Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing the accuracy of estimated terrain elevations across spatial resolution

ABSTRACT Terrain is modelled in Geographic Information Science on a grid, assuming that elevation values are constant within any single pixel of a Digital Elevation Model (DEM). Pixels are considered flat and rigid, for computational simplicity (a ‘rigid pixel’ paradigm). This paradigm does not account for the slope and curvature of terrain within each pixel, generating imprecise measurements, particularly as pixel size increases or in uneven terrain. This paper relaxes the rigid pixel assumption, allowing for possible sub-pixel variations in slope and curvature (a ‘surface-adjusted’ paradigm). This paper compares different interpolation methods to investigate sub-pixel variations for estimating elevation of arbitrary points given a regular grid. Tests interpolating elevation values for 20,000 georeferenced off-centroid random points from a regular grid DEM are presented, using a variety of exact and inexact local deterministic interpolation methods within contiguity configurations incorporating first and second order neighbours. The paper examines the accuracy of surface-adjusted estimations across a progression of spatial resolutions (10 m, 30 m, 100 m, and 1,000 m DEMs) and a suite of terrain types varying in latitude, altitude, slope, and roughness, validating off-centre estimates against direct elevation measurements on 3 m resolution lidar DEM. Results illustrate that the Bi-quadratic and Bi-cubic interpolation methods outperform Weighted Average, Linear, and Bi-linear methods at coarse resolutions and in rough or non-uniform terrain. In smooth or flat terrain and at finest resolutions, the interpolation method impacts estimation accuracy less or not at all. The type of contiguity configuration appears to play a role in estimation errors as well, with tighter neighbourhoods exhibiting higher accuracy. The analysis also examined regularized mathematical surfaces, adding autocorrelated randomly distributed noise to simulate terrain. The results of experiments based on regularized smooth mathematical surfaces do not translate directly to terrain modelling. The analysis also considers the balance between the increased computation times needed to measure surface-adjusted elevation against improvements in accuracy.
Clinical sequencing of the retinitis pigmentosa gene RPGR in over 1,000 cases of vision loss

RPGR pathogenic variants are the major cause of X-linked retinitis pigmentosa. Here, we report the results from 1,033 clinical DNA tests that included sequencing of RPGR . A total of 184 RPGR variants were identified: 78 pathogenic or likely pathogenic, 14 uncertain, and 92 likely benign or benign. Among the pathogenic and likely pathogenic variants, 23 were novel, and most were frameshift or nonsense mutations (87%) and enriched (67%) in RPGR exon 15 (ORF15). Identical pathogenic variants found in different families were largely on different haplotype backgrounds, indicating relatively frequent, recurrent RPGR mutations. None of the 16 mother/affected son pairs showed de novo mutations; all 16 mothers were heterozygous for the pathogenic variant. These last two observations support the occurrence of most RPGR mutations in the male germline.
Distinct seasonal changes and precession forcing of surface and subsurface temperatures in the mid-latitudinal North Atlantic during the onset of the Late Pliocene

The Late Pliocene marks the intensification of Northern Hemisphere Glaciation, offering a unique opportunity to 15 study climate evolution and ice-sheet related feedback mechanisms. In this study, we present high-resolution Mg/Ca-based sea surface (SST) and subsurface temperatures (SubT) derived from foraminiferal species Globigerinoides ruber and Globorotalia hirsuta , respectively, at the Integrated Ocean Drilling Project (IODP) Expedition 306 Site U1313 in the mid-latitudinal North Atlantic during the early Late Pliocene, 3.65 – 3.37 million years ago (Ma). We find distinct differences between our new G. ruber Mg/Ca-based SST record and previously published alkenone-based SST record from the same 20 location. These discrepancies in both absolute values and variations highlight distinct seasonal influences. The G. ruber Mg/Ca-based SST data, reflecting summer temperatures, were primarily influenced by local summer insolation, showing a dominant precession cycle. Conversely, the variations in alkenone-based SST are found to be more indicative of cold season changes, despite previous interpretations of these records as reflecting annual mean temperatures. A simultaneous decline in Mg/Ca-based SST and SubT records from 3.65 to 3.5 Ma suggests a diminished poleward oceanic heat transport, implying a 25 weakening of the North Atlantic Current. A comparison with early Pleistocene G. ruber Mg/Ca-based SST records shows a shift in the dominant climatic cycle from precession to obliquity, alongside a marked increase in amplitude, indicating an enhanced influence of obliquity cycles correlated with the expansion of Northern Hemisphere ice sheets
General mechanisms of coagulation and targets of anticoagulants (Section I)

