Miracle-dz/UniFAR-FTUs huggingface dataset:
Hacking brain development to test models of sensory coding

Animals can discriminate myriad sensory stimuli but can also generalize from learned experience. You can probably distinguish the favorite teas of your colleagues while still recognizing that all tea pales in comparison to coffee. Tradeoffs between detection, discrimination, and generalization are inherent at every layer of sensory processing. During development, specific quantitative parameters are wired into perceptual circuits and set the playing field on which plasticity mechanisms play out. A primary goal of systems neuroscience is to understand how material properties of a circuit define the logical operations— computations--that it makes, and what good these computations are for survival. A cardinal method in biology—and the mechanism of evolution--is to change a unit or variable within a system and ask how this affects organismal function. Here, we make use of our knowledge of developmental wiring mechanisms to modify hard-wired circuit parameters in the Drosophila melanogaster mushroom body and assess the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input number, but not cell number, tunes odor selectivity. Simple odor discrimination performance is maintained when Kenyon cell number is reduced and augmented by Kenyon cell expansion.
Reticulocytes in donor RBC units enhance RBC alloimmunization

Although red blood cell (RBC) transfusions save lives, some patients develop clinically-significant alloantibodies against donor blood group antigens, which then have adverse effects in multiple clinical settings. Few effective measures exist to prevent RBC alloimmunization and/or eliminate alloantibodies in sensitized patients. Donor-related factors may influence alloimmunization; thus, there is an unmet clinical need to identify which RBC units are immunogenic. Repeat volunteer blood donors and donors on iron supplements have elevated reticulocyte counts compared to healthy non-donors. Early reticulocytes retain mitochondria and other components, which may act as danger signals in immune responses. Herein, we tested whether reticulocytes in donor RBC units could enhance RBC alloimmunization. Using a murine model, we demonstrate that transfusing donor RBC units with increased reticulocyte frequencies dose-dependently increase RBC alloimmunization rates and alloantibody levels. Transfusing reticulocyte-rich RBC units was associated with increased RBC clearance from the circulation and a robust proinflammatory cytokine response. As compared to previously reported post-transfusion RBC consumption patterns, erythrophagocytosis from reticulocyte-rich units was increasingly performed by splenic B cells. These data suggest that reticulocytes in a donated RBC unit impact the quality of blood transfused, are targeted to a distinct compartment, and may be an underappreciated risk factor for RBC alloimmunization.
Heterogeneity in killing efficacy of individual effector CD8+ T cells against Plasmodium liver stages

Vaccination strategies in mice inducing high numbers of memory CD8+ T cells specific to a single epitope are able to provide sterilizing protection against infection with Plasmodium sporozoites. We have recently found that Plasmodium-specific CD8+ T cells cluster around sporozoite-infected hepatocytes but whether such clusters are important in elimination of the parasite remains incompletely understood. Here we used our previously generated data in which we employed intravital microscopy to longitudinally image 32 GFP-expressing Plasmodium yoelii parasites in livers of mice that had received activated Plasmodium-specific CD8+ T cells after sporozoite infection. We found significant heterogeneity in the dynamics of the normalized GFP signal from the parasites (termed “vitality index” or VI) that was weakly correlated with the number of T cells near the parasite. We also found that a simple model assuming mass-action, additive killing by T cells well describes the VI dynamics for most parasites and predicts a highly variable killing efficacy by individual T cells. Given our estimated median per capita kill rate of k = 0.031/h we predict that a single T cell is typically incapable to kill a parasite within the 48 hour lifespan of the liver stage in mice. Stochastic simulations of T cell clustering and killing of the liver stage also suggested that 1) three or more T cells per infected hepatocyte are required to ensure sterilizing protection; 2) both variability in killing efficacy of individual T cells and resistance to killing by individual parasites may contribute to the observed variability in VI decline, and 3) the stable VI of some clustered parasites cannot be explained by measurement noise. Taken together, our analysis for the first time provides estimates of efficiency at which individual CD8+ T cells eliminate intracellular parasitic infection in vivo.
Identification of a Specific Biomarker of Acinetobacter baumannii Global Clone 1 by Machine Learning and PCR Related to Metabolic Fitness of ESKAPE Pathogens

