Miracle-dz/UniFAR-FTUs huggingface dataset:
Ferromagnetism in Mn-doped Ge

We have successfully fabricated highly (up to 6%) Mn-doped bulk Ge single crystals. The lattice constant increases linearly with Mn concentration due to the larger Mn atomic radius compared with Ge, strongly indicating that Mn ions are being incorporated into the host Ge lattice. Alloys with lower Mn concentrations showed paramagnetism due to localized magnetic ions. ${\mathrm{Ge}}_{0.94}{\mathrm{Mn}}_{0.06}$ showed ferromagnetic ordering at \ensuremath{\sim}285 K, as determined from temperature-dependent magnetization and resistance measurements. The coersive field was 1260 Oe at 250 K.
Age-dependent structural and morphological changes of the stem cell niche disrupt spatiotemporal regulation of stem cells and drive tissue disintegration

Aging induces a progressive decline in tissue function, which has been attributed to a decrease in stem cell function. A major factor driving this decline is the aging of the stem cell niche but elucidating molecular mechanisms of the niche aging and its effects on stem cell regulation remain a challenge. Here, we use the Caenorhabditis elegans distal tip cell (DTC), the mesenchymal niche that employs Notch signaling to regulate germline stem cells (GSCs), as an in vivo niche aging model and delineate the molecular details of the DTC/niche aging process and its consequences on GSC function and tissue integrity. Using Notch-dependent transcriptional activation as a direct readout of GSC-DTC/niche interaction and its transcriptional activity as a readout for GSC function, we find that an age-dependent reduction in Notch transcription occurs both at the tissue and the cellular levels, but with its activity at the chromosomal loci remains unaffected. This overall reduction is due to an age-dependent progressive shift in the spatial pattern of Notch-dependent transcription in the germline, resulting in a shift of the GSC pool location and disruption of the tissue integrity. We show that the position of the DTC/niche nucleus determines the location of the Notch-responsive GSC pool, with its correlation to the structure and morphology of the DTC/niche, which also changes during aging. Our findings demonstrate that the stem cell niche undergoes structural and morphological changes during aging and reveal a critical link between these changes and the spatiotemporal regulation of stem cell function.
Another involution of moduli of sextics

Let M be the moduli space of sextics with 6 cusps and 3 nodes. A sextic C is called of a 2; 3-torus type (or brie ̄y of a torus type) if its de®ning polynomial f has the expression f x; y  f2 x; y  f3 x; y for some polynomials f2; f3 of degree 2, 3 respectively. We denote by Mtorus the component of M which consists of curves of a torus type and by Mgen the curves of a general type ( not of a torus type). We denote the dual curve of C by C . Recall that C is the image of the Gauss map dualC : C ! P , X ;Y ;Z 7! FX X ;Y ;Z; FY X ;Y ;Z;FZ X ;Y ;Z. In our previous paper [O3], we have shown that the dual curve operation C 7! C gives an involution on M and it preserves the type of the curve in M, i.e., C A Mtorus if and only if C A Mtorus. Let G : PGL 3;C. The quotient moduli spaces are by de®nition the quotient spaces of the moduli spaces by the action of G. The purpose of this note is to show that there exists an involution i on M=G such that i is di ̈erent from the dual curve operation and i preserves the types of the sextics (Theorem 2.4). For the construction of i, we consider the moduli space ~ M of plane curves of degree 12 with 24 cusps and 24 nodes. This moduli space is also self-dual in the sense that C A ~ M if C A ~ M. The construction of i is done as follows. First observe that C has three bi-tangent lines for any C A M. We take g A G so that the three coordinate lines X  0, Y  0, Z  0 are the bi-tangent lines of C g and let F X ;Y ;Z  0 be the de®ning homogeneous polynomial of degree 6. Then consider the curve ~ C de®ned by F X ;Y 2;Z2  0. It turns out that ~ C is contained in ~ M. This operation de®nes a rational mapping c : M=G ! ~ M=G. We de®ne i C  cÿ1 c C g .
Differentiated genomic footprints and connections inferred from 440 Hmong-Mien genomes suggest their isolation and long-distance migration

