Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-Causal Computation

Computation models such as circuits describe sequences of computation steps that are carried out one after the other. In other words, algorithm design is traditionally subject to the restriction imposed by a fixed causal order. We address a novel computing paradigm beyond quantum computing, replacing this assumption by mere logical consistency: We study non-causal circuits, where a fixed time structure within a gate is locally assumed whilst the global causal structure between the gates is dropped. We present examples of logically consistent non- causal circuits outperforming all causal ones; they imply that suppressing loops entirely is more restrictive than just avoiding the contradictions they can give rise to. That fact is already known for correlations as well as for communication, and we here extend it to computation.
When and why do subfertile couples discontinue their fertility care? A longitudinal cohort study in a secondary care subfertility population.

BACKGROUND A substantial number of subfertile couples discontinues fertility care before achieving pregnancy. Most studies on dropouts are related to IVF. The aim here is to examine dropout rates at all stages of fertility care. METHODS We analysed a consecutive cohort of 1391 couples, referred to our secondary care hospital between January 2002 and December 2006. Discontinuation rates were studied at six stages. Stage I: immediately after first visit, Stage II: during diagnostic workup, Stage III: after finishing diagnostic workup but before treatment, Stage IV: during or after non-IVF treatment, Stage V: during IVF, Stage VI: after at least 3 cycles of IVF. Reasons to discontinue and spontaneous pregnancy rates after discontinuation were secondary outcomes. RESULTS In our cohort 319 couples dropped out of fertility care, 76.8%, [95% confidence interval (CI): 72.2-81.4] on their own initiative and 23.2% (95% CI: 18.6-27.8) on doctor's advice. Percentage (95% CI) of couples discontinuing per stage were: Stage I 6.0% (3.4-8.6), Stage II 3.4% (1.5-5.5), Stage III 35.7% (30.5-41.0), Stage IV 23.5% (18.9-28.2), Stage V 17.9% (13.7-22.1) and Stage VI 13.5% (9.7-17.2). Main reasons for dropout (%, 95% CI) were 'emotional distress' (22.3%, 17.7-26.8), 'poor prognosis' (18.8%, 14.5-23.1) and 'reject treatment' (17.2%, 13.1-21.4). The spontaneous ongoing pregnancy rate after discontinuation was 10% (6.7-13.3). CONCLUSION About half of the couples stopped before any fertility treatment was started and one-third stopped after at least one IVF cycle. The main reasons for withdrawal were emotional distress and poor prognosis. This insight may help to improve quality of patient care by making care more responsive to the needs and expectations of subfertile couples.
"Copy and scale" method for doing time-localized M.I.R. estimation:: application to beat-tracking

In this work we propose a "copy and scale" method based on the 1-NN paradigm to estimate time-localized parameters and apply it to the problem of beat-tracking. The 1-NN algorithm consists in assigning the information of the closest item of a pre-annotated database to an unknown target. It can be viewed as a "copy and paste" method. The "copy and scale" method we propose consists in "scaling" this information to adapt it to the properties of the unknown target. For this, we first represent the content of an audio signal using a sampled and tempo-normalized complex DFT. This representation is used as the vectors over which the 1-NN search is performed. Along each vector of the 1-NN space, we store the corresponding annotated beat-marker positions in a normalized form. Once the closest vector is found, its tempo is assigned to the unknown item and the normalized beat-markers are scaled to this tempo in order to provide the estimation of the unknown item beat-markers. We perform a preliminary evaluation of this method and show that, with such a simple method, we can achieve results comparable to the ones obtained with sophisticated approaches.
MIT Open Access

Polarization sensitive optical coherence tomography (PS-OCT) is a functional imaging method that provides additional contrast using the light polarizing properties of a sample. This manuscript describes PS-OCT based on ultrahigh speed swept source / Fourier domain OCT operating at 1050nm at 100kHz axial scan rates using single mode fiber optics and a multiplexing approach. Unlike previously reported PS-OCT multiplexing schemes, the method uses a passive polarization delay unit and does not require active polarization modulating devices. This advance decreases system cost and avoids complex synchronization requirements. The polarization delay unit was implemented in the sample beam path in order to simultaneously illuminate the sample with two different polarization states. The orthogonal polarization components for the depth-multiplexed signals from the two input states were detected using dual balanced detection. PS-OCT images were computed using Jones calculus. 3D PS-OCT imaging was performed in the human and rat retina. In addition to standard OCT images, PS-OCT images were generated using contrast form birefringence and depolarization. Enhanced tissue discrimination as well as quantitative measurements of sample properties was demonstrated using the additional contrast and information contained in the PS-OCT images.
Application of Lung Ultrasonography in the Diagnosis of Childhood Lung Diseases