A. baumannii GC1 is an important high-risk clone that rapidly develops extreme drug resistance in the nosocomial niche. Furthermore, several strains have been identified worldwide in environmental samples, exacerbating the risk of human interactions. ABSTRACT Since the emergence of high-risk clones worldwide, constant investigations have been undertaken to comprehend the molecular basis that led to their prevalent dissemination in nosocomial settings over time. So far, the complex and multifactorial genetic traits of this type of epidemic clones have allowed only the identification of biomarkers with low specificity. A machine learning algorithm was able to recognize unequivocally a biomarker for early and accurate detection of Acinetobacter baumannii global clone 1 (GC1), one of the most disseminated high-risk clones. A support vector machine model identified the U1 sequence with a length of 367 nucleotides that matched a fragment of the moaCB gene, which encodes the molybdenum cofactor biosynthesis C and B proteins. U1 differentiates specifically between A. baumannii GC1 and non-GC1 strains, becoming a suitable biomarker capable of being translated into clinical settings as a molecular typing method for early diagnosis based on PCR as shown here. Since the metabolic pathways of Mo enzymes have been recognized as putative therapeutic targets for ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens, our findings highlight that machine learning can also be useful in knowledge gaps of high-risk clones and provides noteworthy support to the literature to identify relevant nosocomial biomarkers for other multidrug-resistant high-risk clones. IMPORTANCE A. baumannii GC1 is an important high-risk clone that rapidly develops extreme drug resistance in the nosocomial niche. Furthermore, several strains have been identified worldwide in environmental samples, exacerbating the risk of human interactions. Early diagnosis is mandatory to limit its dissemination and to outline appropriate antibiotic stewardship schedules. A region with a length of 367 bp (U1) within the moaCB gene that is not subjected to lateral genetic transfer or to antibiotic pressures was successfully found by a support vector machine model that predicts A. baumannii GC1 strains. At the same time, research on the group of Mo enzymes proposed this metabolic pathway related to the superbug's metabolism as a potential future drug target site for ESKAPE pathogens due to its central role in bacterial fitness during infection. These findings confirm that machine learning used for the identification of biomarkers of high-risk lineages can also serve to identify putative novel therapeutic target sites.
Turbulence mechanism in Klebanoff transition: a quantitative comparison of experiment and direct numerical simulation

The mechanism of turbulence development in periodic Klebanoff transition in a boundary layer has been studied experimentally and in a direct numerical simulation (DNS) with controlled disturbance excitation. In order to compare the results quantitatively, the flow parameters were matched in both methods, thus providing complementary data with which the origin of turbulence in the transition process could be explained. Good agreement was found for the development of the amplitude and shape of typical disturbance structures, the Λ-vortices, including the development of ring-like vortices and spikes in the time traces. The origin and the spatial development of random velocity perturbations were measured in the experiment, and are shown together with the evolution of local high-shear layers. Since the DNS is capable of providing the complete velocity and vorticity fields, further conclusions are drawn based on the numerical data. The mechanisms involved in the flow randomization process are presented in detail. It is shown how the random perturbations which initially develop at the spike-positions in the outer part of the boundary layer influence the flow randomization process close to the wall. As an additional effect, the interaction of vortical structures and high-shear layers of different disturbance periods was found to be responsible for accelerating the transition to a fully developed turbulent flow. These interactions lead to a rapid intensification of a high-shear layer very close to the wall that quickly breaks down because of the modulation it experiences through interactions with vortex structures from the outer part of the boundary layer. The final breakdown process will be shown to be dominated by locally appearing vortical structures and shear layers.
Effects of Jet Temperature on Broadband Shock-Associated Noise

