Miracle-dz/UniFAR-FTUs huggingface dataset:
Netting Gut Disease: Neutrophil Extracellular Trap in Intestinal Pathology

Many gut disease etiologies are attributed to the presence of robust inflammatory cell recruitment. The recruitment of neutrophils plays a vital role in inflammatory infiltration. Neutrophils have various antimicrobial effector mechanisms, including phagocytosis, oxidative burst, and degranulation. It is suggested that neutrophils could release neutrophil extracellular traps (NETs) to kill pathogens. However, recent evidence indicates that neutrophil infiltration within the gut is associated with disrupted local immunological microenvironment and impaired epithelial barrier. Growing evidence implies that NETs are involved in the progression of many diseases, including cancer, diabetes, thrombosis, and autoimmune disease. Increased NET formation was found in acute or chronic conditions, including infection, sterile inflammation, cancer, and ischemia/reperfusion injury (IRI). Here, we present a comprehensive review of recent advances in the understanding of NETs, focusing on their effects in gut disease. We also discuss NETs as a potential therapeutic target in gut disease.
Reopening California: Seeking robust, non-dominated COVID-19 exit strategies

The COVID-19 pandemic required significant public health interventions from local governments. Although nonpharmaceutical interventions often were implemented as decision rules, few studies evaluated the robustness of those reopening plans under a wide range of uncertainties. This paper uses the Robust Decision Making approach to stress-test 78 alternative reopening strategies, using California as an example. This study uniquely considers a wide range of uncertainties and demonstrates that seemingly sensible reopening plans can lead to both unnecessary COVID-19 deaths and days of interventions. We find that plans using fixed COVID-19 case thresholds might be less effective than strategies with time-varying reopening thresholds. While we use California as an example, our results are particularly relevant for jurisdictions where vaccination roll-out has been slower. The approach used in this paper could also prove useful for other public health policy problems in which policymakers need to make robust decisions in the face of deep uncertainty.
Ketogenic diet reduces early mortality following traumatic brain injury in Drosophila via the PPARγ ortholog Eip75B

Traumatic brain injury (TBI) is a common neurological disorder whose outcomes vary widely depending on a variety of environmental factors, including diet. Using a Drosophila melanogaster TBI model that reproduces key aspects of TBI in humans, we previously found that the diet consumed immediately following a primary brain injury has a substantial effect on the incidence of mortality within 24 h (early mortality). Flies that receive equivalent primary injuries have a higher incidence of early mortality when fed high-carbohydrate diets versus water. Here, we report that flies fed high-fat ketogenic diet (KD) following TBI exhibited early mortality that was equivalent to that of flies fed water and that flies protected from early mortality by KD continued to show survival benefits weeks later. KD also has beneficial effects in mammalian TBI models, indicating that the mechanism of action of KD is evolutionarily conserved. To probe the mechanism, we examined the effect of KD in flies mutant for Eip75B, an ortholog of the transcription factor PPARγ (peroxisome proliferator-activated receptor gamma) that contributes to the mechanism of action of KD and has neuroprotective effects in mammalian TBI models. We found that the incidence of early mortality of Eip75B mutant flies was higher when they were fed KD than when they were fed water following TBI. These data indicate that Eip75B/PPARγ is necessary for the beneficial effects of KD following TBI. In summary, this work provides the first evidence that KD activates PPARγ to reduce deleterious outcomes of TBI and it demonstrates the utility of the fly TBI model for dissecting molecular pathways that contribute to heterogeneity in TBI outcomes.
Mid-Upper Arm Circumference Assessment and Comparison With Weight for Length Z-Score in Infants ≤6 Months as an Indicator of Severe Acute Malnutrition

Objective To assess the frequency of severe acute malnutrition (SAM) and to determine the validity of mid-upper arm circumference (MUAC) as compared to weight for length z-score (WLZ-score) as an indicator of the nutritional status in this age group. Methods A cross-sectional study, with a purposive sampling was conducted from March 2018 to November 2018 to enroll 540 infants ≤6 months of age from three different sites in Karachi, Pakistan. The anthropometric measurements (MUAC, length and weight) were taken by experienced community health workers. The data were analyzed using SPSS. MUAC was compared with WLZ-score for sensitivity and specificity to observe the concordant among the two diagnostic measures. The Youden Index was used to determine the ideal cut-off for infants less than 6 months of age in this population and the Kappa coefficient was also calculated to assess the agreement between MUAC and WLZ-score. Results The study findings revealed that SAM was found in 13.6% (n=74) of the children. MUAC cut-off ≤11.5 cm yielded the Youden Index of 0.31 with 59.5% sensitivity and 71.4% specificity. The total area under receiver operating characteristic curve was 0.70 (95% CI: 0.63, 0.77; P < 0.001). The degree of agreement between mid-upper arm circumference and weight for length z-score to diagnose SAM ranged from 0.2 to 0.3. Conclusion The Youden index implied that a MUAC cut-off of ≤11.5 cm can be used as an indicator with acceptable validity for diagnosing SAM in children ≤6 months of age in a low middle income developing country like Pakistan.
Synchronous Rectal Tumours with Different Molecular and Genetic Phenotypes Occurring in a Patient with Lynch Syndrome