In this paper, we focus on the characteristics of LUS in diagnosing childhood pulmonary disease. LUS is convenient, noninvasive, and free of radiation. It helps in the differentiation of lung diseases. Therefore, LUS has the potential to become a reference instrument for bedside dynamic respiratory monitoring. We hope that this review will help clinicians become acquainted with LUS and will accelerate the extensive application of LUS in children.
Preoperative Gabapentin Prevents Intrathecal Morphine-Induced Pruritus After Orthopedic Surgery

BACKGROUND:Pruritus is the most common side effect of intrathecal morphine. Gabapentin is an anticonvulsant and had been reported to be effective in some chronic pruritus conditions. Its effect in intrathecal morphine-induced pruritus has not yet undergone an evaluation. METHODS:We randomly allocated 86 patients scheduled for lower limb surgery under spinal anesthesia into two equal groups that received either gabapentin 1200 mg or placebo 2 h before operation in a prospective, double-blind manner. All patients received an intrathecal injection of 15 mg of 0.5% isobaric bupivacaine and 0.2 mg preservative-free morphine. Pruritus was evaluated at 3, 6, 9, 12, and 24 h after intrathecal morphine administration. RESULTS:The incidence of pruritus was significantly more frequent in the placebo group compared with the gabapentin group (77.5% vs 47.5%; P = 0.01). The onset time of pruritus in the gabapentin group (6.2 ± 1.8 h) was significantly delayed compared with that in the placebo group (3.1 ± 0.8 h) (P < 0.0001). The severity of pruritus was significantly more in the placebo group compared with the gabapentin group at 3 and 6 h after intrathecal morphine injection. CONCLUSION:Preoperative gabapentin prevents pruritus induced by intrathecal morphine in patients undergoing lower limb surgery with spinal anesthesia.
Influenza Viral RNA Detection in Blood as a Marker to Predict Disease Severity in Hematopoietic Cell Transplant Recipients

Abstract Influenza RNA in blood (viremia) was detected in 9 of 79 (11.4%) hematopoietic cell transplant recipients with influenza, and was less frequently observed in patients with upper respiratory tract disease only and more frequently in patients infected with 2009 pandemic influenza A/H1N1 strain (versus seasonal strains). Viremia increased the risk of progression to lower respiratory tract disease (LRD), hypoxemia, respiratory failure, and overall and influenza-related death. Among patients with LRD, viremia was associated with increased hazards of overall and influenza-associated death (hazard ratio 3.5, 1.1–12). Thus, influenza viremia may serve as marker for overall poor outcome.
An update on experimental data obtained at the Säntis Tower

The Säntis Tower was instrumented in May 2010 and, to this date, more than 400 flashes were successfully recorded. Lightning current waveforms and their time-derivatives are measured at two different heights along the tower (24-m and 82-m AGL). In this paper, we present a summary of the obtained experimental data.
A Technique for Performing Electrical Impedance Myography in the Mouse Hind Limb: Data in Normal and ALS SOD1 G93A Animals

Objective To test a method for performing electrical impedance myography (EIM) in the mouse hind limb for the assessment of disease status in neuromuscular disease models. Methods An impedance measuring device consisting of a frame with electrodes embedded within an acrylic head was developed. The head was rotatable such that data longitudinal and transverse to the major muscle fiber direction could be obtained. EIM measurements were made with this device on 16 healthy mice and 14 amyotrophic lateral sclerosis (ALS) animals. Repeatability was assessed in both groups. Results The technique was easy to perform and provided good repeatability in both healthy and ALS animals, with intra-session repeatability (mean ± SEM) of 5% ±1% and 12% ±2%, respectively. Significant differences between healthy and ALS animals were also identified (e.g., longitudinal mean 50 kHz phase was 18±0.6° for the healthy animals and 14±1.0° for the ALS animals, p = 0.0025). Conclusions With this simple device, the EIM data obtained is highly repeatable and can differentiate healthy from ALS animals. Significance EIM can now be applied to mouse models of neuromuscular disease to assess disease status and the effects of therapy.
Convolutional Neural Networks Analyzed via Convolutional Sparse Coding