This paper describes an experimental study of the effects of jet heating on broadband shock-associated noise. The noise measurements are supplemented with schlieren flow visualizations that show that the appearance of a Mach disk in the shock cell structure is consistent with the saturation of the broadband shock-associated noise levels for both highly under- and overexpanded jets. The effects of jet heating are then described for the design Mach-number-1.5 nozzle operating at four Mach numbers: two overexpanded (Mj=1.2 and 1.4), and two underexpanded (Mj=1.7 and 1.9). Total temperature ratios in the range of 1.0 to 2.2 are considered in increments of 0.2. These values are chosen to supplement heated air measurements at higher total temperature ratios (between 1.8 to 3.2) and to examine the effects of low levels of heating. It is shown that the peak broadband shock-associated noise rapidly approaches a saturation value in all cases. In the underexpanded cases, the peak broadband shock-associated noise lev.
High responsivity near-infrared photodetectors in evaporated Ge-on-Si

Germanium is considered the most suitable semiconductor for monolithic integration of near-infrared detectors on silicon photonic chips. Here we report on Ge-on-Si near-infrared photodetectors fabricated by thermal evaporation, demonstrating the use of phosphorus spin-on-dopant to compensate the acceptor states introduced by dislocations. The detectors exhibit 1.55 μm responsivities as high as 0.1 A/W, more than two orders of magnitude larger than in undoped devices and comparing well with state-of-the-art p-i-n photodiodes. This approach enables simple and low-cost monolithic integration of near-infrared sensors with silicon photonics.
Collapse behaviour of three-dimensional brick-block systems using non-linear programming

A two-step procedure for the application of non linear constrained programming to the limit analysis of rigid brick-block systems with no-tension and frictional interface is implemented and applied to various masonry structures. In the first step, a linear problem of programming, obtained by applying the upper bound theorem of limit analysis to systems of blocks interacting through no-tension and dilatant interfaces, is solved. The solution of this linear program is then employed as initial guess for a non linear and non convex problem of programming, obtained applying both the \'mechanism\' and the \'equilibrium\' approaches to the same block system with no-tension and frictional interfaces. The optimiser used is based on the sequential quadratic programming. The gradients of the constraints required are provided directly in symbolic form. Ln this way the program easily converges to the optimal solution even for systems with many degrees of freedom. Various numerical analyses showed that the procedure allows a reliable investigation of the ultimate behaviour of jointed structures, such as stone masonry structures, under statical load conditions.
Suppression of Vortex Shedding and Turbulence behind Oscillating Cylinders

The laminar Karman vortex flow in the wake of a cylinder can be suppressed in a certain Reynolds number range, if the cylinder is stimulated to small oscillations in a direction normal to the mean flow either externally by high‐frequency fluctuations, or internally by negative feedback of a hot‐wire signal picked up in the wake. If suppression is obtained, the transverse mean velocity profiles become deeper in comparison with those of vortex shedding, however the drag is of the same order in both cases. On the other hand the laminar vortex flow can be stabilized and extended to both lower and higher Reynolds numbers, by exciting the cylinder with frequencies, which synchronize the wake fluctuations.
Evidence for nonlinear macroscopic polarization in III-V nitride alloy heterostructures

We provide explicit rules to calculate the nonlinear polarization for nitride alloys of arbitrary composition, and hence, the bound sheet charge induced by polarization discontinuity at the interfaces between different alloy and binary (epi)layers. We then present experimental results and simulations of polarization-related quantities in selected nitride-alloy-based heterostructure systems. The agreement of experiment and simulation, also in comparison to previous approaches, strongly suggests that the macroscopic polarization of nitride alloys is indeed nonlinear as a function of composition.
Complex chain of momentum transfer of body segments in the baseball pitching motion

