Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning of Temporal Motor Patterns: An Analysis of Continuous Versus Reset Timing

Our ability to generate well-timed sequences of movements is critical to an array of behaviors, including the ability to play a musical instrument or a video game. Here we address two questions relating to timing with the goal of better understanding the neural mechanisms underlying temporal processing. First, how does accuracy and variance change over the course of learning of complex spatiotemporal patterns? Second, is the timing of sequential responses most consistent with starting and stopping an internal timer at each interval or with continuous timing? To address these questions we used a psychophysical task in which subjects learned to reproduce a sequence of finger taps in the correct order and at the correct times – much like playing a melody at the piano. This task allowed us to calculate the variance of the responses at different time points using data from the same trials. Our results show that while “standard” Weber’s law is clearly violated, variance does increase as a function of time squared, as expected according to the generalized form of Weber’s law – which separates the source of variance into time-dependent and time-independent components. Over the course of learning, both the time-independent variance and the coefficient of the time-dependent term decrease. Our analyses also suggest that timing of sequential events does not rely on the resetting of an internal timer at each event. We describe and interpret our results in the context of computer simulations that capture some of our psychophysical findings. Specifically, we show that continuous timing, as opposed to “reset” timing, is consistent with “population clock” models in which timing emerges from the internal dynamics of recurrent neural networks.
Singularities in the complex physical plane for deep water waves

Abstract Deep water waves in two-dimensional flow can have curvature singularities on the surface profile; for example, the limiting Stokes wave has a corner of $2\lrm{\pi} / 3$ radians and the limiting standing wave momentarily forms a corner of $\lrm{\pi} / 2$ radians. Much less is known about the possible formation of curvature singularities in general. A novel way of exploring this possibility is to consider the curvature as a complex function of the complex arclength variable and to seek the existence and nature of any singularities in the complex arclength plane. Highly accurate boundary integral methods produce a Fourier spectrum of the curvature that allows the identification of the nearest singularity to the real axis of the complex arclength plane. This singularity is in general a pole singularity that moves about the complex arclength plane. It approaches the real axis very closely when waves break and is associated with the high curvature at the tip of the breaking wave. The behaviour of these singularities is more complex for standing waves, where two singularities can be identified that may collide and separate. One of them approaches the real axis very closely when a standing wave forms a very narrow collapsing column of water almost under free fall. In studies so far, no singularity reaches the real axis in finite time. On the other hand, the surface elevation $y(x)$ has square-root singularities in the complex $x$ plane that do reach the real axis in finite time, the moment when a wave first starts to break. These singularities have a profound effect on the wave spectra.
Deciphering the Genome of Polyphosphate Accumulating Actinobacterium Microlunatus phosphovorus

Polyphosphate accumulating organisms (PAOs) belong mostly to Proteobacteria and Actinobacteria and are quite divergent. Under aerobic conditions, they accumulate intracellular polyphosphate (polyP), while they typically synthesize polyhydroxyalkanoates (PHAs) under anaerobic conditions. Many ecological, physiological, and genomic analyses have been performed with proteobacterial PAOs, but few with actinobacterial PAOs. In this study, the whole genome sequence of an actinobacterial PAO, Microlunatus phosphovorus NM-1T (NBRC 101784T), was determined. The number of genes for polyP metabolism was greater in M. phosphovorus than in other actinobacteria; it possesses genes for four polyP kinases (ppks), two polyP-dependent glucokinases (ppgks), and three phosphate transporters (pits). In contrast, it harbours only a single ppx gene for exopolyphosphatase, although two copies of ppx are generally present in other actinobacteria. Furthermore, M. phosphovorus lacks the phaABC genes for PHA synthesis and the actP gene encoding an acetate/H+ symporter, both of which play crucial roles in anaerobic PHA accumulation in proteobacterial PAOs. Thus, while the general features of M. phosphovorus regarding aerobic polyP accumulation are similar to those of proteobacterial PAOs, its anaerobic polyP use and PHA synthesis appear to be different.
Coronary Plaque Morphology and Frequency of Ulceration Distant From Culprit Lesions in Patients With Unstable and Stable Presentation