Convolutional neural networks (CNN) have led to many state-of-the-art results spanning through various fields. However, a clear and profound theoretical understanding of the forward pass, the core algorithm of CNN, is still lacking. In parallel, within the wide field of sparse approximation, Convolutional Sparse Coding (CSC) has gained increasing attention in recent years. A theoretical study of this model was recently conducted, establishing it as a reliable and stable alternative to the commonly practiced patch-based processing. Herein, we propose a novel multi-layer model, ML-CSC, in which signals are assumed to emerge from a cascade of CSC layers. This is shown to be tightly connected to CNN, so much so that the forward pass of the CNN is in fact the thresholding pursuit serving the ML-CSC model. This connection brings a fresh view to CNN, as we are able to attribute to this architecture theoretical claims such as uniqueness of the representations throughout the network, and their stable estimation, all guaranteed under simple local sparsity conditions. Lastly, identifying the weaknesses in the above pursuit scheme, we propose an alternative to the forward pass, which is connected to deconvolutional, recurrent and residual networks, and has better theoretical guarantees.
Establishment of a particle-counting method for purified elementary bodies of chlamydiae and evaluation of sensitivities of the IDEIA Chlamydia kit and DNA probe by using the purified elementary bodies

To evaluate the sensitivity of commercially available test kits for detection of chlamydiae, we established a method of purifying Chlamydia trachomatis and Chlamydia pneumoniae elementary bodies (EBs). We then subjected the purified EBs, together with the purified EBs of Chlamydia psittaci, to the IDEIA Chlamydia (IDEIA) and DNA probe test kits to determine the EB numbers at the detection limits. The sensitivities of the test kits were thus compared. The results can be summarized as follows. (i) Intact EBs in the purified preparations were present at 100, 96.3, and 97% for the C. psittaci Cal 10, C. trachomatis L2/434/Bu (L2), and C. pneumoniae TW-183 strains, respectively. The preparations of the L2 and TW-183 EBs contained a few EB envelopes, which reacted with antilipopolysaccharide monoclonal antibodies, as did the intact EBs, indicating that elimination of EB envelopes is not required for testing of the IDEIA kit's sensitivity. (ii) We established a method of counting intact EBs and EB envelopes under a scanning electron microscope after sedimentation of EBs on a coverslip by centrifugation. (iii) The EB numbers per assay at the cutoff level, which is set up in the IDEIA kit, were 9.6 x 10(2), 6.5 x 10(3), and 2.5 x 10(4) for the L2, TW-183, and Cal 10 strains, respectively. When the same EB preparations were applied to the DNA probe kit, the EB number at the cutoff level was 7.5 x 10(3) per assay for the L2 strain, but no reaction occurred for the Cal 10 and TW-183 strains at any EB number, indicating that the DNA probe kit is highly specific for C. trachomatis. Although the IDEIA kit designed for detection of C. trachomatis showed a sensitivity superior to that of the DNA probe, the chlamydial species was not determined by the IDEIA kit.
Mesaconase Activity of Class I Fumarase Contributes to Mesaconate Utilization by Burkholderia xenovorans

ABSTRACT Pseudomonas aeruginosa, Yersinia pestis, and many other bacteria are able to utilize the C5-dicarboxylic acid itaconate (methylenesuccinate). Itaconate degradation starts with its activation to itaconyl coenzyme A (itaconyl-CoA), which is further hydrated to (S)-citramalyl-CoA, and citramalyl-CoA is finally cleaved into acetyl-CoA and pyruvate. The xenobiotic-degrading betaproteobacterium Burkholderia xenovorans possesses a P. aeruginosa-like itaconate degradation gene cluster and is able to grow on itaconate and its isomer mesaconate (methylfumarate). Although itaconate degradation proceeds in B. xenovorans in the same way as in P. aeruginosa, the pathway of mesaconate utilization is not known. Here, we show that mesaconate is metabolized through its hydration to (S)-citramalate. The latter compound is then metabolized to acetyl-CoA and pyruvate with the participation of two enzymes of the itaconate degradation pathway, a promiscuous itaconate-CoA transferase able to activate (S)-citramalate in addition to itaconate and (S)-citramalyl-CoA lyase. The first reaction of the pathway, the mesaconate hydratase (mesaconase) reaction, is catalyzed by a class I fumarase. As this enzyme (Bxe_A3136) has similar efficiencies (k cat/Km ) for both fumarate and mesaconate hydration, we conclude that B. xenovorans class I fumarase is in fact a promiscuous fumarase/mesaconase. This promiscuity is physiologically relevant, as it allows the growth of this bacterium on mesaconate as a sole carbon and energy source.
Comprehensive Predictive Biomarker Analysis for MEK Inhibitor GSK1120212