Abstract The increasingly widespread use of immunohistochemistry and next-generation sequencing (NGS) in the detection of microsatellite instability (MSI) and DNA mismatch repair (MMR) status has led to the observation of various unusual tumour types that exhibit MMR protein deficiency in Lynch syndrome (LS). Here, we report a case of two synchronous colorectal cancer (CRC) tumours simultaneously occurring in a 42-year-old woman with a deleterious germline mutation in MSH6, abundant expression of PD-L1 and high tumour mutation burden (TMB). The two CRC tumours (tumours A and B) harboured highly heterogeneous features. One showed loss of MSH6 protein and a microsatellite stable (MSS)/MSI-low (MSI-L) status, while the other presented no loss of MMR protein and MSI-H status. Furthermore, the 9 common mutated genes between the two CRC tumours had no shared mutation sites. Only 4 KEGG pathways were identified as enriched for five of the common mutated genes, while 8 cancer-related pathways were identified as enriched for 9 and 13 unique mutated genes in tumours A and B, respectively. Therefore, we chose immune checkpoint inhibitors (ICIs) as the potential therapy. This case exemplifies the complexity of tumorigenesis and potential ICI treatment in LS patients.
Targeting Extracellular Vesicles to Dendritic Cells and Macrophages

Targeting protein therapeutics to specific cells and tissues is a major challenge in modern medicine. Improving the specificity of protein therapeutic delivery will significantly enhance efficiency in drug development. One of the promising tools for protein delivery is extracellular vesicles (EVs) that are enveloped by a complex lipid bilayer. EVs are secreted by almost all cell types and possess significant advantages: biocompatibility, stability, and the ability to penetrate the blood–brain barrier. Overexpression of the vesicular stomatitis virus protein G (VSV-G) was shown to promote EV formation by the producer cell. We have developed an EV-based system for targeted delivery of protein cargoes to antigen-presenting cells (APCs). In this study, we show that attachment of a recombinant llama nanobody α-CD206 to the N-terminus of a truncated VSV-G increases the selectivity of EV cargo delivery mainly to APCs. These results highlight the outstanding technological and biomedical potential of EV-based delivery systems for correcting the immune response in patients with autoimmune, viral, and oncological diseases.
Size-dependent enhancement of passive microwave rectification in magnetic tunnel junctions with perpendicular magnetic anisotropy

Spintronic rf detectors were demonstrated, recently, for energy harvesting and wireless communication at low input power. Here we report on the optimization of the rectified output dc voltage using magnetic tunnel junctions (MTJ) with strong perpendicular anisotropy (PMA) of both the polarizing and the free layer. The magnetization of the polarizing layer is fixed out-of-plane, while the free layer thickness is adjusted so that its magnetization orientation changes from in-plane to out-of-plane. The rectification dc output voltage lies in the mV range for moderate rf powers, with a signal-to-noise ratio of 10-100 for Prf = –25dBm. It shows a strong dependence on the dimensions of the MTJ: it increases by a factor of 5-6 when reducing the diameter from 150nm to 20nm. This enhancement can be doubled when reducing the FL thickness from 1.8nm to 1.6nm. This dimensional enhancement is attributed to the change of the effective anisotropy of the excited free layer, and the MTJ resistance. The results are of interest for the design of spintronic based rf detectors with optimized sensitivity.
AeCoM: Design, Modeling and Control of a Novel Aerial Continuum Manipulator

