Miracle-dz/UniFAR-FTUs huggingface dataset:
CPR: Understanding and Improving Failure Tolerant Training for Deep Learning Recommendation with Partial Recovery

The paper proposes and optimizes a partial recovery training system, CPR, for recommendation models. CPR relaxes the consistency requirement by enabling non-failed nodes to proceed without loading checkpoints when a node fails during training, improving failure-related overheads. The paper is the first to the extent of our knowledge to perform a data-driven, in-depth analysis of applying partial recovery to recommendation models and identified a trade-off between accuracy and performance. Motivated by the analysis, we present CPR, a partial recovery training system that can reduce the training time and maintain the desired level of model accuracy by (1) estimating the benefit of partial recovery, (2) selecting an appropriate checkpoint saving interval, and (3) prioritizing to save updates of more frequently accessed parameters. Two variants of CPR, CPR-MFU and CPR-SSU, reduce the checkpoint-related overhead from 8.2-8.5% to 0.53-0.68% compared to full recovery, on a configuration emulating the failure pattern and overhead of a production-scale cluster. While reducing overhead significantly, CPR achieves model quality on par with the more expensive full recovery scheme, training the state-of-the-art recommendation model using Criteo's Ads CTR dataset. Our preliminary results also suggest that CPR can speed up training on a real production-scale cluster, without notably degrading the accuracy.
Deciphering the Kinematic Structure of the Small Magellanic Cloud through Its Red Giant Population

We present a new kinematic model for the Small Magellanic Cloud (SMC), using data from the Gaia Data Release 2 catalog. We identify a sample of astrometrically well-behaved red giant (RG) stars belonging to the SMC and cross-match with publicly available radial velocity (RV) catalogs. We create a 3D spatial model for the RGs, using RR Lyrae for distance distributions, and apply kinematic models with varying rotation properties and a novel tidal expansion prescription to generate mock proper motion (PM) catalogs. When we compare this series of mock catalogs to the observed RG data, we find that a combination of moderate rotation (with a magnitude of ∼10–20 km s−1 at 1 kpc from the SMC center, inclination between ∼50 and 80°, and a predominantly north-to-south line-of-nodes position angle of ∼180°) and tidal expansion (with a scaling of ∼10 km s−1 kpc−1) is required to explain the PM signatures. The exact best-fit parameters depend somewhat on whether we assess only the PMs or include the RVs as a qualitative check, leaving some tension remaining between the PM and RV conclusions. In either case, the parameter space preferred by our model is different from previously inferred rotational geometries, including from the SMC H i gas, and from the RG RV-only analyses and new SMC PM analyses, which conclude that a rotation signature is not detectable. Taken together this underscores the need to treat the SMC as a series of different populations with distinct kinematics.
A connection between cut locus, Thom space
and Morse–Bott functions

Associated to every closed, embedded submanifold $N$ in a connected Riemannian manifold $M$, there is the distance function $d_N$ which measures the distance of a point in $M$ from $N$. We analyze the square of this function and show that it is Morse-Bott on the complement of the cut locus $\mathrm{Cut}(N)$ of $N$, provided $M$ is complete. Moreover, the gradient flow lines provide a deformation retraction of $M-\mathrm{Cut}(N)$ to $N$. If $M$ is a closed manifold, then we prove that the Thom space of the normal bundle of $N$ is homeomorphic to $M/\mathrm{Cut}(N)$. We discuss several interesting applications of these results to homotopy type of the cut locus, computing the local homology of the cut locus and deformations of Lie groups.
The Effects of Biconical Outflows on Lyα Escape from Green Peas

