Miracle-dz/UniFAR-FTUs huggingface dataset:
Normalization of unintegrated parton densities

Recently, the deﬁnitions of the Kimber-Martin-Ryskin-Watt (KMRW) unintegrated parton densities (UPDFs) have been discussed by several groups. In the ﬁrst part of this manuscript, we remind the issues encountered with these deﬁnitions and discuss the proposed solutions. In our opinion, none of these solutions is fully satisfactory. We observe that these issues seem to be related to the normalization condition where the UPDFs are related to the collinear PDFs by an integration over transverse momentum cut oﬀ by the factorization scale. Then, we build a modiﬁed version of the angular-ordering KMRW UPDFs, obeying the normalization condition with the transverse momentum integrated up to inﬁnity, and show that the usual issues are absent. Some consequences for the phenomenology are also discussed.
BDIS: Bayesian Dense Inverse Searching Method for Real-Time Stereo Surgical Image Matching

In stereoscope-based minimally invasive surgeries (MISs), dense stereo matching plays an indispensable role in 3-D shape recovery, AR, VR, and navigation tasks. Although numerous deep neural network (DNN) approaches are proposed, the conventional prior-free approaches are still popular in the industry because of the lack of open-source annotated dataset and the limitation of the task-specific pretrained DNNs. Among the prior-free stereo matching algorithms, there is no successful real-time algorithm in none GPU environment for MIS. This article proposes the first CPU-level real-time prior-free stereo matching algorithm for general MIS tasks. We achieve an average $14-17$ Hz on $640 \times 480$ images with a single-core CPU (i5-9400) for surgical images. Meanwhile, it achieves slightly better accuracy than the popular efficient large-scale stereo matching (ELAS) method. The patch-based fast disparity searching algorithm is adopted for the rectified stereo images. A coarse-to-fine Bayesian probability and a spatial Gaussian mixed model were proposed to evaluate the patch probability at different scales. An optional probability density function estimation algorithm was adopted to quantify the prediction variance. Extensive experiments demonstrated the proposed method's capability to handle ambiguities introduced by the textureless surfaces and the photometric inconsistency from the non-Lambertian reflectance and dark illumination. The estimated probability managed to balance the confidences of the patches for stereo images at different scales. It has similar or higher accuracy and fewer outliers than the baseline ELAS in MIS, while it is 4–5 times faster.
Longitudinal cardio-respiratory fitness prediction through free-living wearable sensors

SUMMARY Background Cardiorespiratory ﬁtness is an established predictor of metabolic disease and mortality. Fitness is directly measured as maximal oxygen consumption (VO 2 max ), or indirectly assessed using heart rate response to a standard exercise test. However, such testing is costly and burdensome, limiting its utility and scalability. Fitness can also be approximated using resting heart rate and self-reported exercise habits but with lower accuracy. Modern wearables capture dynamic heart rate data which, in combination with machine learning models that ﬁnd latent patterns in high-dimensional sensor signals, could improve ﬁtness prediction. Methods In this work, we analyze movement and heart rate signals from wearable sensors in free-living conditions from 11,059 participants who also underwent a standard exercise test, along with a longitudinal repeat cohort of 2,675 participants. We design algorithms and models that convert raw sensor data into cardio-respiratory ﬁtness estimates, and validate these estimates’ ability to capture ﬁtness proﬁles in a longitudinal cohort over time while subjects engaged in real-world (non-exercise) behavior. Additionally, we validate our methods with a third external cohort of 181 participants who underwent maximal VO 2 max testing, which is considered the gold standard measurement because it requires reaching one’s maximum heart rate and exhaustion level. Findings Our results show that the developed models yield high correlation ( r = 0.82, 95CI 0.80-0.83), when compared to the ground truth in a holdout sample. These models outperform conventional non-exercise ﬁtness models and traditional bio-markers using measurements of normal daily living without the need of a speciﬁc exercise test. Additionally, we show the adaptability and applicability of this approach for detecting ﬁtness change over time in the longitudinal subsample who repeated measurements after 7 years. Interpretation These results demonstrate the value of wearables for the longitudinal assessment of ﬁtness that today can be measured only with laboratory tests.
Got plenty of nothing: cosmic voids as a probe of particle dark matter