Aerial robotic systems have raised emerging interests in recent years. In this article, we propose a novel aerial manipulator system that is significantly different from conventional aerial discrete manipulators: An Aerial Continuum Manipulator (AeCoM). The AeCoM compactly integrates a quadrotor with a tendon-driven continuum robotic manipulator. Due to the compact design and the payload bearing ability of tendon-driven continuum robotic arms, the proposed system solved the conflict between payload capacity and dexterity lying in conventional aerial manipulators. Two contributions are made in this paper: 1) a sensor-based kinematic model is developed for precise modeling in the presence of variable loading; and 2) a tendon slacking prevention system is developed in the presence of aggressive motions. The detailed design of the system is presented and extensive experimental validations have been performed to validate the system self-initialization, payload capacity, precise kinematic modeling with variable end-effector (EE) loadings during aerial grasping and tendon-slacking prevention. The experimental results demonstrate that the proposed novel aerial continuum manipulator system solves the constraints in conventional aerial manipulators and has more potential applications in clustered environments.
Iterative Teaching by Label Synthesis

In this paper, we consider the problem of iterative machine teaching, where a teacher provides examples sequentially based on the current iterative learner. In contrast to previous methods that have to scan over the entire pool and select teaching examples from it in each iteration, we propose a label synthesis teaching framework where the teacher randomly selects input teaching examples ( e.g. , images) and then synthesizes suitable outputs ( e.g. , labels) for them. We show that this framework can avoid costly example selection while still provably achieving exponential teachability. We propose multiple novel teaching algorithms in this framework. Finally, we empirically demonstrate the value of our framework.
New Theory-driven GENIE Tune for MicroBooNE

P. Abratenko, R. An, J. Anthony, L. Arellano, J. Asaadi, A. Ashkenazi, S. Balasubramanian, B. Baller, C. Barnes, G. Barr, V. Basque, L. Bathe-Peters, O. Benevides Rodrigues, S. Berkman, A. Bhanderi, A. Bhat, M. Bishai, A. Blake, J. Y. Book, L. Camilleri, D. Caratelli, I. Caro Terrazas, F. Cavanna, G. Cerati, Y. Chen, D. Cianci, J. M. Conrad, M. Convery, L. Cooper-Troendle, J. I. Crespo-Anadón, M. Del Tutto, S. R. Dennis, P. Detje, A. Devitt, R. Diurba, R. Dorrill, K. Duffy, S. Dytman, B. Eberly, A. Ereditato, J. J. Evans, R. Fine, G. A. Fiorentini Aguirre, R. S. Fitzpatrick, B. T. Fleming, N. Foppiani, D. Franco, A. P. Furmanski, D. Garcia-Gamez, S. Gardiner, G. Ge, S. Gollapinni, 17 O. Goodwin, E. Gramellini, P. Green, H. Greenlee, W. Gu, R. Guenette, P. Guzowski, L. Hagaman, O. Hen, C. Hilgenberg, G. A. Horton-Smith, A. Hourlier, R. Itay, C. James, X. Ji, L. Jiang, J. H. Jo, R. A. Johnson, Y. -J. Jwa, D. Kalra, N. Kamp, N. Kaneshige, G. Karagiorgi, W. Ketchum, M. Kirby, T. Kobilarcik, I. Kreslo, I. Lepetic, K. Li, Y. Li, K. Lin, B. R. Littlejohn, W. C. Louis, X. Luo, K. Manivannan, C. Mariani, D. Marsden, J. Marshall, D. A. Martinez Caicedo, K. Mason, A. Mastbaum, N. McConkey, V. Meddage, T. Mettler, K. Miller, J. Mills, K. Mistry, A. Mogan, T. Mohayai, J. Moon, M. Mooney, A. F. Moor, C. D. Moore, L. Mora Lepin, J. Mousseau, M. Murphy, D. Naples, A. Navrer-Agasson, M. Nebot-Guinot, R. K. Neely, D. A. Newmark, J. Nowak, M. Nunes, O. Palamara, V. Paolone, A. Papadopoulou, V. Papavassiliou, S. F. Pate, N. Patel, A. Paudel, Z. Pavlovic, E. Piasetzky, I. D. Ponce-Pinto, S. Prince, X. Qian, J. L. Raaf, V. Radeka, A. Rafique, M. Reggiani-Guzzo, L. Ren, L. C. J. Rice, L. Rochester, J. Rodriguez Rondon, M. Rosenberg, M. Ross-Lonergan, G. Scanavini, D. W. Schmitz, A. Schukraft, W. Seligman, M. H. Shaevitz, R. Sharankova, J. Shi, J. Sinclair, A. Smith, E. L. Snider, M. Soderberg, S. Söldner-Rembold, P. Spentzouris, J. Spitz, M. Stancari, J. St. John, T. Strauss, K. Sutton, S. Sword-Fehlberg, A. M. Szelc, W. Tang, K. Terao, C. Thorpe, D. Totani, M. Toups, Y. -T. Tsai, M. A. Uchida, T. Usher, W. Van De Pontseele, 13 B. Viren, M. Weber, H. Wei, Z. Williams, S. Wolbers, T. Wongjirad, M. Wospakrik, K. Wresilo, N. Wright, W. Wu, E. Yandel, T. Yang, G. Yarbrough, L. E. Yates, H. W. Yu, G. P. Zeller, J. Zennamo, and C. Zhang (The MicroBooNE Collaboration)∗
Spin-triplet superconductivity driven by finite-momentum spin fluctuations