We analyze the spectra of 10 Green Pea galaxies, previously studied by Henry et al., using a semi-analytical line transfer model to interpret emission and absorption features observed in UV galactic spectra. We focus our analysis on various ionization states of silicon, associated with the cool (∼104 K) and warm (∼105 K) gas. By analyzing low-ionization lines, we study the relationships between the distribution and kinematics of the outflowing H i gas and the observed Lyα escape fraction, , as well as the Lyα emission peak separation, Δpeak. We find that outflow geometries that leave a portion of the source uncovered along the line of sight create the best conditions for Lyα escape and have narrow peak separations, while geometries that block the observer’s view of the source create the worst conditions for Lyα escape and have large peak separations. To isolate the effects of outflow kinematics, we restrict our testing set to galaxies with spherical outflows and find that and the Lyα luminosity both increase with the extent of the galactic winds. A simple estimate suggests that the collisional excitation of neutral hydrogen by free electrons in the cool gas of the winds can account for the Lyα luminosity observed in these objects. Finally, we speculate on the relationship between outflows and the escape of ionizing radiation from the circumgalactic medium.
A targeted sequence capture array for phylogenetics and population genomics in the Salicaceae

Premise The family Salicaceae has proved taxonomically challenging, especially in the genus Salix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus. Methods We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300–1200 bp of exonic regions of 972 genes. Results We recovered sequence data for nearly all of the targeted genes in three species of Populus and three species of Salix. We present a species tree, discuss concordance among gene trees, and present population genomic summary statistics for these loci. Conclusions Our sequence capture array has extremely high capture efficiency within the genera Populus and Salix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.
Antioxidant and Cytotoxic Activity of Beauveria bassiana Crude Mycelia Extracts against A-549 Cell Line

Entomopathogenic fungus Beauveria bassiana widely used as biopesticide that specifically infect and kill insect pests. The present study was aimed to evaluate antioxidant and cytotoxic potentials of mycelia extracts of ten Beauveria bassiana isolates. Mycelia of Beauveria bassiana were extracted with hexane, ethyl acetate, methanol and water. Antioxidant activity possessed by the mycelial extracts was studied using the 1,1-diphenyl-2-picrylhydrazyl radical assay. Cytotoxic activity of mycelia extracts was tested using A-549 cell lines employing sulforhodamine B assay. Among all the mycelial extracts of Beauveria bassiana isolates, ethyl acetate extract exhibited highest antioxidant activity with an IC50 of 202.45 µg/ml. Highest cytotoxic activity was observed with the ethyl acetate extract (116 %) while standard cisplatin showed 102 %. Further investigations needed on isolation and characterization of secondary metabolites that could be responsible for these activities in a bid to develop new compounds for cancer.
Learning to Approximate Functions Using Nb-Doped SrTiO3 Memristors

Memristors have attracted interest as neuromorphic computation elements because they show promise in enabling efficient hardware implementations of artificial neurons and synapses. We performed measurements on interface-type memristors to validate their use in neuromorphic hardware. Specifically, we utilized Nb-doped SrTiO3 memristors as synapses in a simulated neural network by arranging them into differential synaptic pairs, with the weight of the connection given by the difference in normalized conductance values between the two paired memristors. This network learned to represent functions through a training process based on a novel supervised learning algorithm, during which discrete voltage pulses were applied to one of the two memristors in each pair. To simulate the fact that both the initial state of the physical memristive devices and the impact of each voltage pulse are unknown we injected noise into the simulation. Nevertheless, discrete updates based on local knowledge were shown to result in robust learning performance. Using this class of memristive devices as the synaptic weight element in a spiking neural network yields, to our knowledge, one of the first models of this kind, capable of learning to be a universal function approximator, and strongly suggests the suitability of these memristors for usage in future computing platforms.
Interdependent Phenotypic and Biogeographic 3 Evolution Driven by Biotic Interactions

