cell recordings of DMV neurones identified by retrograde DiI tracing to pharmacologically characterize nAChRs. Pressure ejection of acetylcholine (ACh, 250 μm for 200 ms) from a patch pipette placed ≈10‐20 μm from the surface of the recorded cell produced an inward current in most DMV neurones sampled. The average currents for neurones projecting to the fundus, antrum and caecum were 149 ± 38 (n= 25), 115 ± 18 (n= 29) and 117 ± 23 pA (n= 6), respectively. Blockade of the α7 subtype of nAChR with either α‐bungarotoxin (α‐BGT) or methyllycaconitine (MLA) counteracted 60‐75 % of the ACh‐evoked current in DMV neurones projecting to the fundus, antrum and caecum. In neurones projecting to the fundus and the antrum, currents resistant to α‐BGT were significantly blocked by dihydro‐β‐erythroidine (10‐20 nm), an antagonist of the α4β2 subtype of nAChR. In neurones projecting to the caecum, currents resistant to α‐BGT were significantly depressed by a low concentration of mecamylamine (1 μm). Cytisine (100 μm), an agonist of nAChRs that contain the α7 or the β4 subunit, evoked significant currents in caecum‐projecting neurones that were previously exposed to α‐BGT. In contrast, cytisine had no effect on DMV neurones previously exposed to α‐BGT that project to the fundus or antrum. Our data indicate that the prevailing nAChR subtype in DMV neurones projecting to the GI tract is the α7 subtype. In addition, we obtained evidence for the co‐expression of the α4β2 nAChR subtype on DMV neurones projecting to the fundus and antrum, and the α3β4 nAChR subtype on DMV neurones projecting to the caecum.
Research on zero-sequence signal of space vector modulation for three-level neutral-point-clamped inverter based on vector diagram partition

This paper proposes a novel method for analyzing the zero-sequence signal of three-level voltage-source inverter based on vector diagram partition. The inherent relationship between carried-based PWM and SVPWM is demonstrated. It is shown that the two method can worked equivalently through proper selection of active time for the redundant vector in the case of space vector modulation, or zero-sequence signal injections in the case of carried-based modulation. Furthermore, a novel balancing control strategy of NP potential is proposed based the zero-sequence signal injections. Both simulation and experiment result verify the effectiveness of proposed approach.
Water as a Digression Relative to the Dielectric Response in the Frequency Domain for Polymer Composites

The presence of water in insulating solids is known to affect the dielectric properties. Although relaxation processes evolved with the excitation frequency and temperature, further characteristics unfold when contaminant with a high dielectric constant, such as water is involved. When the material consists of a microcomposite, and especially in the advent of incorporation of nanofillers, it is speculated that water molecules may intervene in several different manners. In order to investigate further the potential digression caused by water, dielectric spectroscopy was used on prepared composite specimen. Different types of epoxy microcomposites exhibiting a high content of quartz, i.e. 60% wt. , were prepared. The effects due to the variation of the water content and presence of nanostructures (nanoclay) on the dielectric response will be discussed. With a weight intake of 0.2% of water, the capacity of the epoxy microcomposite exhibits a slight increase (2%) at lower frequencies and losses are found to increase while a shift towards higher frequencies occurs.
Unsupervised learning technique identifies bronchiectasis phenotypes with distinct clinical characteristics.

BACKGROUND Unsupervised learning technique allows researchers to identify different phenotypes of diseases with complex manifestations. OBJECTIVES To identify bronchiectasis phenotypes and characterise their clinical manifestations and prognosis. METHODS We conducted hierarchical cluster analysis to identify clusters that best distinguished clinical characteristics of bronchiectasis. Demographics, lung function, sputum bacteriology, aetiology, radiology, disease severity, quality-of-life, cough scale and capsaicin sensitivity, exercise tolerance, health care use and frequency of exacerbations were compared. RESULTS Data from 148 adults with stable bronchiectasis were analysed. Four clusters were identified. Cluster 1 (n = 69) consisted of the youngest patients with predominantly mild and idiopathic bronchiectasis with minor health care resource use. Patients in cluster 2 (n = 22), in which post-infectious bronchiectasis predominated, had the longest duration of symptoms, greater disease severity, poorer lung function, airway Pseudomonas aeruginosa colonisation and frequent health care resource use. Cluster 3 (n = 16) consisted of elderly patients with shorter duration of symptoms and mostly idiopathic bronchiectasis, and predominantly severe bronchiectasis. Cluster 4 (n = 41) constituted the most elderly patients with moderate disease severity. Clusters 2 and 3 tended to have a greater risk of bronchiectasis exacerbations (P = 0.06) than clusters 1 and 4. CONCLUSION Identification of distinct phenotypes will lead to greater insight into the characteristics and prognosis of bronchiectasis.
Catastrophic pulmonary alveolar hemorrhage complicating warfarin therapy.