Objective—Intravascular ultrasound studies describe ruptured coronary plaques at sites remote from the culprit lesion in patients with acute myocardial infarction (MI), suggesting multifocal plaque vulnerability. However, the role of intravascular ultrasound in the diagnosis of lesion vulnerability before rupture is unclear. Methods and Results—We compared morphology and frequency of ulceration of additional plaques proximal to the culprit lesion in 105 patients treated with emergent stenting during an evolving, acute MI in the CADILLAC study and 92 patients with stable/subacute presentation who underwent elective stenting. Additional plaques proximal to the culprit lesion were found in 52 (50%) and 54 (59%) patients in the acute MI and stable/subacute group, respectively. The prevalence of ulceration was significantly higher in the acute MI than in the stable/subacute group (19% versus 4%; P =0.014). However, there was no significant difference in other morphological lesion characteristics. Conclusions—Additional plaques are frequently found adjacent to the culprit lesions in patients undergoing percutaneous coronary intervention independent of clinical presentation. The increased prevalence of plaque ulceration but otherwise similar morphology of additional lesions in patients with acute MI versus stable/subacute presentation demonstrates the limitations of imaging in the assessment of plaque vulnerability.
Noninfectious endophthalmitis associated with intravitreal triamcinolone injection.

BACKGROUND Intravitreal injection of triamcinolone has been advocated to treat exudative macular diseases such as macular edema and choroidal neovascularization. OBJECTIVE To describe 7 patients who developed a clinical picture simulating endophthalmitis after intravitreal triamcinolone injection. METHODS Intravitreal triamcinolone injections were performed to treat refractory cystoid macular edema or diffuse macular edema associated with diabetic retinopathy, macular pucker, branch retinal vein occlusion, or pseudophakia. One patient received an injection in an attempt to treat exudation associated with occult choroidal neovascularization. RESULTS Preinjection visual acuity ranged from 20/50 to 20/400. An extensive inflammatory response developed 1 to 2 days after injection in all 7 eyes. Five eyes had previously undergone vitrectomy. Four eyes had a layered hypopyon. All 7 eyes had an anterior chamber cellular reaction and vitritis. Visual acuity ranged from 20/400 to hand movements. The first 6 patients were treated for presumed endophthalmitis with vitreous cultures and intravitreal injections of antibiotics. All 6 cultures were negative for any organisms, and the eyes resolved their inflammatory response, with recovery to preinjection visual acuity or better. The seventh patient was treated with topical prednisolone without antibiotic therapy, and the inflammation resolved, with resolution of the macular edema seen before the intravitreal triamcinolone injection. CONCLUSION It may be appropriate to closely observe noninfectious, toxic endophthalmitis in patients treated with intravitreal triamcinolone before assuming it to be infectious, especially in the absence of eye pain.
The Importance of Interphase Contacts in Li Ion Electrodes: The Meaning of the High-Frequency Impedance Arc

Li insertion electrodes are made by pressing a mixture of active material and additives on a metallic substrate. Here we estimate how various interphase contacts affect the electrode kinetics. We apply variable external mechanical pressure onto different cathodes and measure their impedance response. Similar experiments are performed on dry composites in contact with: Al or Cu foil, or Ag paste. Most surprisingly, we find that the high-frequency impedance arc is due to the contact impedance between the metal and the electrode material. This is in fundamental contradiction with previous interpretations. We propose an equivalent circuit explaining the observed phenomena.
Donor‐derived human herpes virus 8‐related Kaposi's sarcoma in renal allograft ureter