Abstract Baseball pitching requires contributions from and interaction among all limb segments. Most previous investigators have concentrated on the throwing arm itself, but the center of mass (COM) and contribution of all segments in the pitching motion have not been studied. The purpose of this study was to investigate the momentum transfer of all body segments in the pitching motion. The kinematics pitching motion data were captured from three experienced pitchers (one is professional, two are amateurs). A ten‐segment body system was modeled in this study. The results showed that the lowest position of the COM during the pitching cycle occurred around the ball release time and the fastest velocity (2.81±0.18 m/sec) of the COM was in the late cocking phase. The trunk and thigh on the throwing side showed the largest linear momentum among all segments in the late cocking phase. The upper throwing arm and forearm had peak linear momentum in the acceleration phase. The trunk also had the largest angular momentum during the pitching cycle and reached the maximum rotational momentum (4.17±1.22 Kg‐m2/sec) in the late cocking phase and medial bending momentum (9.03±5.78 Kg‐m2/sec) at the end of the late cocking phase. From the time sequence of linear momentum changes, especially in the leading direction, the force transfer from the foot to the trunk then through the upper extremity during the pitching motion was identified. The largest change rate of angular momentum found in the trunk meant that the trunk contributed the largest torque in the pitching motion. Better coordination of the body segments in the pitching motion not only enhances performance but also avoids injury. The coordination of motion by athletes in the pitching motion provides a guideline for better coaching and training.
Methods of theoretical physics

Allis and Herlin Thermodynamics and Statistical Mechanics Becker Introduction to Theoretical Mechanics Clark Applied X-rays Collin Field Theory of Guided Waves Evans The Atomic Nucleus Finkelnburg Atomic Physics Ginzton Microwave Measurements Green Nuclear Physics Gurney Introduction to Statistical Mechanics Hall Introduction to Electron Microscopy Hardy and Perrin The Principles of Optics Harnwell Electricity and Electromagnetism Harnwell and Livingood Experimental Atomic Physics Harnwell and Stephens Atomic Physics Henley and Thirring Elementary Quantum Field Theory Houston Principles of Mathematical Physics Hund High-frequency Measurements Kennard Kinetic Theory of Gases Lane Superfluid Physics Leighton Principles of Modern Physics Lindsay Mechanical Radiation Livingston and Blewett Particle Accelerators Middleton An Introduction to Statistical Communication Theory Morse Vibration and Sound Morse and Feshbach Methods of Theoretical Physics Muskat Physical Principles of Oil Production Present Kinetic Theory of Gases Read Dislocations in Crystals Richtmyer, Kennard, and Lauritsen Introduction to Modern Physics Schiff Quantum Mechanics Seitz The Modern Theory of Solids Slater Introduction to Chemical Physics Slater Quantum Theory of Matter Slater Quantum Theory of Atomic Structure, Vol. I Slater Quantum Theory of Atomic Structure, Vol. II Slater Quantum Theory of Molecules and Solids, Vol. 1 Slater and Frank Electromagnetism Slater and Frank Introduction to Theoretical Physics Slater and Frank Mechanics Smythe Static and Dynamic Electricity Stratton Electromagnetic Theory Thorndike Mesons: A Summary of Experimental Facts Townes and Schawlow Microwave Spectroscopy White Introduction to Atomic Spectra
Probing the trapping and thermal activation dynamics of excitons at single twin defects in GaAs–AlGaAs core–shell nanowires

Time resolved and time-integrated photoluminescence (PL) spectroscopy is used to investigate the trapping and thermal activation dynamics of excitons bound to single twin defects in individual GaAs–AlGaAs core–shell nanowires. The GaAs core exhibits two distinct spectral emission features that are attributed to free and bound excitons. Time resolved measurements reveal lifetimes of τFE∼1.4ns? > and τBE∼4.0ns? > for the free and bound excitons, respectively. For temperatures above 30 K, the global PL intensity is quenched due to non-radiative carrier recombination. In contrast, for temperatures below 20 K we observe clear evidence for thermal detrapping of bound excitons into the continuum. By comparing the time-resolved PL spectra with a two-level rate equation model, quantitative values are obtained for both the exciton trapping and detrapping rates. Our data is consistent with a temperature independent exciton trapping rate >20 GHz that dominates the population dynamics of bound excitons at T = 6 K. At elevated temperature, the detrapping rate is found to adhere to a thermally activated behavior characterized by a thermal activation energy of EA=5.8±1.0meV? >, very close to the energy spacing of bound and free exciton emission features. This observation implies that bound excitons are thermally activated into the excitonic continuum without the need to overcome additional energetic barriers.
Clinical effectiveness and safety of spinal anaesthesia compared with general anaesthesia in patients undergoing hip fracture surgery using a consensus-based core outcome set and patient-and public-informed outcomes: a systematic review and meta-analysis