Summary Contrary to previous models based on plasma, coagulation processes are currently believed to be mostly cell surface-based, including three overlapping phases: initiation, when tissue factor-expressing cells and microparticles are exposed to plasma; amplification, whereby small amounts of thrombin induce platelet activation and aggregation, and promote activation of factors (F)V, FVIII and FXI on platelet surfaces; and propagation, in which the Xase (tenase) and prothrombinase complexes are formed, producing a burst of thrombin and the cleavage of fibrinogen to fibrin. Thrombin exerts a number of additional biological actions, including platelet activation, amplification and self-inhibition of coagulation, clot stabilisation and anti-fibrinolysis, in processes occurring in the proximity of vessel injury, tightly regulated by a series of inhibitory mechanisms. ″Classical″ anticoagulants, including heparin and vitamin K antagonists, typically target multiple coagulation steps. A number of new anticoagulants, already developed or under development, target specific steps in the process, inhibiting a single coagulation factor or mimicking natural coagulation inhibitors.
Effect of flexibility and cis residues in single-molecule FRET studies of polyproline

Polyproline has recently been used as a spacer between donor and acceptor chromophores to help establish the accuracy of distances determined from single-molecule Förster resonance energy transfer (FRET) measurements. This work showed that the FRET efficiency in water is higher than expected for a rigid spacer and was attributed to the flexibility of the polypeptide. Here, we investigate this issue further, using a combination of single-molecule fluorescence intensity and lifetime measurements, NMR, theory, and molecular dynamics simulations of polyproline-20 that include the dyes and their linkers to the polypeptide. NMR shows that in water ≈30% of the molecules contain internal cis prolines, whereas none are detectable in trifluoroethanol. Simulations suggest that the all-trans form of polyproline is relatively stiff, with persistence lengths of 9–13 nm using different established force fields, and that the kinks arising from internal cis prolines are primarily responsible for the higher mean FRET efficiency in water. We show that the observed efficiency histograms and distributions of donor fluorescence lifetimes are explained by the presence of multiple species with efficiencies consistent with the simulations and populations determined by NMR. In calculating FRET efficiencies from the simulation, we find that the fluctuations of the chromophores, attached to long flexible linkers, also play an important role. A similar simulation approach suggests that the flexibility of the chromophore linkers is largely responsible for the previously unexplained high value of R0 required to fit the data in the classic study of Stryer and Haugland.
A quantitative morphometric analysis of rat spinal cord remyelination following transplantation of allogenic Schwann cells

Quantitative morphometric techniques were used to assess the extent and pattern of remyelination produced by transplanting allogenic Schwann cells into demyelinated lesions in adult rat spinal cords. The effects of donor age, prior culturing of donor cells, prior lesioning of donor nerves, and host immunosuppression were evaluated by transplanting suspensions of 30,000 acutely dissociated or cultured Schwann cells from neonatal, young adult, or aged adult rat sciatic nerves into X‐irradiation and ethidium bromide‐induced demyelinated dorsal column lesions, with or without co‐transplantation of neonatal optic nerve astrocytes. Three weeks after transplantation, spinal cords were processed for histological analysis. Under all Schwann cell transplant protocols, large areas containing many Schwann cell‐like myelinated axon profiles could be readily observed throughout most of the lesion length. Within these “myelin‐rich” regions, the vast majority of detectable axons showed a peripheral‐like pattern of myelination. However, interaxonal spacing also increased, resulting in densities of myelinated axons that were more similar to peripheral nerve than intact dorsal columns. Freshly isolated Schwann cells remyelinated more axonal length than cultured Schwann cells, and cells from younger donors remyelinated slightly more axon length than cells from older donors, but all Schwann cell transplant protocols remyelinated tens of thousands of millimeters of axon length and remyelinated axons at similar densities. These results indicate that Schwann cells prepared under a variety of conditions are capable of eliciting remyelination, but that the density of remyelinated axons is much lower than the myelinated axon density in intact spinal cords. J. Comp. Neurol. 443:259–274, 2002. © 2002 Wiley‐Liss, Inc.
Antiretroviral treatment changes in adults from Côte d'Ivoire: the roles of tuberculosis and pregnancy