The MEK1 and MEK2 inhibitor GSK1120212 is currently in phase II/III clinical development. To identify predictive biomarkers, sensitivity to GSK1120212 was profiled for 218 solid tumor cell lines and 81 hematologic malignancy cell lines. For solid tumors, RAF/RAS mutation was a strong predictor of sensitivity. Among RAF/RAS mutant lines, co-occurring PIK3CA/PTEN mutations conferred a cytostatic response instead of a cytotoxic response for colon cancer cells that have the biggest representation of the comutations. Among KRAS mutant cell lines, transcriptomics analysis showed that cell lines with an expression pattern suggestive of epithelial-to-mesenchymal transition were less sensitive to GSK1120212. In addition, a proportion of cell lines from certain tissue types not known to carry frequent RAF/RAS mutations also seemed to be sensitive to GSK1120212. Among these were breast cancer cell lines, with triple negative breast cancer cell lines being more sensitive than cell lines from other breast cancer subtypes. We identified a single gene DUSP6, whose expression was associated with sensitivity to GSK1120212 and lack of expression associated with resistance irrelevant of RAF/RAS status. Among hematologic cell lines, acute myeloid leukemia and chronic myeloid leukemia cell lines were particularly sensitive. Overall, this comprehensive predictive biomarker analysis identified additional efficacy biomarkers for GSK1120212 in RAF/RAS mutant solid tumors and expanded the indication for GSK1120212 to patients who could benefit from this therapy despite the RAF/RAS wild-type status of their tumors. Mol Cancer Ther; 11(3); 720–9. ©2011 AACR.
PRESIDENTIAL GUEST ADDRESS: The Swedish Hip Registry: Increasing the Sensitivity by Patient Outcome Data

The Swedish Hip Register was initiated in 1979. The mission of the register is to improve the outcome of THA. The hypothesis is that feedback of data stimulates participating clinics to reflect and improve. In addition to revision surgery, patient-based outcome measures and radiographic results are included to improve sensitivity. All patients who have a total hip arthroplasty answer a questionnaire preoperatively and again after 1, 6, and 10 years postoperatively. The questionnaire includes the Charnley classification, EQ-5D and visual analog scales concerning pain and overall satisfaction and is used by 31 of 81 units. Average costs for the procedure ($11,000) are obtained from a national database. The mean gain in the EQ-5D index after 1 year for 3900 patients was 0.37, giving a low cost of $3000 per quality adjusted life year. Patient satisfaction and pain amelioration generally was high. The national average 7-year survival (revision as endpoint), has improved from 93.5% (± 0.15) to 95.8 (± 0.15) between the two periods 1979 to 1991 and 1992 to 2003. National implant registers define the epidemiology of primary and revision surgery. In conjunction with individual subjective patient data and radiography they contribute to development of evidence-based THA surgery.
Exploring the effects of graphene oxide concentration on properties and antifouling performance of PEES/GO ultrafiltration membranes

In this study, asymmetric polyphenylene-ether-ether-sulfone (PEES) ultrafiltration (UF) membranes containing graphene oxide (GO) were prepared via non-solvent-induced phase separation process and N-methyl pyrrolidone was used as a solvent. The synthesis of GO was confirmed by Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction analysis. The morphology of the prepared GO nanosheets was observed by field emission scanning electron microscope (FESEM) and transmission electron microscope. The membranes prepared with increasing concentrations of GO nanosheets were characterized by attenuated total reflectance-FTIR, SEM, atomic force microscopy (AFM), contact angle, and UF studies. The FTIR spectra of the GO embedded membranes reveal large amounts of –OH groups present due to the existence of GO nanosheets which improved its surface hydrophilicity. The contact angle of PEES/GO membrane was significantly lower than PEES membrane. The SEM pictures showed that PEES/GO UF membranes had a sponge-like substructure with the increased porosity and pore size. An AFM topography imaging showed that roughnesses of the modified membranes were improved compared to the pristine PEES membrane. The UF studies showed that the pure water flux (JW ) and the bovine serum albumin flux (JP ) were increased with the incorporation of GO into the blend solution. For the membrane with 0.1% GO content, JW increased by 75% and JP improved twofold which correspond to the maximum values of 186 and 113 L m−2 h−1, respectively. Furthermore, the flux recovery ratio results suggested that PEES/GO membranes have better antifouling characteristics due to the changes in membrane morphology and surface hydrophilicity.
Changes in Electrocardiographic P Wave Parameters after Cryoballoon Ablation and Their Association with Atrial Fibrillation Recurrence