— Biotic interactions are hypothesized to be one of the main processes shaping 11 trait and biogeographic evolution during lineage diversification. Theoretical and empirical 12 evidence suggests that species with similar ecological requirements either spatially exclude 13 each other, by preventing the colonization of competitors or by driving coexisting 14 populations to extinction, or show niche divergence when in sympatry. However, the extent 15 and generality of the effect of interspecific competition in trait and biogeographic evolution 16 has been limited by a dearth of appropriate process-generating models to directly test the 17 effect of biotic interactions. Here, we formulate a phylogenetic parametric model that 18 . CC-BY-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint . http://dx.doi. org/10.1101/560912 doi: bioRxiv preprint first posted online Feb. 25, 2019;
Altered Brain Structural Networks in Patients with Brain Arteriovenous Malformations Located in Broca's Area

Focal brain lesions, such as stroke and tumors, can lead to remote structural alterations across the whole-brain networks. Brain arteriovenous malformations (AVMs), usually presumed to be congenital, often result in tissue degeneration and functional displacement of the perifocal areas, but it remains unclear whether AVMs may produce long-range effects upon the whole-brain white matter organization. In this study, we used diffusion tensor imaging and graph theory methods to investigate the alterations of brain structural networks in 14 patients with AVMs in the presumed Broca's area, compared to 27 normal controls. Weighted brain structural networks were constructed based on deterministic tractography. We compared the topological properties and network connectivity between patients and normal controls. Functional magnetic resonance imaging revealed contralateral reorganization of Broca's area in five (35.7%) patients. Compared to normal controls, the patients exhibited preserved small-worldness of brain structural networks. However, AVM patients exhibited significantly decreased global efficiency (p = 0.004) and clustering coefficient (p = 0.014), along with decreased corresponding nodal properties in some remote brain regions (p < 0.05, family-wise error corrected). Furthermore, structural connectivity was reduced in the right perisylvian regions but enhanced in the perifocal areas (p < 0.05). The vulnerability of the left supramarginal gyrus was significantly increased (p = 0.039, corrected), and the bilateral putamina were added as hubs in the AVM patients. These alterations provide evidence for the long-range effects of AVMs on brain white matter networks. Our preliminary findings contribute extra insights into the understanding of brain plasticity and pathological state in patients with AVMs.
Cytomegalovirus and Epstein-Barr Infections: Prevalence and Impact on Patients with Hematological Diseases

Cytomegalovirus (CMV) and Epstein-Barr virus (EBV) infections are widely distributed throughout the world. EBV is linked to various hematological and autoimmune disorders whereas CMV might play important role in the progression of chronic hematological diseases, such as hemoglobinopathies, lymphomas, myelomas, hemophilia, and aplastic and sickle cell anemia. Both viruses produce a viral homolog of human interleukin-10 that can cause general suppression of immune response, increasing susceptibility to other infections. These viruses can remain latent in the host cells and be reactivated when the host immune system is compromised. Studies showing the impact of CMV and EBV infections on hematological disorders are scarce and unclear in the context of coinfection. This review intends to present the biology, prevalence, and impact of CMV and EBV infections in patients with hematological diseases.
Neurogenesis Makes a Crucial Contribution to the Neuropathology of Alzheimer’s Disease

One unexplained feature of Alzheimer’s disease (AD) is that the lateral entorhinal cortex undergoes neurodegeneration before other brain areas. However, this brain region does not have elevated levels of amyloid peptides in comparison with undamaged regions. What is the cause of this special vulnerability of the entorhinal cortex? One special feature of the lateral entorhinal cortex is that it projects to newborn neurons that have undergone adult neurogenesis in the dentate gyrus of the hippocampus. Neurogenesis is abnormal in human AD brains, and modulation of neurogenesis in experimental animals influences the course of AD. This complex process of neurogenesis may expose axon terminals originating from neurons of the entorhinal cortex to a unique combination of molecules that can enhance toxic effects of amyloid. Retrograde degeneration of neurons with axons terminating in the dentate gyrus provides a likely explanation for the spatial patterns of neuronal cell death seen in AD. Specialized astrocytes in the dentate gyrus participate in adult neurogenesis and produce fatty acid binding protein7 (FABP7). These FABP7+ cells undergo an aging-related mitochondrial pathology that likely impairs their functions. This age-related abnormality may contribute to the impairment in neurogenesis seen in aging and Alzheimer’s disease. Also, a compromised function of these astrocytes likely results in local elevations of palmitic acid, iron, copper, and glucose, which all enhance the toxicity of amyloid peptides. Treatments that modulate neurogenesis or diminish the production of these toxic substances may prove more successful than treatments that are solely aimed at reducing the amyloid burden alone.
Risk factors for postoperative complications after elective ileocolic resection for Crohn’s disease: a retrospective study