Abstract: We present a case of human herpes virus 8 (HHV8)‐associated Kaposi sarcoma (KS) occurring in a renal allograft ureter from a male donor. The female patient presented with a rising creatinine due to ureteric obstruction, and subsequent histological examination of the excised tumor revealed a KS. The tumor tested positive for HHV8 antigen and, using in situ hybridization to identify X and Y chromosomes, we were able to demonstrate that the tumor was of male origin. In the absence of any other KS lesions, this suggested that the tumor arose due to reactivation of latent HHV8 in the donor tissue, permitted by the recipient's immunosuppression. The patient was managed by a gradual reduction in immunosuppression and there has been no subsequent recurrence of the tumor. KS in renal transplantation is discussed in detail including the possible utility of pre‐transplant HHV8 screening.
Last-Level Cache Side-Channel Attacks are Practical

We present an effective implementation of the Prime+Probe side-channel attack against the last-level cache. We measure the capacity of the covert channel the attack creates and demonstrate a cross-core, cross-VM attack on multiple versions of GnuPG. Our technique achieves a high attack resolution without relying on weaknesses in the OS or virtual machine monitor or on sharing memory between attacker and victim.
Critical Flaws in the Female Sexual Function Index and the International Index of Erectile Function

The Female Sexual Function Index (FSFI; Rosen et al., 2000) and International Index of Erectile Function (IIEF; Rosen et al., 1997) are two of the most widely used measures of sexual dysfunction. However, they have potential measurement and psychometric flaws that have not been addressed in the literature. This article examines the measurement capabilities of these measures based on data collected from an online study in 2010. A convenience sample of 518 sexually active adults (65% female) drawn from the general community were included in the analyses. Both measures displayed critical theoretical and measurement problems for the assessment of sexual problems beyond sexual arousal, and for the sexual desire domains in particular. Based on these results, we encourage clinicians and researchers to think critically about whether the FSFI and IIEF are appropriate measures for their practice and research. In particular, these measures are inappropriate for use among individuals who are not currently sexually active, and research with a focus other than sexual arousal should consider supplementary measures of sexual function. The psychometric properties of these measures should be reassessed in clinical samples, but the theoretical issues with the measures raised in this article are relevant across clinical and research contexts.
Silicon Carbide-Silicon Dioxide Transition Layer Mobility

We present transition layer electron mobility versus field curves for several 4H-SiC/SiO2 structures, simulated by a newly developed Monte Carlo simulator that uses density of states calculated by density functional theory (DFT). Our calculations show that among all structures, abrupt SiC/SiO2 has the highest transition layer mobility.
Accuracy of symptoms, signs, and C-reactive protein for early chronic obstructive pulmonary disease.

BACKGROUND Guidelines recommend detection of early chronic obstructive pulmonary disease (COPD), but evidence on the diagnostic work-up for COPD only concerns advanced and established COPD. AIM To quantify the accuracy of symptoms and signs for early COPD, and the added value of C-reactive protein (CRP), in primary care patients presenting with cough. DESIGN AND SETTING Cross-sectional diagnostic study of 73 primary care practices in the Netherlands. METHOD Four hundred primary care patients (182 males, mean age 63 years) older than 50 years, presenting with persistent cough (>14 days) without established COPD participated, of whom 382 completed the study. They underwent a systematic diagnostic work-up of symptoms, signs, conventional laboratory CRP level, and hospital lung functions tests, including body plethysmography, and an expert panel decided whether COPD was present (reference test). The independent value of all items was estimated by multivariable logistic regression analysis. RESULTS According to the expert panel, 118 patients had COPD (30%). Symptoms and signs with independent diagnostic value were age, sex, current smoking, smoking more than 20 pack-years, cardiovascular comorbidity, wheezing complaints, diminished breath sounds, and wheezing on auscultation. Combining these items resulted in an area under the receiver operating characteristic curve (ROC area) of 0.79 (95% confidence interval = 0.74 to 0.83) after internal validation. The proportion of subjects with elevated CRP was higher in those with early COPD, but CRP added no relevant diagnostic information above symptoms and signs. CONCLUSION In subjects presenting with persistent cough, the CRP level has no added value for detection of early COPD.
Interpretative strategies for lung function tests