Background: We conducted a systematic review and meta-analysis of contemporary RCTs to determine the clinical effectiveness of spinal vs general anaesthesia (SA vs GA) in patients undergoing hip fracture surgery using a consensus-based core outcome set, and outcomes deﬁned as important by patient and public involvement (PPI) initiatives. Methods: RCTs comparing any of the core outcomes (mortality, time from injury to surgery, acute coronary syndrome, hypotension, acute kidney injury, delirium, pneumonia, orthogeriatric input, being out of bed at day 1 postoperatively, and pain) or PPI-deﬁned outcomes (return to preoperative residence, quality of life, and mobility status) between SA and GA were identiﬁed from MEDLINE, Embase, Cochrane Library, and Web of Science (2000 to February 2022). Pooled relative risks (RRs) and mean differences (95% conﬁdence intervals [CIs]) were estimated. Results: There was no signiﬁcant difference in the risk of delirium comparing SA vs GA (RR ¼ 1.07; 95% CI, 0.90 e 1.29). Comparing SA vs GA, the RR for mortality was 0.56 (95% CI, 0.22 e 1.44) in-hospital, 1.07 (95% CI, 0.52 e 2.23) at 30 days, and 1.08 (95% CI, 0.55 e 2.12) at 90 days. Spinal anaesthesia reduced the risk of acute kidney injury compared with GA: RR ¼ 0.59 (95% CI, 0.39 e 0.89). There were no signiﬁcant differences in the risk of other outcomes. Few studies reported PPI-deﬁned outcomes, with most studies reporting on one to three core outcomes. Conclusions: Except for acute kidney injury, there were no differences between SA and GA in hip fracture surgery when using a consensus-based core outcome set and patient and public involvement-deﬁned outcomes. Most studies reported limited outcomes from the core outcome set, and few reported outcomes important to patients, which should be considered when designing future RCTs.
Determination of the Aggregate Binding Site of Amyloid Protofi-brils Using Electron Capture Dissociation Tandem MS

: Amyloid fibril formation is a hallmark in a range of human diseases. Analysis of the molecular details of amyloid aggregation, however, are limited by the difficulties in solubilising, separating, and identifying the aggregated biomolecules. Additional labelling or protein modification are required in many current analytical techniques in order to provide molecular details of amyloid protein aggregation, but these modifications may result in protein structure disruption.
“Ain’t that a Shame”: False Tax Declarations and Fraudulent Benefit Claims. Some Analysis and Evidence

This paper begins by listing three ‘uncomfortable’ implications of the standard expected utility model of individual decision-making concerning participation in fiscal crimes: that tax evasion and benefit fraud can be treated identically; fiscal crimes should be endemic; and that all individuals, depending on parameter values, should be either honest or dishonest. Levitt and List’s (2007) utility function relating to decisions with a moral dimension is adapted to offer insight into these implications involving an individual’s ‘optimal honesty’ and ‘moral hinterland’. Predictions are developed that include moral costs as a determinant of dishonest intentions and are tested with reference to some 2,942 questionnaire responses to a 2016 national (UK) survey. This paper offers insight into the way moral costs inform perceptions of the intrinsic value of ‘doing the right thing’ thereby providing a richer analysis of fiscal crimes. The account has particular relevance for policy prescriptions that involve aspects of ‘shame’.