Background The incidence of postoperative complications (POC) in patients with Crohn’s disease (CD) who undergo intestinal resection is high. The literature provides conflicting data about the risk factors for POC, especially regarding preoperative immunosuppressive medications. The purpose of this study was to evaluate the impact of anti-tumor necrosis factor (TNF) agents on the postoperative course and identify other predictors for POC after ileocolic resection (ICR). Methods This was a single-center retrospective study that included 153 CD patients who underwent elective ICR in a Greek tertiary center between January 2010 and December 2018. Risk factors for overall POC and intra-abdominal septic complications (IASC) were assessed with univariate and multivariate analyses. Results Overall POC and IASC occurred in 35 (22.9%) and 19 (12.4%) patients, respectively. In multivariate analysis, anti-TNF agents (n=61), as either monotherapy or combination treatment, were not associated with an increased risk for overall POC (21.3% vs. 23.9%, P=0.71) or IASC (13.1% vs. 12.0%, P=0.83). Similarly, no combined immunosuppressive regimen significantly correlated with POC. Patients with perianal disease, disease duration >10 years, or previous intestinal resections had significantly higher rates of both overall POC and IASC. In multivariate analysis, previous resection was the only independent risk factor for overall POC (odds ratio [OR] 3.90, 95% confidence interval [CI] 1.38-11.06; P=0.010) and IASC (OR 4.56, 95%CI 1.51-13.77; P=0.007). Conclusions Preoperative administration of anti-TNF agents or other immunosuppressive regimens was not a risk factor for total POC or IASC. A history of previous resection independently correlated with both overall POC and IASC.
Comparative Analysis of Visual Performance and Astigmatism Tolerance with Monofocal, Bifocal, and Extended Depth-of-Focus Intraocular Lenses Targeting Slight Myopia

Purpose To compare the visual performance and astigmatism tolerance of 3 intraocular lens (IOL) groups: monofocal, bifocal, and extended depth-of-focus (EDOF) IOLs targeting slight myopia. Methods Overall, there were 60 cataract surgery eyes from 60 patients with implantation of a monofocal, bifocal, or EDOF IOL (20 eyes in each IOL group). The EDOF IOLs targeted slight myopia (−0.25 D to −0.75 D). Intragroup comparison of visual acuity, defocus curve, objective optical quality, contrast sensitivity, visual function questionnaire scores, patients' overall satisfaction, and the astigmatism tolerance was performed 3 months after surgery. Results The EDOF group provided equivalently excellent distance visual outcomes (0.06 ± 0.12) as the monofocal (0.06 ± 0.09) and bifocal (0.03 ± 0.09) groups (P=0.554), better intermediate vision than the other 2 groups (P < 0.05), and similarly satisfactory near visual outcomes (0.23 ± 0.16 at 20 cm, and 0.17 ± 0.14 at 33 cm) as the bifocal group (0.28 ± 0.14 at 20 cm and 0.08 ± 0.10 at 33 cm) (P > 0.05). The contrast sensitivity of EDOF IOL was slightly decreased compared to that of monofocal IOL, but it was better than that of bifocal IOL. The EDOF group showed significantly higher satisfaction than the bifocal group did when preoperative corneal astigmatism was 0.75 D or greater (P=0.009). A significant negative correlation between the corneal astigmatism and patient satisfaction was observed in only the bifocal group. Conclusions The EDOF IOLs targeting slight myopia offered satisfactory visual outcomes at an extended range from far to near distances. The EDOF and monofocal IOLs showed a better tolerance to astigmatism than did the bifocal IOL.
Gastrointestinal fistula endoscopic closure techniques

