Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic review and meta‐analysis of the prognostic impact of lymph node micrometastasis and isolated tumour cells in patients with stage I–IIIA non‐small cell lung cancer

Lymph node micrometastases could be one of the reasons for the high recurrence rate after complete surgical resection in stage I–IIIA non‐small cell lung cancer (NSCLC). The standard evaluation of a single haematoxylin and eosin (H&E) slide of a paraffin‐embedded section of a lymph node is insufficient for the detection of micrometastases, and there is a need for additional histopathological evaluation. The association of lymph node micrometastases with survival remains as yet unresolved. The aim of this systematic review and meta‐analysis is to investigate if lymph node micrometastases and isolated tumour cells in patients with stage I–IIIA NSCLC, detected with multiple sectioning and/or immunohistochemistry (IHC) and/or reverse transcriptase polymerase chain reaction (RT‐PCR), are associated with overall survival (OS) and disease‐free survival (DFS) after surgical resection. We performed a meta‐analysis of time‐to‐event outcomes based on 15 articles using ancillary techniques to detect micrometastases. We extracted the OS and DFS every 3–6 months after surgery, for patients with and without occult lymph node micrometastasis, from the survival curves published in each article. These data were used to reconstruct OS and DFS for ‘micrometastasis’ and ‘no micrometastasis’ groups. Based on all included studies that used IHC, serial sectioning, or RT‐PCR, we found a 5‐year OS of 55% (micrometastasis) vs. 75% (no micrometastasis), and a 5‐year DFS of 53% (micrometastasis) vs. 75% (no micrometastasis). Patients with stage I–IIIA NSCLC with lymph node micrometastases detected by ancillary histopathological and molecular techniques have a significantly poorer OS and DFS compared to patients without lymph node micrometastases.
Initial value formalism for dust collapse

Formulating a dust filled spherically symmetric metric utilizing the 3+1 formalism for general relativity, we show that the metric coefficients are completely determined by the matter distribution throughout the spacetime. Furthermore, the metric describes both inhomogeneous dust regions and also vacuum regions in a single coordinate patch, thus alleviating the need for complicated matching schemes at the interfaces. In this way, the system is established as an initial-boundary value problem, which has many benefits for its numerical evolution. We show the dust part of the metric is equivalent to the class of Lemaitre-Tolman-Bondi (LTB) metrics under a coordinate transformation. In this coordinate system, shell crossing singularities (SCS) are exhibited as fluid shock waves, and we therefore discuss possibilities for the dynamical extension of shell crossings through the initial point of formation by borrowing methods from classical fluid dynamics. This paper fills a void in the present literature associated with these collapse models by fully developing the formalism in great detail. Furthermore, the applications provide examples of the benefits of the present model.
SHINING, A Survey of Far-infrared Lines in Nearby Galaxies. I. Survey Description, Observational Trends, and Line Diagnostics

We use the Herschel/PACS spectrometer to study the global and spatially resolved far-infrared (FIR) fine-structure line emission in a sample of 52 galaxies that constitute the SHINING survey. These galaxies include star-forming, active-galactic nuclei (AGNs), and luminous infrared galaxies (LIRGs). We find an increasing number of galaxies (and kiloparsec-size regions within galaxies) with low line-to-FIR continuum ratios as a function of increasing FIR luminosity (LFIR), dust infrared color, LFIR to molecular gas mass ratio (LFIR/Mmol), and FIR surface brightness (ΣFIR). The correlations between the [C ii]/FIR or [O i]/FIR ratios with ΣFIR are remarkably tight (∼0.3 dex scatter over almost four orders of magnitude in ΣFIR). We observe that galaxies with and ΣFIR ≳ 1011 L⊙ kpc−2 tend to have weak fine-structure line-to-FIR continuum ratios, and that LIRGs with infrared sizes ≳1 kpc have line-to-FIR ratios comparable to those observed in typical star-forming galaxies. We analyze the physical mechanisms driving these trends in Paper II. The combined analysis of the [C ii], [N ii] 122 μm, and [O iii] 88 μm lines reveals that the fraction of the [C ii] line emission that arises from neutral gas increases from 60% to 90% in the most active star-forming regions and that the emission originating in the ionized gas is associated with low-ionization, diffuse gas rather than with dense gas in H ii regions. Finally, we report the global and spatially resolved line fluxes of the SHINING galaxies to enable the comparison and planning of future local and high-z studies.
Bovine and human endometrium-derived hydrogels support organoid culture from healthy and cancerous tissues