The search for a particle dark matter signal in terms of radiation produced by dark matter annihilation or decay has to cope with the extreme faintness of the predicted signal and the presence of masking astrophysical backgrounds. It has been shown that using the correlated information between the dark matter distribution in the Universe with the fluctuations of the cosmic radiation fields has the potential to allow setting apart a pure dark matter signal from astrophysical emissions, since spatial fluctuations in the radiation field due to astrophysical sources and dark matter emission have different features. The cross-correlation technique has been proposed and adopted for dark matter studies by looking at dark matter halos (overdensities). In this paper we extend the technique by focusing on the information on dark matter distribution offered by cosmic voids, and by looking specifically at the gamma-ray dark matter emission: we show that, while being underdense and therefore producing a reduced emission as compared to halos, nevertheless in voids the relative size of the cross-correlation signal due to decaying dark matter vs. astrophysical sources is significantly more favourable, producing signal-to-background ratios S/B (even significantly) larger than 1 for decay lifetimes up to 2 × 1030 s. This is at variance with the case of halos, where S/B is typically (even much) smaller than 1. We show that forthcoming galaxy surveys such as Euclid combined with future generation gamma-ray detectors with improved specifications have the ability to provide a hint of such a signal with a predicted significance up to 5. 7σ for galaxies and 1. 6σ for the cosmic shear. The bound on the dark matter lifetime attainable exploiting voids is predicted to improve on current bounds in a mass range for the WIMP of 25 ÷ 900 GeV.
PR-PL: A Novel Transfer Learning Framework with Prototypical Representation based Pairwise Learning for EEG-Based Emotion Recognition

Affective brain-computer interfaces based on electroencephalography (EEG) is an important branch in the field of affective computing. However, individual differences and noisy labels seriously limit the effectiveness and generalizability of EEG-based emotion recognition models. In this paper, we propose a novel transfer learning framework with Prototypical Representation based Pairwise Learning (PR-PL) to learn discriminative and generalized prototypical representations for emotion revealing across individuals and formulate emotion recognition as pairwise learning for alleviating the reliance on precise label information. Extensive experiments are conducted on two benchmark databases under four cross-validation evaluation protocols (cross-subject cross-session, cross-subject within-session, within-subject cross-session, and within-subject within-session). The experimental results demonstrate the superiority of the proposed PR-PL against the state-of-the-arts under all four evaluation protocols, which shows the effectiveness and generalizability of PR-PL in dealing with the ambiguity of EEG responses in affective studies. The source code is available at https://github.com/KAZABANA/PR-PL.
Dynamics simulation and numerical analysis of arbitrary time-dependent $\mathcal{PT}$-symmetric system based on density operators

PT -symmetric system has attracted extensive attention in recent years because of its unique properties and applications. How to simulate PT -symmetric system in traditional quantum mechanical system has not only fundamental theoretical signiﬁcance but also practical value. We propose a dynamics simulation scheme of arbitrary time-dependent PT -symmetric system based on density operators, and the results are compatible with previous methods based on pure-state vectors. Based on the above, we are able to study the inﬂuence of quantum noises on the simulation results with the technique of vectorization of density operators and matrixization of superoperators (VDMS), and we show the depolarizing (Dep) noise is the most fatal and should be avoided as much as possible. Meanwhile, we also give a numerical analysis. We ﬁnd that the problem of chronological product usually has to be solved not only in the numerical calculation, but also even in the experiment, because the dilated higher-dimensional Hamiltonian is usually time-dependent. Through theoretical analysis and numerical calculation, we ﬁnd that on the premise of meeting the goal of calculation accuracy and saving computing resources, the time step of calculation and the cut-oﬀ term of Magnus series have to be carefully balanced.
Wake asymmetry weakening in viscoelastic fluids: Numerical discovery and mechanism exploration

Viscoelasticity weakens the asymmetry of laminar shedding flow behind a blunt body in a free domain. In the present study, this finding is confirmed by four unsteady viscoelastic flows with asymmetric flow configuration, i.e., flow over an inclined flat plate with various angles of incidence, flow over a rotating circular cylinder, flow over a circular cylinder with asymmetric slip boundary distribution, and flow over an inclined row of eight equally closely spaced circular cylinders (which can be considered as a single large blunt body) through direct numerical simulation combined with the Peterlin approximation of the finitely extensible nonlinear elastic (FENE-P) model. At high Weissenberg number, an arc shape region with high elastic stress, which is similar to shock wave, forms in the frontal area of the blunt body. This region acts as a stationary shield to separate the flow into different regions. Thus, the free stream resembles to pass this shield instead of the original blunt body. As this shield has symmetric feature, the wake flow restores symmetry.
The effect of dietary chitin on Atlantic salmon (Salmo salar) chitinase activity, gene expression, and microbial composition

Background Chitin is a common component in the natural diet of many fish, and a range of chitinases with the potential to down chitin have been identified. Yet whether chitin is metabolized in fish is still unclear. Here we used a combination of chitinase activity assay, transcriptomics, and 16S rRNA bacterial analysis to assess the effect of chitin supplementation on Atlantic salmon gene expression and microbial community. Results Atlantic salmon express multiple genes associated with chitin metabolism, and we show that the expression and activity of Atlantic salmon chitinases are not affected by the addition of dietary chitin. We do, however, demonstrate an association between gut microbial composition, chitinase activity in the gut, and host chitinase expression. Conclusion The findings presented here support the idea that chitin metabolism genes are linked to the maintenance of a chitin-based barrier in the teleost gut. These results contribute to a greater understanding of chitin metabolism in fish.
Sigh breathing rhythm depends on intracellular calcium oscillations in a population of inspiratory rhythmogenic preBötzinger complex neurons in mice