With the improvement in flexible endoscopic technology and the availability of new endoscopic devices, current endoscopic therapies spare many patients who would otherwise undergo surgical repair of gastrointestinal fistulas. These endoscopic techniques include gastrointestinal stents, endoscopic suturing, cardiac septal occluders, endo-sponge, vacuum therapy and others. This review elaborates on the indications, evidence, procedural details, efficacy, and complications of various endoscopic techniques for the management of gastrointestinal fistulas.
Clinical Characteristics and Gene Mutation Analysis of the Chinese Han Population with Gitelman Syndrome: 3 Case Reports and a Literature Review

The present study reported clinical characteristics and the results of gene mutation analysis of 3 Chinese patients with Gitelman syndrome (GS). Three patients manifested with normal blood pressure, recurrent hypokalemia, and metabolic alkalosis. Only case 2 had obvious hypomagnesemia. Gene sequencing showed a compound heterozygous mutation in SCL12A3 in case 1 and a homozygous mutation in SCL12A3 in case 2. Heterozygous mutations in SCL12A3 and CLCNKB were found in case 3. Then, the literature was reviewed. The keyword “Gitelman syndrome” was inputted into the PubMed, Wanfang Database, and CNK to search all Chinese patients with GS diagnosed by gene mutations and to extract complete clinical data from December 1998 to 2018. Finally, a total of 124 cases of GS were included. No significant differences in the levels of serum potassium and magnesium were observed among the different gene mutations, and the serum magnesium levels in adults were lower than those of the juvenile. GS with reduced blood magnesium had a serious clinical phenotype. Therefore, GS had a diverse phenotype, and its final diagnosis required genetic profiling. The relationship of gene mutation and clinical phenotype needed further study.
Hand and Foot Musculature of Anura: Structure, Homology, Terminology, and Synapomorphies for Major Clades

ABSTRACT Although studies of anuran hand and foot musculature began in the first half of the 19th century, all studies to date have been taxonomically or anatomically restricted in scope, and none has considered the diversity of autopodial myology in Anura as a whole. As a model for future comparisons, we thoroughly describe the hand and foot musculature of an arboreal species (the hylid Triprion petasatus), define the layers in which these muscles are arranged, and attribute presumed functions. On the basis of our myological analysis of 155 species representing 46 of the 54 currently recognized families and main clades of anurans, we describe 20 characters related to hand and foot muscles. Optimization of these characters on the most recent and inclusive phylogenetic hypothesis of Anura results in synapomorphies for several major clades (Bombinatoridae, Alytidae, Xenoanura + Acosmanura, Xenoanura, Pipidae, Acosmanura, Anomocoela, Scaphiopodidae, Pelodytidae + Pelobatidae + Megophryidae, Megophryidae, Neobatrachia, Heleophrynidae, Sooglossidae, Laurentobatrachia, Calyptocephalellidae, Myobatrachoidea, and Nobleobatrachia), including new, nonhomoplastic synapomorphies for clades previously supported only by molecular evidence and a few conflicting phenotypic characters (e.g., Acosmanura, Anomocoela, Neobatrachia). Additionally, we (1) address controversies regarding the homology of anuran and caudate muscles in the context of putative synapomorphies for Ascaphidae + Leiopelmatidae and its sister clade Lalagobatrachia; (2) evaluate a recently proposed terminology for anuran hand and foot musculature; (3) discuss the identities of several hand and foot muscles with problematic homologies; (4) establish a unified terminology for anuran hand and foot muscles, including a list of synonyms for all names employed in the literature; and (5) propose hypotheses for the origin of several myological novelties (neomorphs).