A small number of superconductors are believed to exhibit intrinsic spin triplet pairing, and they are often discussed in terms of a simple, 3 He-like picture where ferromagnetic spin ﬂuctuations pro-vide the “glue”. However, in some cases in which reliable inelastic neutron scattering measurements are available, spin excitations are found to be peaked at ﬁnite momentum q rather than q = 0. Here we investigate some simple models that exhibit triplet pairing arising from antiferromagnetic spin ﬂuctuations. We show that a strong peak at larger q in the magnetic susceptibility can drive such states and can give rise to pairing states with nodes in the k z plane even in the presence of a pure 2D Fermi surface. In these situations, dominant pair scattering processes occur between Fermi surface segments with like signs of the superconducting order parameter, yet they are consistent with an overall odd parity state. We examine the applicability of these scenarios to putative triplet superconductors UTe 2 by calculations based on three dimensional Fermi surfaces.
On Competitive Permutations for Set Cover by Intervals

We revisit the problem of computing an optimal partial cover of points by intervals. We show that the greedy algorithm computes a permutation $\Pi = \pi_1, \pi_2,\ldots$ of the intervals that is $3/4$-competitive for any prefix of $k$ intervals. That is, for any $k$, the intervals $\pi_1 \cup \cdots \cup \pi_k$ covers at least $3/4$-fraction of the points covered by the optimal solution using $k$ intervals. We also provide an approximation algorithm that, in $O(n + m/\varepsilon)$ time, computes a cover by $(1+\varepsilon)k$ intervals that is as good as the optimal solution using $k$ intervals, where $n$ is the number of input points, and $m$ is the number of intervals (we assume here the input is presorted). Finally, we show a counter example illustrating that the optimal solutions for set cover do not have the diminishing return property -- that is, the marginal benefit from using more sets is not monotonically decreasing. Fortunately, the diminishing returns does hold for intervals.
Development of a high bandwidth readout chain for the CMS Phase-2 pixel upgrade

The CMS collaboration is building a new inner tracking pixel detector for the HighLuminosity LHC. Each pixel readout chip will be controlled with a single serial input stream at 160 Mbps and will send out data via four current mode logic (CML) 1.28 Gbps outputs. The readout chips will be grouped in modules and connected with up to 1.6 m long low-mass electrical links to Low-Power Gigabit Transceivers (lpGBT) and Versatile Link PLUS Transceiver (VTRx+) modules that send the data optically to off-detector electronics at 10 Gbps. The development and the characterization of these components is presented along with system tests of the readout chain.
ALMA Survey of Orion Planck Galactic Cold Clumps (ALMASOP): Detection of a Dense SiO Jet in the Evolved Protostellar Phase

Jets and outflows trace the accretion history of protostars. High-velocity molecular jets have been observed from several protostars in the early Class 0 phase of star formation, detected with the high-density tracer SiO. Until now, no clear jet has been detected with SiO emission from isolated evolved Class I protostellar systems. We report a prominent dense SiO jet from a Class I source G205S3 (HOPS-315: T bol ∼ 180 K, spectral index ∼0.417), with a moderately high mass-loss rate (∼0.59 × 10−6 M ⊙ yr−1) estimated from CO emission. Together, these features suggest that G205S3 is still in a high-accretion phase, similar to that expected of Class 0 objects. We compare G205S3 to a representative Class 0 system G206W2 (HOPS-399) and literature Class 0/I sources to explore the possible explanations behind the SiO emission seen at the later phase. We estimate a high inclination angle (∼40°) for G205S3 from CO emission, which may expose the infrared emission from the central core and mislead the spectral classification. However, the compact 1.3 mm continuum, C18O emission, location in the bolometric luminosity to submillimeter fluxes diagram, outflow force (∼3.26 × 10−5 M ⊙ km s−1 yr−1) are also analogous to that of Class I systems. We thus consider G205S3 to be at the very early phase of Class I, and in the late phase of high accretion. The episodic ejection could be due to the presence of an unknown binary, a planetary companion, or dense clumps, where the required mass for such high accretion could be supplied by a massive circumbinary disk.
Multi-Frequency Image Completion via a Biologically-Inspired Sub-Riemannian Model with Frequency and Phase