Background The underrepresentation of Hmong-Mien (HM) people in Asian genomic studies has hindered our comprehensive understanding of population history and human health. South China is an ethnolinguistically diverse region and indigenously settled by ethnolinguistically diverse HM, Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), and Sino-Tibetan (ST) people, which is regarded as East Asia’s initial cradle of biodiversity. However, previous fragmented genetic studies have only presented a fraction of the landscape of genetic diversity in this region, especially the lack of haplotype-based genomic resources. The deep characterization of demographic history and natural-selection-relevant architecture in HM people was necessary. Results We comprehensively reported the population-specific genomic resources and explored the fine-scale genetic structure and adaptative features inferred from the high-density SNP data in 440 individuals from 34 ethnolinguistic populations, including previously unreported She. We identified solid genetic differentiation between inland (Miao/Yao) and coastal (She) southern Chinese HM people, and the latter obtained more gene flow from northern East Asians. Multiple admixture models further confirmed that extensive gene flow from surrounding ST, TK, and AN people entangled in forming the gene pool of coastal southeastern East Asian HM people. Population genetic findings of isolated shared unique ancestral components based on the sharing alleles and haplotypes deconstructed that HM people from Yungui Plateau carried the breadth of genomic diversity and previously unknown genetic features. We identified a direct and recent genetic connection between Chinese and Southeast Asian HM people as they shared the most extended IBD fragments, supporting the long-distance migration hypothesis. Uniparental phylogenetic topology and Network relationship reconstruction found ancient uniparental lineages in southwestern HM people. Finally, the population-specific biological adaptation study identified the shared and differentiated natural-selection signatures among inland and coastal HM people associated with physical features and immune function. The allele frequency spectrum (AFS) of clinical cancer susceptibility alleles and pharmacogenomic genes showed significant differences between HM and northern Chinese people. Conclusions Our extensive genetic evidence combined with the historic documents supported the view that ancient HM people originated in Yungui regions associated with ancient ‘Three-Miao tribes’ descended from the ancient Daxi-Qujialing-Shijiahe people. And then, some recently rapidly migrated to Southeast Asia, and some culturally dispersed eastward and mixed respectively with Southeast Asian indigenes, coastal Liangzhu-related ancient populations, and incoming southward Sino-Tibetan people. Generally, complex population migration, admixture, and adaptation history contributed to their specific patterns of non-coding or disease-related genetic variations.
Specificity Guides Interpretation: On H3K4 Methylation at Enhancers and Broad Promoters

In 2018, we used internally calibrated chromatin immunoprecipitation (ICeChIP) to find that many of the most commonly used antibodies against H3K4 methylforms had significant off-target binding, which compromised the findings of at least eight literature paradigms that used these antibodies for ChIP-seq (Shah et al., 2018). In many cases, we were able to recapitulate the prior findings in K562 cells with the original, low-quality antibody, only to find that the models did not hold up to scrutiny with highly specific reagents and quantitative calibration. In a recent preprint originally prepared as a Letter to the Editor of Molecular Cell, though they agree with our overarching conclusions, Pekowska and colleagues take issue with analyses presented for two relatively minor points of the paper (Pekowska et al., 2023). We are puzzled by the assertion that these two points constitute the “bulk” of our findings, nor is it clear which components of our “analytical design” they find problematic. We feel their critique, however mild, is misguided.
The evolution of parthenogen fertilization rates in switching environments: from facultative cell-fusion to oogamy

Organisms with external fertilisation exhibit a broad range of reproductive modes, from simple parthenogenesis to sexual reproduction encompassing isogamy, anisogamy, and oogamy, and including environmentally-mediated facultative sex. Here we develop a unifying mathematical model which explains the emergence of these modes via the coevolution of fertilization rate and cell size. Using a minimal assumption that survival is dependent on cell mass, and by carefully accounting for biological and evolutionary time scales, we find two distinct evolutionary outcomes: high fertilization rate (obligate sexuality) is selected when costs to cell fusion are low, while zero fertilization rate (obligate asexuality) is selected for when these costs are high. Surprisingy, in high fertilization rate scenarios evolving populations can transition from isogamy to anisogamy and oogamy via evolutionary branching. Furthermore, in variable environments we show that, without phenotypic plasticity, intermediate fertilization rates and isogamy can be maintained through bet-hedging. Allowing phenotypic plasticity can give rise to facultative sex; sexual reproduction in harsh environmental conditions, and asexuality in more benign conditions. These results parsimoniously explain a large range of empirically observed parthenogen reproduction strategies, and offer an hypothesis for the origin of binary cell fusion, a key step in the evolution of syngamy and sexual reproduction itself.
3D building modeling using images and LiDAR: a review