SERIES “ATS/ERS TASK FORCE: STANDARDISATION OF LUNG FUNCTION TESTING” Edited by V. Brusasco, R. Crapo and G. Viegi Number 5 in this Series This section is written to provide guidance in interpreting pulmonary function tests (PFTs) to medical directors of hospital-based laboratories that perform PFTs, and physicians who are responsible for interpreting the results of PFTs most commonly ordered for clinical purposes. Specifically, this section addresses the interpretation of spirometry, bronchodilator response, carbon monoxide diffusing capacity ( D L,CO) and lung volumes. The sources of variation in lung function testing and technical aspects of spirometry, lung volume measurements and D L,CO measurement have been considered in other documents published in this series of Task Force reports 1–4 and in the American Thoracic Society (ATS) interpretative strategies document 5. An interpretation begins with a review and comment on test quality. Tests that are less than optimal may still contain useful information, but interpreters should identify the problems and the direction and magnitude of the potential errors. Omitting the quality review and relying only on numerical results for clinical decision making is a common mistake, which is more easily made by those who are dependent upon computer interpretations. Once quality has been assured, the next steps involve a series of comparisons 6 that include comparisons of test results with reference values based on healthy subjects 5, comparisons with known disease or abnormal physiological patterns ( i.e. obstruction and restriction), and comparisons with self, a rather formal term for evaluating change in an individual patient. A final step in the lung function report is to answer the clinical question that prompted the test. Poor choices made during these preparatory steps increase the risk of misclassification, i.e. a falsely negative or falsely positive interpretation for a lung function abnormality or a change …
Multiple Regulation of Rad51-Mediated Homologous Recombination by Fission Yeast Fbh1

Fbh1, an F-box helicase related to bacterial UvrD, has been proposed to modulate homologous recombination in fission yeast. We provide several lines of evidence for such modulation. Fbh1, but not the related helicases Srs2 and Rqh1, suppressed the formation of crossover recombinants from single HO-induced DNA double-strand breaks. Purified Fbh1 in complex with Skp1 (Fbh1-Skp1 complex) inhibited Rad51-driven DNA strand exchange by disrupting Rad51 nucleoprotein filaments in an ATP-dependent manner; this disruption was alleviated by the Swi5-Sfr1 complex, an auxiliary activator of Rad51. In addition, the reconstituted SCFFbh1 complex, composed of purified Fbh1-Skp1 and Pcu1-Rbx1, displayed ubiquitin-ligase E3 activity toward Rad51. Furthermore, Fbh1 reduced the protein level of Rad51 in stationary phase in an F-box-dependent, but not in a helicase domain-independent manner. These results suggest that Fbh1 negatively regulates Rad51-mediated homologous recombination via its two putative, unrelated activities, namely DNA unwinding/translocation and ubiquitin ligation. In addition to its anti-recombinase activity, we tentatively suggest that Fbh1 might also have a pro-recombination role in vivo, because the Fbh1-Skp1 complex stimulated Rad51-mediated strand exchange in vitro after strand exchange had been initiated.
A high‐throughput screen for antibiotic drug discovery

We describe an ultra‐high‐throughput screening platform enabling discovery and/or engineering of natural product antibiotics. The methodology involves creation of hydrogel‐in‐oil emulsions in which recombinant microorganisms are co‐emulsified with bacterial pathogens; antibiotic activity is assayed by use of a fluorescent viability dye. We have successfully utilized both bulk emulsification and microfluidic technology for the generation of hydrogel microdroplets that are size‐compatible with conventional flow cytometry. Hydrogel droplets are ∼25 pL in volume, and can be synthesized and sorted at rates exceeding 3,000 drops/s. Using this technique, we have achieved screening throughputs exceeding 5 million clones/day. Proof‐of‐concept experiments demonstrate efficient selection of antibiotic‐secreting yeast from a vast excess of negative controls. In addition, we have successfully used this technique to screen a metagenomic library for secreted antibiotics that kill the human pathogen Staphylococcus aureus. Our results establish the practical utility of the screening platform, and we anticipate that the accessible nature of our methods will enable others seeking to identify and engineer the next generation of antibacterial biomolecules. Biotechnol. Bioeng. 2014;111: 232–243. © 2013 Wiley Periodicals, Inc.
Automatic prediction of polysaccharide utilization loci in Bacteroidetes species