We present a novel cortically-inspired image completion algorithm. It uses five-dimensional sub-Riemannian cortical geometry, modeling the orientation, spatial frequency and phase-selective behavior of the cells in the visual cortex. The algorithm extracts the orientation, frequency and phase information existing in a given two-dimensional corrupted input image via a Gabor transform and represents those values in terms of cortical cell output responses in the model geometry. Then, it performs completion via a diffusion concentrated in a neighborhood along the neural connections within the model geometry. The diffusion models the activity propagation integrating orientation, frequency and phase features along the neural connections. Finally, the algorithm transforms the diffused and completed output responses back to the two-dimensional image plane.
Heterogeneous Multi-player Multi-armed Bandits: Closing the Gap and Generalization

Despite the significant interests and many progresses in decentralized multi-player multi-armed bandits (MP-MAB) problems in recent years, the regret gap to the natural centralized lower bound in the heterogeneous MP-MAB setting remains open. In this paper, we propose BEACON -- Batched Exploration with Adaptive COmmunicatioN -- that closes this gap. BEACON accomplishes this goal with novel contributions in implicit communication and efficient exploration. For the former, we propose a novel adaptive differential communication (ADC) design that significantly improves the implicit communication efficiency. For the latter, a carefully crafted batched exploration scheme is developed to enable incorporation of the combinatorial upper confidence bound (CUCB) principle. We then generalize the existing linear-reward MP-MAB problems, where the system reward is always the sum of individually collected rewards, to a new MP-MAB problem where the system reward is a general (nonlinear) function of individual rewards. We extend BEACON to solve this problem and prove a logarithmic regret. BEACON bridges the algorithm design and regret analysis of combinatorial MAB (CMAB) and MP-MAB, two largely disjointed areas in MAB, and the results in this paper suggest that this previously ignored connection is worth further investigation.
Particle Dark Matter Density and Entropy Production in the Early Universe

Dark Matter (DM) density is reduced if entropy production takes place after DM particles abundance is frozen out in the early universe. We study a possibility of such reduction due to entropy production in the electroweak phase transition (EWPT). We compare scenarios of entropy production in the standard model (SM) and its simplest extension, the two-Higgs doublet model (2HDM). Assuming the EWPT is of second order in the SM scenario and the first order in the 2HDM, we calculate the entropy release in these scenarios and the corresponding dilution of preexisting DM density in the early universe. We find the effect of dilution in EWPT significant for confrontation with observations of any form of possible DM (including primordial black holes (PBHs)), which is frozen out, decoupled, frozen in, or formed before EWPT.
Neural-PIL: Neural Pre-Integrated Lighting for Reflectance Decomposition

Decomposing a scene into its shape, reflectance and illumination is a fundamental problem in computer vision and graphics. Neural approaches such as NeRF have achieved remarkable success in view synthesis, but do not explicitly perform decomposition and instead operate exclusively on radiance (the product of reflectance and illumination). Extensions to NeRF, such as NeRD, can perform decomposition but struggle to accurately recover detailed illumination, thereby significantly limiting realism. We propose a novel reflectance decomposition network that can estimate shape, BRDF, and per-image illumination given a set of object images captured under varying illumination. Our key technique is a novel illumination integration network called Neural-PIL that replaces a costly illumination integral operation in the rendering with a simple network query. In addition, we also learn deep low-dimensional priors on BRDF and illumination representations using novel smooth manifold auto-encoders. Our decompositions can result in considerably better BRDF and light estimates enabling more accurate novel view-synthesis and relighting compared to prior art. Project page: https://markboss.me/publication/2021-neural-pil/
Porcine Anterior Cruciate Ligament Delay of 2 or 6 Weeks Adversely Affects the Functional Outcome of Augmented Primary Repair of the

http://ajs.sagepub. com/content/38/12/2528 The online version of this article can be found at: DOI: 10.1177/0363546510377416 2010 38: 2528 originally published online September 20, 2010 Am J Sports Med Murray Elise M. Magarian, Braden C. Fleming, Sophia L. Harrison, Ashley N. Mastrangelo, Gary J. Badger and Martha M. Porcine Anterior Cruciate Ligament Delay of 2 or 6 Weeks Adversely Affects the Functional Outcome of Augmented Primary Repair of the