A 60-year-old male was admitted with sudden onset of fever, cough, severe breathlessness and hemoptysis. He was taking warfarin 5mg daily following mitral valve replacement 20 years earlier, for rheumatic mitral valve disease. His follow-up was irregular. Physical examination revealed: respiratory rate of 46/ min, pulse 108 / min, blood pressure 110/70 mmHg, temperature 39.20C, prosthetic valve sounds on cardiac auscultation and coarse crackles in the lung fields. Investigation showed: Hb 8.2 gm/ dL, TLC 14500/ mm3, P 82%, L 18% and PCV 32%. Urine 30-40 RBC’s/ HPF. ECg sinus tachycardia. X-ray chest showed bilateral fluffy opacities (Fig. 1). The prothrombin time was 8 minutes (control 13 sec). Oxygen saturation 60% while inhaling 100% oxygen. Other hematological and biochemical laboratory values were normal. CT-scan of the thorax revealed diffuse pulmonary alveolar hemorrhage (Fig. 2). The patient died within 2 hours of hospitalization despite treatment with transfusions with multiple units of fresh frozen plasma and ventilatory support. Diffuse pulmonary alveolar hemorrhage represents a medical emergency, characterized by widespread hemorrhage from the pulmonary microvasculature and often presents with the clinical triad of hemoptysis, anemia and diffuse alveolar consolidation. The causes of diffuse alveolar hemorrhage, include vasculitides, Goodpasture’s syndrome, SLE, leptospirosis hantavirus, and rarely anticoagulant therapy. Diffuse pulmonary alveolar hemorrhage complicating warfarin therapy is associated with a high mortality rate.
FKS2 Mutations Associated with Decreased Echinocandin Susceptibility of Candida glabrata following Anidulafungin Therapy

ABSTRACT This is the first case report of Candida glabrata-disseminated candidiasis describing the acquisition of echinocandin resistance following anidulafungin treatment. The initial isolates recovered were susceptible to echinocandins. However, during 27 days of anidulafungin treatment, two resistant strains were isolated (from the blood and peritoneal fluid). The resistant peritoneal fluid isolate exhibited a Ser663Pro mutation in position 1987 of FKS2 HS1 (hot spot 1), whereas the resistant blood isolate displayed a phenylalanine deletion (Phe659).
Expression cloning of a gibberellin 20-oxidase, a multifunctional enzyme involved in gibberellin biosynthesis.

In the biosynthetic pathway to the gibberellins (GAs), carbon-20 is removed by oxidation to give the C19-GAs, which include the biologically active plant hormones. We report the isolation of a cDNA clone encoding a GA 20-oxidase [gibberellin, 2-oxoglutarate:oxygen oxidoreductase (20-hydroxylating, oxidizing) EC 1.14. 11. -] by screening a cDNA library from developing cotyledons of pumpkin (Cucurbita maxima L.) for expression of this enzyme. When mRNA from either the cotyledons or the endosperm was translated in vitro using rabbit reticulocyte lysates, the products contained GA12 20-oxidase activity. A polyclonal antiserum was raised against the amino acid sequence of a peptide released by tryptic digestion of purified GA 20-oxidase from the endosperm. A cDNA expression library in lambda gt11 was prepared from cotyledon mRNA and screened with the antiserum. The identity of positive clones was confirmed by the demonstration of GA12 20-oxidase activity in single bacteriophage plaques. Recombinant protein from a selected clone catalyzed the three-step conversions of GA12 to GA25 and of GA53 to GA17, as well as the formation of the C19-GAs, GA1, GA9, and GA20, from their respective aldehyde precursors, GA23, GA24, and GA19. The nucleotide sequence of the cDNA insert contains an open reading frame of 1158 nt encoding a protein of 386 amino acid residues. The predicted M(r) (43,321) and pI (5.3) are similar to those determined experimentally for the native GA 20-oxidase. Furthermore, the derived amino acid sequence includes sequences obtained from the N terminus and two tryptic peptides from the native enzyme. It also contains regions that are highly conserved in a group of non-heme Fe-containing dioxygenases.
The renal biopsy.