The preBötzinger Complex (preBötC) of the lower brainstem generates two breathing-related rhythms: one for inspiration on a timescale of seconds and another that produces larger amplitude sighs on the order of minutes. Their underlying mechanisms and cellular origins remain incompletely understood. We resolve these problems via a joint experiment and modeling approach. Blocking purinergic gliotransmission does not perturb either rhythm and imaging experiments show that both rhythms emanate from the same glutamatergic neuron population. We hypothesized that these two disparate rhythms emerge in tandem wherein recurrent excitation gives rise to inspiratory rhythm while a calcium oscillator generates sighs; there is no obligatory role for gliotransmission, hyperpolarization activated mixed cationic current (Ih) in neurons, or synaptic inhibition-mediated coupling of separate populations. We developed a mathematical model that instantiates our working hypothesis. Tests of model predictions validate the single-population rhythmogenic framework, reproducing disparate breathing-related frequencies and the ability for inspiratory and sigh rhythms to be separately regulated in support of respiration under a wide array of conditions. Here we show how a single neuron population exploits two cellular tool-kits: one involving voltage-dependent membrane properties and synaptic excitation for inspiratory breathing (eupnea) and an intracellular biochemical oscillator for sighs, which ventilate and maintain optimal function in the compliant mammalian lung. SIGNIFICANCE STATEMENT Breathing consists of two vital rhythms: one for eupnea that serves periodic physiological gas exchange and the other for sighs, which are larger breaths that occur minutes apart and serve to optimize pulmonary function. These rhythms with disparate frequencies emerge via a mechanism that is simpler than previously envisaged: it results from one neuron population (not two as previously thought) without need for gliotransmission or synaptic inhibition-mediated coupling of neuronal populations. We show that a low-frequency intracellular calcium oscillation underlies sighs and functions in parallel with the higher-frequency voltage-dependent network oscillation that drives eupnea. Exploiting two separate cellular tool kits enables quasi-independent breathing rhythms, which are unique features of breathing in mammals with compliant lungs.
Sucrose rather than GA transported by AtSWEET13 and AtSWEET14 supports pollen fitness at late anther development stages

Summary Both sugar and hormone gibberellin (GA) are essential for anther-enclosed pollen development and thus for plant productivity in flowering plants. Arabidopsis (Arabidopsis thaliana) AtSWEET13 and AtSWEET14, which are expressed in anthers and associated with seed yield, transport both sucrose and GA. However, it is still unclear which substrate transported by them directly affects anther development and seed yield. Histochemical staining, cross-sectioning and microscopy imaging techniques were used to investigate and interpret the phenotypes of AtSWEET13 and AtSWEET14 double mutant during anther development. Genetic complementation of atsweet13;14 using AtSWEET9 that transports sucrose but not GA was conducted to test the substrate preference relevant to the biological process. The loss of AtSWEET13 and AtSWEET14 resulted in reduced pollen viability and therefore decreased pollen germination. AtSWEET9 fully rescued the defects in pollen fertility of atsweet13;14, indicating AtSWEET13/14 mediated sucrose rather than GA is essential to pollen fertility. AtSWEET13 and AtSWEET14 mainly function at the anther wall during late anther development stages and are likely responsible for sucrose efflux into locules to support pollen development to maturation, which is vital for subsequent pollen viability and germination.
Testing the link between isoaspartate and Alzheimer’s disease etiology

Isoaspartate (isoAsp) is a damaging amino acid residue formed in proteins as a result of spontaneous deamidation. IsoAsp disrupts the secondary and higher order structures of proteins, damaging their functions and making them prone to aggregation. An association has been suggested between isoAsp and Alzheimer’s Disease (AD). Here we strengthened the link between isoAsp and AD by novel approaches to isoAsp analysis in blood human serum albumin (HSA), the most abundant blood protein, a major carrier of amyloid beta (Aß) peptide and phosphorylated tau (pTau) protein in blood and a key participant in their clearance pathway. We discovered a reduced amount of anti-isoAsp antibodies (P < .0001), an elevated isoAsp level in HSA (P < .001), more HSA aggregates (P < .0001) and increased levels of free Aß (P < .01) in AD blood compared to healthy controls. We also found that deamidation significantly reduces HSA capacity to bind with Aß and pTau (P < .05). These findings support the presence in AD of a bottleneck in clearance of Aß and pTau leading to their increased concentrations in brain and facilitating their aggregations there. RESEARCH IN CONTEXT Systematic review: We reviewed the evidence that associates isoaspartate (isoAsp) residue in blood proteins with the etiology of Alzheimer’s disease (AD). However, the link between isoAsp in blood and aggregation of amyloid beta (Aß) peptide and phosphorylated tau (pTau) protein in brain remained unclear. Interpretation: For the first time we demonstrate that isoAsp-containing human serum albumin (HSA) forms aggregates with reduced binding capacity toward Aß peptide and pTau protein. Using a novel ELISA, we discovered in AD blood elevated levels of isoAsp in HSA, together with reduced endogenous anti-isoAsp antibody levels, suggesting hampered Aß and pTau clearance in AD. Future directions: As degradation of the innate anti-isoAsp defenses may take years to develop, investigation of the isoAsp role in early stages of AD is warranted. And enrollment of different neurodegenerative disease cohorts will illustrate if isoAsp is AD-specific or universal to diseases related to aging.
GliaMorph: a modular image analysis toolkit to quantify Müller glial cell morphology