3D modeling from images and LiDAR (Light Detection And Ranging) has been an active research area in the photogrammetry, computer vision, and computer graphics communities. In terms of literature review, a comprehensive survey on 3D building modeling that contains methods from all these fields will be beneficial. This article attempts to survey the state-of-the-art 3D building modeling methods in the areas of photogrammetry, computer vision, and computer graphics. The existing methods are grouped into three categories: 3D reconstruction from images, 3D modeling using range data, and 3D modeling using images and range data. The use of both data for 3D modeling is a sensor fusion approach, in which methods of image-to-LiDAR registration, upsampling, and image-guided segmentation are reviewed. For each category, the key problems are identified and solutions are addressed.
Learning fast and fine-grained detection of amyloid neuropathologies from coarse-grained expert labels

Precise, scalable, and quantitative evaluation of whole slide images is crucial in neuropathology. We release a deep learning model for rapid object detection and precise information on the identification, locality, and counts of cored plaques and cerebral amyloid angiopathies (CAAs). We trained this object detector using a repurposed image-tile dataset without any human-drawn bounding boxes. We evaluated the detector on a new manually-annotated dataset of whole slide images (WSIs) from three institutions, four staining procedures, and four human experts. The detector matched the cohort of neuropathology experts, achieving 0.64 (model) vs. 0.64 (cohort) average precision (AP) for cored plaques and 0.75 vs. 0.51 AP for CAAs at a 0.5 IOU threshold. It provided count and locality predictions that correlated with gold-standard CERAD-like WSI scoring (p=0.07± 0.10). The openly-available model can quickly score WSIs in minutes without a GPU on a standard workstation.
Gene Expression and Evolution in the Smalltooth Sawfish, Pristis pectinata

Sawfishes (Pristidae) are large, highly threatened rays named for their tooth-studded rostrum, which is used for prey sensing and capture. Of all five species, the smalltooth sawfish, Pristis pectinata, has experienced the greatest decline in range, currently found in only ∼20% of its historic range. To better understand the genetic underpinnings of these taxonomically and morphologically unique animals, we collected transcriptomic data from several tissue types, mapped them to the recently completed reference genome and contrasted the patterns observed with comparable data from other elasmobranchs. Evidence of positive selection was detected in 79 genes in P. pectinata, several of which are involved in growth factor/receptor tyrosine kinase signaling and specification of organ symmetry, suggesting a role in morphogenesis. Data acquired also allow for examination of the molecular components of P. pectinata electrosensory systems, which are highly developed in sawfishes and have likely been influential in their evolutionary success.
T492I mutation alters SARS-CoV-2 properties via modulating viral non-structural proteins

The historically dominant SARS-CoV-2 Delta variants and the currently dominant Omicron variants carry a T492I substitution within the non-structural protein 4 (NSP4). Based on a combination of in silico analyses, we predicted that the T492I mutation increases the transmissibility and adaptability of the virus. We confirmed this hypothesis by performing competition experiments in hamsters and in human airway tissue culture models. Furthermore, we show that the T492I mutation also increases the replication capacity and infectiveness of the virus, and improves its ability to evade antibody neutralization induced by previous variants. Mechanistically, the T492I mutation increases cleavage efficiency of the viral main protease NSP5 by enhancing enzyme-substrate binding, resulting in increased production of nearly all non-structural proteins processed by NSP5. Importantly, T492I mutation suppresses the viral RNA associated chemokines in monocytic macrophages, which may contribute to the attenuated pathogenicity of Omicron variants. Our results highlight the importance of the NSP4 mutation in the evolutionary dynamics of SARS-CoV-2 and identify a novel target for the development of broad-spectrum antiviral agents.
Evidence of Lactate Shuttling in the Human Brain using Hyperpolarized 13C-MRI