Objective:To determine the rates and causes of first antiretroviral treatment changes in HIV-infected adults in Côte d'Ivoire. Methods:We evaluated adults who initiated antiretroviral treatment in an outpatient clinic in Abidjan. We recorded baseline and follow-up data, including drug prescriptions and reasons for changing to alternative first-line regimens (drug substitution for any reason but failure) or second-line regimens (switch for failure). Results:Two thousand and twelve HIV-infected adults (73% women) initiated antiretroviral treatment. At baseline, 9% of all patients were on treatment for tuberculosis and 3% of women were pregnant. First-line antiretroviral treatment consisted of two nucleoside reverse transcriptase inhibitors (58% stavudine–lamivudine, 42% zidovudine–lamivudine) and efavirenz (63%), nevirapine (32%) or indinavir (5%). Median follow-up time was 16.9 months. During this time, 205 (10%) patients died and 261 (13%) were lost to follow-up. Overall, the rate of treatment modifications was 20.7/100 patient-years. The most common modifications were drug substitutions for intolerance (12.4/100 patient-years), pregnancy (4.5/100 patient-years) and tuberculosis (2.5/100 patient-years). The rates of intolerance-related substitutions were 17.9/100 patient-years for stavudine, 6.3/100 patient-years for nevirapine, 3.9/100 patient-years for zidovudine and 0.1/100 patient-years for efavirenz. Twenty percent of efavirenz substitutions resulted from pregnancy and 18% of nevirapine substitutions were related to tuberculosis treatment. Conclusion:During the first months following antiretroviral treatment initiation, a third of all treatment changes occurred for reasons other than intolerance to the drug or treatment failure. In Africa, drug forecasting is crucial to ensuring the success of HIV treatment programmes. Drugs that do not require interruptions during pregnancy or tuberculosis treatment should be made more readily available as first-line drugs in sub-Saharan Africa.
Change in choroidal thickness after intravitreal aflibercept in pretreated and treatment-naive eyes for neovascular age-related macular degeneration

Aim Evaluation of effects of intravitreal aflibercept therapy on choroidal thickness (CT) in neovascular age-related macular degeneration. Methods Retrospective cohort study evaluating the change in CT following a loading dose of three intravitreal aflibercept injections at 4 weeks interval. Pretreated and treatment-naive eyes as well as untreated fellow eyes were evaluated at five retinal locations (subfoveal, 300 and 2500 µm nasal and temporal to the fovea) using spectral domain optical coherence tomography prior to and 4 weeks after a loading dose of three intravitreal aflibercept injections. Results A total of 84 treated eyes (61 pretreated, 23 treatment naive) and 48 fellow eyes were enrolled into the study. Treatment-naive and pretreated eyes showed a significant reduction in CT at all retinal locations. The effect was more pronounced in treatment-naive eyes. In the pretreated group, the mean reduction in CT was greatest at 2500 µm temporal to the fovea at 10.7 µm compared with 22.4 at 300 µm nasal to the fovea in the treatment-naive group. Only the fellow eyes in the treatment-naive group showed a significant CT reduction 12 weeks after initiation of therapy to the partner eye. Conclusions Aflibercept induces a reduction in CT in treatment-naive and pretreated eyes with neovascular age-related macular degeneration. There is some evidence of a systemic effect of aflibercept reflected by CT reduction in untreated fellow eyes.
Private Self-Consciousness, Self-Awareness, and the Reliability of Self-Reports

Two studies found that individuals high in private self-consciousness provide self-reports of greater reliability across time than individuals low in private self-consciousness. In addition, Study 2 found that a successful manipulation of self-awareness did not affect test-retest reliability of self-reports among Ss either high or low in private self-consciousness. The hypothesis that individuals high in private self-consciousness have articulated self-schemata of greater temporal stability than individuals low in private self-consciousness received support. The discussion considers (a) how private selfconsciousness, but not self-awareness, influenced test-retest reliability of self-reports, (b) how private self-consciousness and self-awareness may both influence, albeit differentially, the eriterionrelated validity of self-reports, and (c) the possibility that current models of self-consciousness-selfawareness require reformulation.
Edinburgh Research Explorer 1 Cellular protein TTC4 and its cofactor HSP90 are pro-viral for bovine herpesvirus 1