Significance The human endometrium represents one of the most-regenerative tissues, known for its ability to undergo cyclic breakdown and scarless repair in a few days. Endometrial organoids have provided unprecedented insights into human endometrial biology, functions, and diseases. However, the broader application of organoids in basic and clinical research is hampered by the use of an ill-defined mixture of extracellular matrix proteins and growth factors derived from mouse cancer cells. We have developed endometrial extracellular matrix-based hydrogels. Human organoids developed in these hydrogels are biochemically similar to the native tissue from which they are derived. Our endometrial hydrogels overcome a major limitation of current organoid technology and would support the development of more physiologically and translationally relevant endometrial organoid models.
Starting to have sexual intercourse is associated with increases in cervicovaginal immune mediators in young women: a prospective study and meta-analysis

Background: Adolescent girls and young women (AGYW) are at high risk of sexually transmitted infections (STIs). It is unknown whether beginning to have sexual intercourse results in changes to immune mediators in the cervicovaginal tract that contribute to this risk. Methods: We collected cervicovaginal lavages from Kenyan AGYW in the months before and after first penile-vaginal sexual intercourse and measured the concentrations of 20 immune mediators. We compared concentrations pre- and post-first sex using mixed effect models. We additionally performed a systematic review to identify similar studies and combined them with our results by meta-analysis of individual participant data. Results: We included 180 samples from 95 AGYW, with 44% providing only pre-first sex samples, 35% matched pre and post, and 21% only post. We consistently detected 19/20 immune mediators, all of which increased post-first sex (p<0.05 for 13/19; Holm-Bonferroni-adjusted p<0.05 for IL-1β, IL-2, and CXCL8). Effects remained similar after excluding samples with STIs and high Nugent scores. Concentrations increased cumulatively over time after date of first sex, with an estimated doubling time of about 5 months. Our systematic review identified two eligible studies, one of 93 Belgian participants, and the other of 18 American participants. Nine immune mediators were measured in at least two-thirds of studies. Meta-analysis confirmed higher levels post-first sex for 8/9 immune mediators (p<0.05 for six mediators, most prominently IL-1α, IL-1β, and CXCL8). Conclusions: Cervicovaginal immune mediator concentrations were higher in women who reported that they started sexual activity. Results were consistent across three studies conducted on three different continents. Funding: This research was funded by R01 HD091996-01 (ACR), by P01 AI 030731-25 (Project 1) (AW), R01 AI116292 (FH), R03 AI154366 (FH) and by the Center for AIDS Research (CFAR) of the University of Washington/Fred Hutchinson Cancer Research Center AI027757.
Genomic prediction for the Germplasm Enhancement of Maize project

The Germplasm Enhancement of Maize (GEM) project was initiated in 1993 as a cooperative effort of public‐ and private‐sector maize (Zea mays L.) breeders to enhance the genetic diversity of the U.S. maize crop. The GEM project selects progeny lines with high topcross yield potential from crosses between elite temperate lines and exotic parents. The GEM project has released hundreds of useful breeding lines based on phenotypic selection within selfing generations and multienvironment yield evaluations of GEM line topcrosses to elite adapted testers. Developing genomic selection (GS) models for the GEM project may contribute to increases in the rate of genetic gain. Here we evaluated the prediction ability of GS models trained on 6 yr of topcross evaluations from the two GEM programs in Raleigh, NC, and Ames, IA, documenting prediction abilities ranging from 0.36 to 0.75 for grain yield and from 0.78 to 0.96 for grain moisture when models were cross‐validated within program and heterotic group. Predicted genetic gain from GS ranged from 0.95 to 2.58 times the gain from phenotypic selection. Prediction ability across program and heterotic group was generally poorer than within groups. Based on observed genomic relationships between GEM breeding lines and their tropical ancestors, GS for either yield or moisture would reduce recovery of exotic germplasm only slightly. Using GS models trained within program, the GEM programs should be able to more effectively deliver on its mission to broaden the genetic base of U.S. germplasm.
The Connection between Different Tracers of the Diffuse Interstellar Medium: Kinematics