Changes in P wave parameters after circumferential pulmonary vein isolation (CPVI) have been previously identified. In this study, we aimed to determine the changes in P wave parameters surface electrocardiogram (ECG) after cryoballoon ablation (CBA) for atrial fibrillation (AF) and evaluate their relationship with AF recurrence.
Defects and Nanocrystals Generated by Si Implantation into aSiO 2

Electrical charge-trapping characteristics have been studied in thermal oxides that were implanted with Si, experimentally using electron spin resonance (ESR), capacitance versus voltage (CV) measurements, transmission electron microscopy (TEM), atomic force microscopy (AFM), and theoretically with Density Functional Theory (DFT) using plane waves. Our study examines possible defect structures associated with excess Si in thermal oxides.
5-HT3 and 5-HT4 antagonists inhibit peristaltic contractions in guinea-pig distal colon by mechanisms independent of endogenous 5-HT

Recent studies have shown that endogenous serotonin is not required for colonic peristalsis in vitro, nor gastrointestinal (GI) transit in vivo. However, antagonists of 5-Hydroxytryptamine (5-HT) receptors can inhibit peristalsis and GI-transit in mammals, including humans. This raises the question of how these antagonists inhibit GI-motility and transit, if depletion of endogenous 5-HT does not cause any significant inhibitory changes to either GI-motility or transit? We investigated the mechanism by which 5-HT3 and 5-HT4 antagonists inhibit distension-evoked peristaltic contractions in guinea-pig distal colon. In control animals, repetitive peristaltic contractions of the circular muscle were evoked in response to fixed fecal pellet distension. Distension-evoked peristaltic contractions were unaffected in animals with mucosa and submucosal plexus removed, that were also treated with reserpine (to deplete neuronal 5-HT). In control animals, peristaltic contractions were blocked temporarily by ondansetron (1–10 μM) and SDZ-205–557 (1–10 μM) in many animals. Interestingly, after this temporary blockade, and whilst in the continued presence of these antagonists, peristaltic contractions recovered, with characteristics no different from controls. Surprisingly, similar effects were seen in mucosa-free preparations, which had no detectable 5-HT, as detected by mass spectrometry. In summary, distension-evoked peristaltic reflex contractions of the circular muscle layer of the guinea-pig colon can be inhibited temporarily, or permanently, in the same preparation by selective 5-HT3 and 5-HT4 antagonists, depending on the concentration of the antagonists applied. These effects also occur in preparations that lack any detectable 5-HT. We suggest caution should be exercised when interpreting the effects of 5-HT3 and 5-HT4 antagonists; and the role of endogenous 5-HT, in the generation of distension-evoked colonic peristalsis.
Mammalian DNA methyltransferases show different subnuclear distributions

In mammalian cells, DNA methylation patterns are precisely maintained after DNA replication with defined changes occurring during development. The major DNA methyltransferase (Dnmt1) is associated with nuclear replication sites during S‐phase, which is consistent with a role in maintenance methylation. The subcellular distribution of the recently discovered de novo DNA methyltransferases, Dnmt3a and Dnmt3b, was investigated by immunofluorescence and by epitope tagging. We now show that both Dnmt3a and Dnmt3b are distributed throughout the nucleoplasm but are not associated with nuclear DNA replication sites during S‐phase. These results suggest that de novo methylation by Dnmt3a and Dnmt3b occurs independently of the replication process and might involve an alternative mechanism for accessing the target DNA. The different subcellular distribution of mammalian DNA methyltransferases might thus contribute to the regulation of DNA methylation. J. Cell. Biochem. 83: 373–379, 2001. © 2001 Wiley‐Liss, Inc.