11 Bovine Herpesvirus Type 1 (BoHV-1) infection causes infectious bovine rhinotracheitis and 12 genital disease in cattle, with significant economic and welfare impacts. However, the role of 13 cellular host factors during viral replication remains poorly characterised. A previously 14 performed genome-wide CRISPR knockout screen identified pro-and antiviral host factors 15 acting during BoHV-1 replication. Herein we validate a pro-viral role for a candidate from this 16 screen: the cellular protein tetracopeptide repeat protein 4 (TTC4). We show that TTC4 17 transcript production is upregulated during BoHV-1 infection. Depletion of TTC4 protein 18 impairs BoHV-1 protein production but does not reduce production of infectious virions, 19 whereas overexpression of exogenous TTC4 results in a significant increase in production of 20 infectious BoHV-1 virions. TTC4 itself is poorly characterized (especially in the context of virus 21 infection), but is a known co-chaperone of heat shock protein 90 (HSP90). HSP90 has a well-22 characterized pro-viral role during the replication of diverse herpesviruses, and we therefore 23 hypothesized that HSP90 is also pro-viral for BoHV-1. Drug-mediated inhibition of HSP90 24 using geldanamycin at sub-cytotoxic concentrations inhibited both BoHV-1 protein production 25 and viral genome replication, indicating a pro-viral role for HSP90 during BoHV-1 infection. 26 Our data demonstrates pro-viral roles for both TTC4 and HSP90 during BoHV-1 replication; 27 possibly, interactions between these two proteins are required for optimal BoHV-1 replication, 28 or the two proteins may have independent pro-viral roles.
Intraoperative pathologic diagnosis of thyroid neoplasms. Report on experience with 504 specimens

Intraoperative pathologic examination with frozen section (FS) was performed on 504 specimens of thyroid tissue obtained from 457 patients over a period of 9 years. After examination of permanent sections (PS) a malignant neoplasm was diagnosed in 57 specimens (11.3%); 50 (87%) of these were primary thyroid carcinoma, four (8%) metastatic carcinoma, and three (5%) malignant lymphoma. The FS diagnosis was “benign” in 448 (88.9%), “malignant” in (30) 5.9%, and “deferred” in 26 (5.2%). The sensitivity of FS diagnosis of malignancy was 53% and the specificity and positive predictive value 100%. The negative predictive value was 97.8% and overall accuracy 97.9%. The PS disclosed a malignant neoplasm in 62% of specimens in which FS diagnosis was “deferred. ” Sixty‐eight percent of papillary carcinomas, 87% of undifferentiated carcinomas, and a single case of medullary carcinoma were diagnosed with FS examination. A FS diagnosis of malignancy was not made in any of the ten specimens containing follicular carcinoma; in all ten the neoplasms were well‐differentiated and eight were encapsulated and minimally invasive. The inability to diagnose follicular carcinoma intraoperatively with FS is the most significant factor accounting for the relatively low sensitivity of FS diagnosis of malignant thyroid neoplasms.
The cell biology of peritrichous flagella in Bacillus subtilis

Bacterial flagella are highly conserved molecular machines that have been extensively studied for assembly, function and gene regulation. Less studied is how and why bacteria differ based on the number and arrangement of the flagella they synthesize. Here we explore the cell biology of peritrichous flagella in the model bacterium Bacillus subtilis by fluorescently labelling flagellar basal bodies, hooks and filaments. We find that the average B. subtilis cell assembles approximately 26 flagellar basal bodies and we show that basal body number is controlled by SwrA. Basal bodies are assembled rapidly (< 5 min) but the assembly of flagella capable of supporting motility is rate limited by filament polymerization (> 40 min). We find that basal bodies are not positioned randomly on the cell surface. Rather, basal bodies occupy a grid‐like pattern organized symmetrically around the midcell and that flagella are discouraged at the poles. Basal body position is genetically determined by FlhF and FlhG homologues to control spatial patterning differently from what is seen in bacteria with polar flagella. Finally, spatial control of flagella in B. subtilis seems more relevant to the inheritance of flagella and motility of individual cells than the motile behaviour of populations.
Topical undecylenic acid for herpes simplex labialis: a multicenter, placebo-controlled trial.