Using visible, radio, microwave, and submillimeter data, we study several lines of sight toward stars generally closer than 1 kpc on a component-by-component basis. We derive the component structure seen in absorption at visible wavelengths from Ca ii, Ca i, K i, CH, CH+, and CN and compare it to emission from H i, CO and its isotopologues, and C+ from the GOT C+ survey. The correspondence between components in emission and absorption helps create a more unified picture of diffuse atomic and molecular gas in the interstellar medium. We also discuss how these tracers are related to the CO-dark H2 gas probed by C+ emission and discuss the kinematic connections among the species observed.
DRNet: Double Recalibration Network for Few-Shot Semantic Segmentation

Few-shot segmentation aims at learning to segment query images guided by only a few annotated images from the support set. Previous methods rely on mining the feature embedding similarity across the query and the support images to achieve successful segmentation. However, these models tend to perform badly in cases where the query instances have a large variance from the support ones. To enhance model robustness against such intra-class variance, we propose a Double Recalibration Network (DRNet) with two recalibration modules, i.e., the Self-adapted Recalibration (SR) module and the Cross-attended Recalibration (CR) module. In particular, beyond learning robust feature embedding for pixel-wise comparison between support and query as in conventional methods, the DRNet further exploits semantic-aware knowledge embedded in the query image to help segment itself, which we call ‘self-adapted recalibration’. More specifically, DRNet first employs guidance from the support set to roughly predict an incomplete but correct initial object region for the query image, and then reversely uses the feature embedding extracted from the incomplete object region to segment the query image. Also, we devise a CR module to refine the feature representation of the query image by propagating the underlying knowledge embedded in the support image’s foreground to the query. Instead of foreground global pooling, we refine the response at each pixel in the query feature map by attending to all foreground pixels in the support feature map and taking the weighted average by their similarity; meanwhile, feature maps of the query image are also added back to weighted feature maps as a residual connection. Our DRNet can effectively address the intra-class variance under the few-shot setting with such two recalibration modules, and mine more accurate target regions for query images. We conduct extensive experiments on the popular benchmarks PASCAL-<inline-formula> <tex-math notation="LaTeX">$5^{i}$ </tex-math></inline-formula> and COCO-<inline-formula> <tex-math notation="LaTeX">$20^{i}$ </tex-math></inline-formula>. The DRNet with the best configuration achieves the mIoU of <inline-formula> <tex-math notation="LaTeX">$\textbf {63.6}\%$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\textbf {64.9}\%$ </tex-math></inline-formula> on PASCAL-<inline-formula> <tex-math notation="LaTeX">$5^{i}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\textbf {44.7}\%$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\textbf {49.6}\%$ </tex-math></inline-formula> on COCO-<inline-formula> <tex-math notation="LaTeX">$20^{i}$ </tex-math></inline-formula> for 1-shot and 5-shot settings respectively, significantly outperforming the state-of-the-arts without any bells and whistles. Code is available at: <uri>https://github.com/fangzy97/drnet</uri>.
Weighted local Hardy spaces associated to Schr\"{o}dinger operators

In this paper, we characterize the weighted local Hardy spaces $h^p_\rho(\omega)$ related to the critical radius function $\rho$ and weights $\omega\in A_{\infty}^{\rho,\,\infty}(\mathbb{R}^{n})$ which locally behave as Muckenhoupt's weights and actually include them, by the local vertical maximal function, the local nontangential maximal function and the atomic decomposition. By the atomic characterization, we also prove the existence of finite atomic decompositions associated with $h^{p}_{\rho}(\omega)$. Furthermore, we establish boundedness in $h^p_\rho(\omega)$ of quasi- Banach-valued sublinear operators. As their applications, we establish the equivalence of the weighted local Hardy space $h^1_\rho(\omega)$ and the weighted Hardy space $H^1_{\cal L}(\omega)$ associated to Schr\"{o}dinger operators $\cal L$ with $\omega \in A_1^{\rho,\infty}(\mathbb{R}^{n})$
Effects of Low-Intensity Pulsed Ultrasound on the Migration and Homing of Human Amnion–Derived Mesenchymal Stem Cells to Ovaries in Rats With Premature Ovarian Insufficiency