MOTIVATION A bacterial polysaccharide utilization locus (PUL) is a set of physically linked genes that orchestrate the breakdown of a specific glycan. PULs are prevalent in the Bacteroidetes phylum and are key to the digestion of complex carbohydrates, notably by the human gut microbiota. A given Bacteroidetes genome can encode dozens of different PULs whose boundaries and precise gene content are difficult to predict. RESULTS Here, we present a fully automated approach for PUL prediction using genomic context and domain annotation alone. By combining the detection of a pair of marker genes with operon prediction using intergenic distances, and queries to the carbohydrate-active enzymes database (www.cazy.org), our predictor achieved above 86% accuracy in two Bacteroides species with extensive experimental PUL characterization. AVAILABILITY AND IMPLEMENTATION PUL predictions in 67 Bacteroidetes genomes from the human gut microbiota and two additional species, from the canine oral sphere and from the environment, are presented in our database accessible at www.cazy. org/PULDB/index.php.
Can money heal all wounds? Social exchange norm modulates the preference for monetary versus social compensation

Compensation is a kind of pro-social behavior that can restore a social relationship jeopardized by interpersonal transgression. The effectiveness of a certain compensation strategy (e.g., repaying money, sharing loss, etc.) may vary as a function of the social norm/relationship. Previous studies have shown that two types of norms (or relationships), monetary/exchange and social/communal, differentially characterize people’s appraisal of and response to social exchanges. In this study, we investigated how individual differences in preference for these norms affect individuals’ perception of others’ as well as the selection of their own reciprocal behaviors. In a two-phase experiment with interpersonal transgression, we asked the participant to perform a dot-estimation task with two partners who occasionally and unintentionally inflicted noise stimulation upon the participant (first phase). As compensation one partner gave money to the participant 80% of the time (the monetary partner) and the other bore the noise for the participant 80% of the time (the social partner). Results showed that the individuals’ preference for compensation (repaying money versus bearing noise) affected their relationship (exchange versus communal) with the partners adopting different compensation strategies: participants tended to form communal relationships and felt closer to the partner whose compensation strategy matched their own preference. The participants could be differentiated into a social group, who tended to form communal relationship with the social partner, and a monetary group, who tended to form communal relationship with the monetary partner. In the second phase of the experiment, when the participants became transgressors and were asked to compensate for their transgression with money, the social group offered more compensation to the social partners than to the monetary partners, while the monetary group compensated less than the social group in general and showed no difference in their offers to the monetary and social partners. These findings demonstrate that the effectiveness of compensation varies as a function of individuals’ preference for communal versus monetary norm and that monetary compensation alone does not heal all wounds.
Electro-Stimulated Piezo-Spectroscopy for Measuring Nano-Scale Residual Stress Fields in Ceramics

Electro-stimulated piezo-spectroscopy (PS) can be quantitatively used for obtaining information about applied and residual stress fields piled up in ceramic materials and devices. PS experiments can be conducted in a field-emission-gun scanning electron microscope (FEG-SEM) equipped with a high spectral resolution cathodoluminescence (CL) spectrometer. Micromechanical information can be thus added to the microscopic crystallographic and chemical information already available in conventional SEM devices. Independent of the physical mechanisms behind CL emission, the spectral position of selected bands in ceramics is shown to possess high stress sensitivity. In addition, given the high scanning flexibility and spatial resolution of the electron beam, residual stress assessments can be performed on relatively large areas with significantly improved spatial resolution as compared with the more popular photo-stimulated PS approach (i.e., using a laser beam as the excitation source). In this paper, we first quantitatively characterize the stress dependence of the spectroscopic bands observed in ruby. Then, based on this knowledge, an application is shown of bi-dimensional residual stress mapping around an indentation print.