A multicenter, patient-initiated, double-blind, placebo-controlled trial of 15% undecylenic acid cream was conducted with 573 patients with recurrent herpes labialis. Treatment was applied 5 or 6 times daily until crusting and then thrice daily until healing. Patients were assessed daily until 48 h after crusting and then every other day until healing. Undecylenic acid significantly reduced the incidence and duration of viral shedding and the duration and severity of itching but did not increase abortive episodes or reduce times to healing, crusting, or progression of lesion size. When treatment was initiated during the prodrome, the time to crusting was reduced (P = .02) and the area under the symptom-time curve for pain and tenderness was reduced, approaching statistical significance (P = .06). Active treatment was well tolerated but caused dysgeusia and local irritation. Undecylenic acid 15% cream reduces viral shedding in recurrent herpes labialis, but clinical benefits are minimal and largely restricted to patients initiating therapy during the prodrome.
NEO-PI-R Neuroticism Scores in Substance-Dependent Outpatients: Internal Consistency and Self-Partner Agreement

We evaluated internal consistency reliabilities and self-partner agreement on Revised NEO Personality Inventory (Costa & McCrae, 1992) Neuroticism (N) domain and facet scores (anxiety, angry hostility, depression, self-consciousness, impulsiveness, vulnerability) in a sample of 48 substance-dependent outpatients. Low internal consistency was seen for self-rated impulsiveness (α = .36). Agreement between self and partner reports was low for impulsiveness (.22) and vulnerability (.24) and was modest for the remaining facets of N (.31 to .34) and the N domain score (.31).
Lower Bounds: From Circuits to QBF Proof Systems

A general and long-standing belief in the proof complexity community asserts that there is a close connection between progress in lower bounds for Boolean circuits and progress in proof size lower bounds for strong propositional proof systems. Although there are famous examples where a transfer from ideas and techniques from circuit complexity to proof complexity has been effective, a formal connection between the two areas has never been established so far. Here we provide such a formal relation between lower bounds for circuit classes and lower bounds for Frege systems for quantified Boolean formulas (QBF). Starting from a propositional proof system P we exhibit a general method how to obtain a QBF proof system P+∀red{P}, which is inspired by the transition from resolution to Q-resolution. For us the most important case is a new and natural hierarchy of QBF Frege systems C-Frege+∀red that parallels the well-studied propositional hierarchy of C-Frege systems, where lines in proofs are restricted to belong to a circuit class C. Building on earlier work for resolution [Beyersdorff, Chew and Janota, 2015a] we establish a lower bound technique via strategy extraction that transfers arbitrary lower bounds for the circuit class C to lower bounds in C-Frege+∀red. By using the full spectrum of state-of-the-art circuit lower bounds, our new lower bound method leads to very strong lower bounds for QBF \FREGE systems: exponential lower bounds and separations for the QBF proof system ACo[p]-Frege+∀red for all primes p; an exponential separation of ACo[p]-Frege+∀red from TCo/d-Frege+∀red; an exponential separation of the hierarchy of constant-depth systems ACo/d-Frege+∀red by formulas of depth independent of d. In the propositional case, all these results correspond to major open problems.
A quasi-sliding mode speed and position observer with a chattering elimination filter

This paper proposes a quasi-sliding mode rotor speed and position observer for surface permanent magnet synchronous motors. The proposed algorithm features a chattering elimination filter used for suppress the chattering over the waveforms of the estimated electromotive forces, from which speed and position are estimated. Such filter is formulated by using equations that ensure a simple design procedure for the observer gains. This chattering elimination strategy is based on the pondered average between the chattering amplitudes of two different estimated electromotive force signals. This technique is viable only because the rotor speed and position observer are designed in a way that guarantees that the estimated electromotive force crosses the sliding surface at each discretization period. Theoretic issues and design procedures for the developed algorithm are discussed on this paper. Simulation results show evidences for the good dynamic performance of this system in a surface permanent magnet synchronous sensorless vector drive. It is achieved despite any parameter uncertainties and load torque disturbances.