CONTEXT The first renal biopsy was carried out more than a century ago, but its widespread introduction into clinical use, beginning in the 1950s, helped develop nephrology into the powerful subspecialty of internal medicine that it is today. In the past 25 years, the use of the spring-loaded biopsy gun, in combination with newer visualization techniques, including ultrasound and computed axial tomography scanning, has led to greater tissue yield and to a much lower risk of complication. During this same time, our understanding of renal pathology has increased many fold. Correct fixation and processing of renal biopsy tissue is critical, and the laboratory must be skilled with renal biopsy light microscopy, immunohistochemistry, and transmission electron microscopy preparation. OBJECTIVES To provide an overview of the renal biopsy, including the techniques and its complications, and to summarize proper laboratory methods for processing renal biopsy tissue. DATA SOURCES This article is based on a review of the literature and on the experience of the author. CONCLUSIONS The experienced nephropathologist, knowledgeable in both renal medicine and pathology and thus able to correlate subtle tissue-derived information with appropriate clinical data, remains the most important key to the development of an accurate clinicopathologic diagnosis.
La Autoantigen Is Cleaved in the COOH Terminus and Loses the Nuclear Localization Signal during Apoptosis*

La autoantigen is a 47-kDa nuclear protein that binds to nascent polymerase III transcripts and a number of viral RNAs. We show that La protein was cleaved to generate a 43-kDa fragment during apoptosis of human leukemic HL-60 cells treated with camptothecin or etoposide. Immunofluorescence microscopy showed that the La protein level was increased in the cytoplasm during apoptosis of HL-60 cells. In addition, UV irradiation of HeLa cells led to the cleavage and redistribution of La protein upon apoptosis. Several lines of evidence show that La protein is cleaved by caspase-3 or closely related proteases at Asp-374 in the COOH terminus. When the full-length (La) and COOH-terminally truncated (LaΔC374) forms of La protein were expressed as fusion proteins with green fluorescence protein (GFP), GFP-LaΔC374 was predominantly cytoplasmic, whereas GFP-La was localized in the nucleus. These results suggest that La protein loses the nuclear localization signal residing in the COOH terminus upon cleavage and is thus redistributed to the cytoplasm during apoptosis.
Solution structure and basis for functional activity of stromal cell‐derived factor‐1; dissociation of CXCR4 activation from binding and inhibition of HIV‐1

The three‐dimensional structure of stromal cell‐derived factor‐1 (SDF‐1) was determined by NMR spectroscopy. SDF‐1 is a monomer with a disordered N‐terminal region (residues 1–8), and differs from other chemokines in the packing of the hydrophobic core and surface charge distribution. Results with analogs showed that the N‐terminal eight residues formed an important receptor binding site; however, only Lys‐1 and Pro‐2 were directly involved in receptor activation. Modification to Lys‐1 and/or Pro‐2 resulted in loss of activity, but generated potent SDF‐1 antagonists. Residues 12–17 of the loop region, which we term the RFFESH motif, unlike the N‐terminal region, were well defined in the SDF‐1 structure. The RFFESH formed a receptor binding site, which we propose to be an important initial docking site of SDF‐1 with its receptor. The ability of the SDF‐1 analogs to block HIV‐1 entry via CXCR4, which is a HIV‐1 coreceptor for the virus in addition to being the receptor for SDF‐1, correlated with their affinity for CXCR4. Activation of the receptor is not required for HIV‐1 inhibition.
The Medical Oncologist's Role in Palliative Care: AIOM's Position

1UOC Oncologia, Ospedale SG Calibita, Rome; 2UOC Oncologia Medica, AO Civile, Piacenza; 3Divisione Clinicizzata Oncologia Medica, Policlinico GB Rossi, Verona; 4UOC Oncologia, IDI, IRCCS, Rome; 5UOC Oncologia Medica, AO Universitaria, Parma; 6UOC Oncologia, AO MorgagniPierantoni, Forli; 7UOC Oncologia, AO S. Orsola Malpighi, Bologna; 8UOC Oncologia, Ospedale SS. Giovanni e Paolo, Venice; 9DH Oncologia, Policlinico Umberto I, Rome; 10UOC Oncologia, Ospedali Riuniti, Bergamo; 11UOC Oncologia Medica, Ospedale S. Salvatore, L’Aquila; 12Terapia del dolore e cure palliative, Dip Oncologia, ULSS6, Vicenza; 13AIOM’s President. *Coordinator