Purpose To test the hypothesis that lactate shuttling contributes to the 13C-lactate and 13C-bicarbonate signal observed in the awake human brain using hyperpolarized 13C MRI. Methods Healthy human volunteers (n = 6) were scanned twice using hyperpolarized 13C-MRI, with reduced radiofrequency saturation of 13C-lactate on one set of scans. 13C-lactate, 13C-bicarbonate, and 13C-pyruvate signals for 132 brain regions across each set of scans were compared using a clustered Wilcoxon sum rank test. Results Reduced 13C-lactate radiofrequency saturation resulted in a significantly greater 13C-bicarbonate signal (p = 0.04). These changes were observed across the majority of brain regions. Conclusion Radiofrequency saturation of 13C-lactate leads to a decrease in 13C-bicarbonate signal, demonstrating that the 13C-lactate generated from the injected 13C-pyruvate is being converted back to 13C-pyruvate and oxidized throughout the human brain.
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data

Gene set scoring (GSS) has been routinely conducted for gene expression analysis of bulk or single-cell RNA-seq data, which helps to decipher single-cell heterogeneity and cell-type-specific variability by incorporating prior knowledge from functional gene sets. Single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) is a powerful technique for interrogating single-cell chromatin-based gene regulation, and genes or gene sets with dynamic regulatory potentials can be regarded as cell-type specific markers as if in scRNA-seq. However, there are few GSS tools specifically designed for scATAC-seq, and the applicability and performance of RNA-seq GSS tools on scATAC-seq data remain to be investigated. We systematically benchmarked ten GSS tools, including four bulk RNA-seq tools, five single-cell RNA-seq (scRNA-seq) tools, and one scATAC-seq method. First, using matched scATAC-seq and scRNA-seq datasets, we find that the performance of GSS tools on scATAC-seq data is comparable to that on scRNA-seq, suggesting their applicability to scATAC-seq. Then the performance of different GSS tools were extensively evaluated using up to ten scATAC-seq datasets. Moreover, we evaluated the impact of gene activity conversion, dropout imputation, and gene set collections on the results of GSS. Results show that dropout imputation can significantly promote the performance of almost all GSS tools, while the impact of gene activity conversion methods or gene set collections on GSS performance is more GSS tool or dataset dependent. Finally, we provided practical guidelines for choosing appropriate pre-processing methods and GSS tools in different scenarios.
BRIGHT-HΑ STARS IN IC 348

The important discovery has recently been made by A. Blaauw that a group of Oand B-type stars in Perseus forms an aggregate whose expansion has been under way for only about 1.3 million years. The expansion of the group (whose brightest star is Ç Persei) was inferred from the space motions of only its brightest members, for obvious reasons. Since the assumption is often made that the formation of main-sequence stars of later type is a continuing process, it is of interest to inquire whether the event that produced the high-luminosity members of the X> Persei group also resulted in the formation of stars of low luminosity. This question will probably be answered when extensive proper motion data become available for faint stars in the region of the aggregate. It is the purpose of this note to point out that evidence of quite a different kind, now available, indicates that an affirmative answer is probably correct. The fundamental assumption in the reasoning to follow is that Blaauw has correctly interpreted the motions of the stars in the Persei group. The brightest member of the small open cluster IC 348 (= IC 1985) is the eighth-magnitude B-type star BD -f31°643, which very probably belongs to the Ç Persei group. Relative proper motion data show that a number of the stars in IC 348 share the motion of —[-31 °643, and hence that the cluster probably is a physical one, and a member of the Ç Persei aggregate. The cluster is situated in a moderately obscured lane between two large dark clouds ; the reddening of its brighter members indicates a photographic absorption of 2 to 4 magnitudes. This fact, together with the presence of reflection nebulosity around +31°643 and other stars in the cluster, shows that IC 348 must be situated either in or behind the dark material upon which it is seen projected. If IC 348 is actually within the dark nebulosity, and if, in addition, this cluster possesses low-luminosity members, then the faint stars might exhibit emission spectra and light variations, such as those observed in objects of the T Tauri type. For the foregoing reasons, a search was made for emission-
Lymph node tuberculosis mimicking axillary hidradenitis: a case report