Premature ovarian insufficiency (POI) can cause multiple sequelae and is currently incurable. Mesenchymal stem cell (MSC) transplantation might provide an effective treatment method for POI. However, the clinical application of systemic MSC transplantation is limited by the low efficiency of cell homing to target tissue in vivo, including systemic MSC transplantation for POI treatment. Thus, exploration of methods to promote MSC homing is necessary. This study was to investigate the effects of low-intensity pulsed ultrasound (LIPUS) on the migration and homing of transplanted human amnion–derived MSCs (hAD-MSCs) to ovaries in rats with chemotherapy-induced POI. For LIPUS treatment, hAD-MSCs were exposed to LIPUS or sham irradiation. Chemokine receptor expressions in hAD-MSCs were detected by polymerase chain reaction (PCR), Western blot, and immunofluorescence assays. hAD-MSC migration was detected by wound healing and transwell migration assays. Cyclophosphamide-induced POI rat models were established to evaluate the effects of LIPUS on the homing of systemically transplanted hAD-MSCs to chemotherapy-induced POI ovaries in vivo. We found that hAD-MSCs expressed chemokine receptors. The LIPUS promoted the expression of chemokine receptors, especially CXCR4, in hAD-MSCs. SDF-1 induced hAD-MSC migration. The LIPUS promoted hAD-MSC migration induced by SDF-1 through SDF-1/CXCR4 axis. SDF-1 levels significantly increased in ovaries induced by chemotherapy in POI rats. Pretreating hAD-MSCs with LIPUS increased the number of hAD-MSCs homing to ovaries in rats with chemotherapy-induced POI to some extent. However, the difference was not significant. Both hAD-MSC and LIPUS-pretreated hAD-MSC transplantation reduced ovarian injuries and improved ovarian function in rats with chemotherapy-induced POI. CXCR4 antagonist significantly reduced the number of hAD-MSCs- and LIPUS-pretreated hAD-MSCs homing to POI ovaries, and further reduced their efficacy in POI treatment. According to these findings, pretreating MSCs with LIPUS before transplantation might provide a novel, convenient, and safe technique to explore for improving the homing of systemically transplanted MSCs to target tissue.
Work extraction and fully entangled fraction

For a bipartite state with equal local dimension d, we prove that one can obtain work gain under Landauer's erasure process on one party in identically and independently distributed (iid) limit when the corresponding fully entangled fraction is larger than 1/d. By processing a given state to the maximally mixed state, we give an approximation for the largest extractable work with an error in the energy scale, which becomes negligible in the large system limit. As a step to link quantum thermodynamics and quantum nonlocality, we also provide a simple picture to approximate the optimal work extraction and suggest a potential thermodynamic interpretation of fully entangled fraction for isotropic states.
Search for heavy bottom-like quarks decaying to an electron or muon and jets in $p\bar{p}$ collisions at $\sqrt{s}=1.96$ TeV

We report the most sensitive direct search for pair production of fourth-generation bottom-like chiral quarks ($b'$) each decaying promptly to $tW$. We search for an excess of events with an electron or muon, at least five jets (one indentified as due to a $b$ or $c$ quark) and an imbalance of transverse momentum using data from $p\bar{p}$ collisions collected by the CDF II detector at Fermilab with an integrated luminosity of 4.8 fb$^{-1}$. We observe events consistent with background expectation and calculate upper limits on the $b'$ pair production cross section ($\sigma_{b\bar{b'}}\lesssim 30$ fb for $m_{b'}>$375 GeV/$c^2$) and exclude $m_{b'}<372$ \gevcc at 95% confidence level.
Juglone promotes antitumor activity against prostate cancer via suppressing glycolysis and oxidative phosphorylation