Cell morphology is critical for all cell functions. This is particularly true for glial cells as they rely on their complex shape to contact and support neurons. However, methods to quantify complex glial cell shape accurately and reproducibly are lacking. To address this gap in quantification approaches, we developed an analysis pipeline called “GliaMorph”. GliaMorph is a modular image analysis toolkit developed to perform (i) image pre-processing, (ii) semi-automatic region-of-interest (ROI) selection, (iii) apicobasal texture analysis, (iv) glia segmentation, and (v) cell feature quantification. Müller Glia (MG) are the principal retinal glial cell type with a stereotypic shape linked to their maturation and physiological status. We here characterized MG on three levels, including (a) global image-level, (b) apicobasal texture, and (c) apicobasal vertical-to-horizontal alignment. Using GliaMorph, we show structural changes occurring in the developing retina. Additionally, we study the loss of cadherin2 in the zebrafish retina, as well as a glaucoma mouse disease model. The GliaMorph toolkit enables an in-depth understanding of MG morphology in the developing and diseased retina. Graphical Abstract Highlights Glial morphology is complex, making it challenging to accurately quantify 3D cell shape. We developed the GliaMorph toolkit for image pre-processing, glial segmentation, and quantification of Müller glial cells. Müller glia elaborate their morphology and rearrange subcellular features during embryonic development. GliaMorph accurately identifies subcellular changes in models with disrupted glia cells, including zebrafish cadherin2 loss of function and a mouse glaucoma model.
Population genomics of post-glacial western Eurasia

Western Eurasia witnessed several large-scale human migrations during the Holocene1–5. To investigate the cross-continental impacts we shotgun-sequenced 317 primarily Mesolithic and Neolithic genomes from across Northern and Western Eurasia. These were imputed alongside published data to obtain diploid genotypes from >1,600 ancient humans. Our analyses revealed a ‘Great Divide’ genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers (HGs) were highly genetically differentiated east and west of this zone, and the impact of the neolithisation was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacements of HGs in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, while east of the Urals relatedness remained high until ∼4,000 BP, consistent with persistence of localised HG groups. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive but we demonstrate that HGs from the Middle Don region contributed ancestry to them. Yamnaya-groups later admixed with individuals associated with the Globular Amphora Culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a ‘Neolithic steppe’ cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
NPC1 Confers Metabolic Flexibility in Triple Negative Breast Cancer

Triple negative breast cancer (TNBC) often undergoes at least partial epithelial-to-mesenchymal transition (EMT) to facilitate metastasis. Identifying EMT-associated characteristics can reveal novel dependencies that may serve as therapeutic vulnerabilities in this aggressive breast cancer subtype. We find that NPC1, which encodes the lysosomal cholesterol transporter Niemann-Pick Type C1 is highly expressed in TNBC as compared to estrogen receptor-positive (ER+) breast cancer and is significantly elevated in high grade disease. We demonstrate that NPC1 is directly targeted by microRNA-200c (miR-200c) a potent suppressor of EMT, providing a mechanism for its differential expression in breast cancer subtypes. Silencing of NPC1 in TNBC causes an accumulation of cholesterol-filled lysosomes and drives decreased growth on soft agar and invasive capacity. Conversely, overexpression of NPC1 in an ER+ cell line increases invasion and growth on soft agar. We further identify TNBC cell lines as cholesterol auxotrophs, however, they do not solely depend on NPC1 for adequate cholesterol supply. Genetic inhibition of NPC1 in TNBC cell lines led to altered mitochondrial function and morphology, suppression of mTOR signaling, and accumulation of autophagosomes. A small-molecule inhibitor of NPC1, U18666A, decreased TNBC proliferation and synergized with the chemotherapeutic drug, paclitaxel. This work suggests that NPC1 promotes aggressive characteristics in TNBC and identifies NPC1 as a potential therapeutic target.