Hidradenitis is a chronic benign pathology with acute manifestations, mainly occurring among young patients with hyper seborrhea. Its clinical presentation is an inflammatory, nodular and fistulized aspect. It affects many body parts, making its location a referral criterion for diagnosis. Our patient had, indeed, a clinical aspect of hidradenitis. However, pathology revealed that it is tuberculosis lymphadenitis.
Algorithmic analysis of the BMAP/D/k system in discrete time

We exploit the structural properties of the BMAP/D/k system to carry out its algorithmic analysis. Specifically, we use these properties to develop algorithms for studying the distributions of waiting times in discrete time and the busy period. One of the structural properties used results from considering the system as having customers assigned in a cyclic order—which does not change the waiting-time distribution—and then studying only one arbitrary server. The busy period is defined as the busy period of an arbitrary single server based on this cyclic assignment of customers to servers. Finally, we study the marginal distribution of the joint queue length and phase of customer arrival. The structural property used for studying the queue length is based on the observation of the system every interval that is the length of one customer service time.
Implementation and Impact of Critical Care Pharmacist Addition to a Telecritical Care Network

IMPORTANCE: Critical care pharmacists when incorporated into the ICU team, have been shown to improve outcomes in critically ill patients by decreasing mortality, improving morbidity and reducing cost. As telehealth continues to evolve, the incorporation of a critical care pharmacist into a comprehensive telecritical care (TCC) service will allow increased comprehensive pharmacotherapeutic care for those in smaller, community or rural hospitals. OBJECTIVES: To describe the implementation of a TCC pharmacist into an established TCC network, classify interventions performed, and quantify cost avoidance generated through pharmacist interventions. DESIGN: Multicenter, observational cohort study and retrospective return on investment, performed between December 2019 and December 2021. SETTING AND PARTICIPANTS: Critically ill adult patients, admitted to an ICU located in any of our eight community hospitals (50 ICU beds) within a large, 25-hospital integrated healthcare system (563 ICU beds total) in the United States. MAIN OUTCOMES AND MEASURES: The TCC pharmacist service was implemented in 8-hour shifts, initially available 5 days per week, then expanded to 7 days per week. Critical care pharmacist interventions were categorized by clinical type established utilizing American Society of Health-System Pharmacists benchmarking standards and the latest cost avoidance data. RESULTS: During the 2-year analysis period, TCC pharmacists documented 2,838 interventions generating $1,664,254 of gross cost avoidance and a return on investment of 4.5:1. CONCLUSIONS AND RELEVANCE: It is feasible to implement a TCC pharmacist within an established TCC network. Our experience showed enhanced comprehensive care of critically ill patients located in community hospitals within a large, integrated healthcare system, demonstrated significant cost avoidance, and has led to other initiatives, including a collaborative clinical/operational partnership with Life Flight.
Red Flag/Blue Flag visualization of a common CNN for text classification

Abstract A shallow convolutional neural network (CNN), TextCNN, has become nearly ubiquitous for classification among clinical and medical text. This research presents a novel eXplainable-AI (X-AI) software, Red Flag/Blue Flag (RFBF), designed for binary classification with TextCNN. RFBF visualizes each convolutional filter’s discriminative capability. This is a more informative approach than direct assessment of logit contribution, features that overfit to train set nuances on smaller datasets may indiscriminately activate large logits on validation samples from both classes. RFBF enables model diagnosis, term feature verification, and overfit prevention. We present 3 use cases of (1) filter consistency assessment; (2) predictive performance improvement; and (3) estimation of information leakage between train and holdout sets. The use cases derive from experiments on TextCNN for binary prediction of surgical misadventure outcomes from physician-authored operative notes. Due to TextCNN’s prevalence, this X-AI can benefit clinical text research, and hence improve patient outcomes.