The treatments currently used for prostate cancer (PC) do not meet clinical needs, and thus, new therapies with greater effectiveness are urgently required. Metabolic reprogramming of tumor cells is emerging as an exciting field for cancer therapy. Although the Warburg effect is a common feature of glucose metabolism in many cancers, PC cells have a unique metabolic phenotype. Non‐neoplastic prostate cells show reduced oxidative phosphorylation (OXPHOS) because large, accumulated zinc inhibits citrate oxidation. During transformation, there are low levels of zinc in PC cells, and the tricarboxylic acid (TCA) cycle is reactivated. However, metastatic PC exhibits the Warburg effect. Due to metabolic differences in prostate tissue, targeting metabolic alterations in PC cells is an attractive therapeutic strategy. In this study, we investigated the effect of juglone on energy metabolism in PC cells. We found that juglone inhibited cell proliferation and induced apoptosis. Mechanistically, we demonstrated that juglone suppressed OXPHOS and glycolysis due to its inhibition of hexokinase (HK), phosphofructokinase (PFK), and pyruvate kinase (PK) activity. Furthermore, downregulation of PFK and PK, but not HK contributed to the inhibition of these enzyme activities. The current study indicates that further development of juglone for PC treatment would be beneficial.
Applications of machine learning tools for ultra-sensitive detection of lipoarabinomannan with plasmonic grating biosensors in clinical samples of tuberculosis

Background Tuberculosis is one of the top ten causes of death globally and the leading cause of death from a single infectious agent. Eradicating the Tuberculosis epidemic by 2030 is one of the top United Nations Sustainable Development Goals. Early diagnosis is essential to achieving this goal because it improves individual prognosis and reduces transmission rates of asymptomatic infected. We aim to support this goal by developing rapid and sensitive diagnostics using machine learning algorithms to minimize the need for expert intervention. Methods and findings A single molecule fluorescence immunosorbent assay was used to detect Tuberculosis biomarker lipoarabinomannan from a set of twenty clinical patient samples and a control set of spiked human urine. Tuberculosis status was separately confirmed by GeneXpert MTB/RIF and cell culture. Two machine learning algorithms, an automatic and a semiautomatic model, were developed and trained by the calibrated lipoarabinomannan titration assay data and then tested against the ground truth patient data. The semiautomatic model differed from the automatic model by an expert review step in the former, which calibrated the lower threshold to determine single molecules from background noise. The semiautomatic model was found to provide 88.89% clinical sensitivity, while the automatic model resulted in 77.78% clinical sensitivity. Conclusions The semiautomatic model outperformed the automatic model in clinical sensitivity as a result of the expert intervention applied during calibration and both models vastly outperformed manual expert counting in terms of time-to-detection and completion of analysis. Meanwhile, the clinical sensitivity of the automatic model could be improved significantly with a larger training dataset. In short, semiautomatic, and automatic Gaussian Mixture Models have a place in supporting rapid detection of Tuberculosis in resource-limited settings without sacrificing clinical sensitivity.
Towards Dark Energy : design, development, and preliminary data from ACT

Recent cosmological observations resulted in the surprising discovery that our universe is dominated by a dark energy, causing acceleration of the expansion of the universe. Understanding the dark energy (Λ) and the cosmic acceleration may require a revolution in our understanding of the laws of physics, and more precise data will be critical to this endeavor. The remainder of the universe is dominated by cold dark matter (CDM), while only ∼4% of the universe comprises baryonic matter. To improve our understanding of dark energy and the ΛCDM model of our universe, we have developed a novel telescope and receiver technology to map the universe at millimeter wavelengths on arcminute angular scales. The Atacama Cosmology Telescope (ACT) and its receiver, the Millimeter Bolometer Array Camera (MBAC), are optimized to measure temperature anisotropies in the primordial cosmic microwave background radiation (CMB). On the smallest angular scales measured by ACT the anisotropies are dominated by secondary interactions of CMB photons, such as gravitational interactions and the Sunyaev-Zel’dovich (SZ) effects: the interaction of CMB photons with ionized gas in galaxy clusters. We can use these measurements to probe dark energy in multiple ways. The CMB bispectrum quantifies the non-Gaussian nature of the secondary anisotropies and when combined with measurements from the Wilkinson Microwave Anisotropy Probe, will provide constraints on dark energy. By combining and cross-correlating measurements of the SZ effects with galaxy cluster redshifts, we can constrain the equation of state of dark energy and its evolution. In addition, by measuring the CMB on arcminute angular scales, we will probe the details of the ΛCDM cosmological model that describes our universe.