Miracle-dz/UniFAR-FTUs huggingface dataset:
Glacial refugia and modern genetic diversity of 22 western North American tree species

North American tree species, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American trees since the last glacial maximum using species distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 tree species. We find that species with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas species with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r2 = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles.
The 45 pocket of HLA-A2.1 plays a role in presentation of influenza virus matrix peptide and alloantigens.

Amino acid substitutions were introduced into the 45 pocket of HLA-A2.1 to determine the potential role of this structurally defined feature of class I molecules in viral peptide and alloantigen presentation. The 45 pocket lies below the alpha 1-domain alpha-helix and is composed of five amino acids, three of which differ between HLA-A2.1 and HLA-B37. These two class I molecules have previously been shown to have largely non-overlapping peptide-binding specificities. Site-directed mutagenesis was used to replace the hydrophobic residues at positions 24, 45, and 67 in the 45 pocket of HLA-A2.1 with the hydrophilic amino acids found in these positions in HLA-B37. Thus, three single amino acid mutants were produced: 24A----S, 45 M----T, and 67V----S. These mutants were transfected into HMy2.C1R cells and assessed for their ability to present influenza virus matrix M1 57-68 peptide and HTLV-I Tax-1 2-25 peptide to HLA-A2.1-restricted, peptide-specific CTL and to present alloantigens to HLA-A2-allospecific CTL lines. Each of these substitutions in the 45 pocket produced a molecule that failed to present the M1 peptide to most M1 peptide-specific CTL lines. In contrast, none of these mutations affected presentation of the Tax-1 peptide to Tax-1-specific CTL lines, which indicates that these mutant HLA-A2 molecules can function in viral peptide presentation. Two of the three substitutions in the 45 pocket resulted in lack of recognition by a subset of HLA-A2 allospecific CTL lines. These results demonstrate that the amino acid side chains in the 45 pocket can strongly influence peptide presentation and suggest that the 45 pocket may play a role in determining peptide-binding specificity.
Detection and Quantification of Left Atrial Structural Remodeling With Delayed-Enhancement Magnetic Resonance Imaging in Patients With Atrial Fibrillation

Background— Atrial fibrillation (AF) is associated with diffuse left atrial fibrosis and a reduction in endocardial voltage. These changes are indicators of AF severity and appear to be predictors of treatment outcome. In this study, we report the utility of delayed-enhancement magnetic resonance imaging (DE-MRI) in detecting abnormal atrial tissue before radiofrequency ablation and in predicting procedural outcome. Methods and Results— Eighty-one patients presenting for pulmonary vein antrum isolation for treatment of AF underwent 3-dimensional DE-MRI of the left atrium before the ablation. Six healthy volunteers also were scanned. DE-MRI images were manually segmented to isolate the left atrium, and custom software was implemented to quantify the spatial extent of delayed enhancement, which was then compared with the regions of low voltage from electroanatomic maps from the pulmonary vein antrum isolation procedure. Patients were assessed for AF recurrence at least 6 months after pulmonary vein antrum isolation, with an average follow-up of 9.6±3.7 months (range, 6 to 19 months). On the basis of the extent of preablation enhancement, 43 patients were classified as having minimal enhancement (average enhancement, 8.0±4.2%), 30 as having moderate enhancement (21.3±5.8%), and 8 as having extensive enhancement (50.1±15.4%). The rate of AF recurrence was 6 patients (14.0%) with minimal enhancement, 13 (43.3%) with moderate enhancement, and 6 (75%) with extensive enhancement (P<0.001). Conclusions— DE-MRI provides a noninvasive means of assessing left atrial myocardial tissue in patients suffering from AF and might provide insight into the progress of the disease. Preablation DE-MRI holds promise for predicting responders to AF ablation and may provide a metric of overall disease progression.
Requirement for a bone marrow-derived component in the expression of cell-mediated antibacterial immunity

Mice were X irradiated with 400 R and 1 week post-irradiation were found to be unable to develop antilisterial immunity after active or passive immunization with immunologically committed spleen lymphocytes from Listeria-immune donors. This consequence of irradiation disappeared spontaneously within 21 days of exposure to X rays. Mice irradiated with as much as 900 R could be passively protected by immunologically committed lymphoid cells from Listeria-immune donors 10 days after irradiation if they had been given normal bone marrow cells on the day or irradiation. It is concluded that, in addition to immunologically committed lymphocytes, a second cellular component is needed for the expression of antibacterial immunity. This second component is bone marrow derived.
Unification of force and substance

Maxwell’s mature presentation of his equations emphasized the unity of electromagnetism and mechanics, subsuming both as ‘dynamical systems’. That intuition of unity has proved both fruitful, as a source of pregnant concepts, and broadly inspiring. A deep aspect of Maxwell’s work is its use of redundant potentials, and the associated requirement of gauge symmetry. Those concepts have become central to our present understanding of fundamental physics, but they can appear to be rather formal and esoteric. Here I discuss two things: the physical significance of gauge invariance, in broad terms; and some tantalizing prospects for further unification, building on that concept, that are visible on the horizon today. If those prospects are realized, Maxwell’s vision of the unity of field and substance will be brought to a new level. This article is part of the themed issue ‘Unifying physics and technology in light of Maxwell's equations’.
Hemodialysis-associated hypotension as an independent risk factor for two-year mortality in hemodialysis patients.

BACKGROUND The relationship between blood pressure (BP) and mortality in hemodialysis patients has remained controversial. Some studies suggested that a lower pre- or postdialysis BP was associated with excess mortality, while others showed poorer outcome in patients with uncontrolled hypertension. We conducted a multicenter prospective cohort study to evaluate the impact of hemodialysis-associated hypotension on mortality. METHODS We recruited 1244 patients (685 males; mean age, 60 +/- 13 years) who underwent hemodialysis in 28 units during the two-year study period beginning in December 1999. Pre-, intra-, and postdialysis BP, and BP upon standing soon after hemodialysis, were measured in all patients at entry. Logistic regression analysis was used to assess the effect on mortality of pre-, intra-, and postdialysis BP, a fall in BP during hemodialysis, and a fall in BP upon standing soon after hemodialysis. RESULTS During the study period, 149 patients died. Logistic models identified the lowest intradialysis systolic blood pressure (SBP) and degree of fall in SBP upon standing soon after hemodialysis as significant factors affecting mortality, but not pre- or postdialysis SBP and diastolic BP. The adjusted odds ratio for death was 0.79 (95% CI 0.64-0.98) when the lowest intradialysis SBP was analyzed in increments of 20 mm Hg, and was 0.82 (95% CI 0.67-0.98) when the fall in SBP upon standing soon after hemodialysis was analyzed in increments of 10 mm Hg. CONCLUSION These results suggest that intradialysis hypotension and orthostatic hypotension after hemodialysis are significant and independent factors affecting mortality in hemodialysis patients.
Integrated CPU and l2 cache voltage scaling using machine learning

Embedded systems serve an emerging and diverse set of applications. As a result, more computational and storage capabilities are added to accommodate ever more demanding applications. Unfortunately, adding more resources typically comes on the expense of higher energy costs. New chip design with Multiple Clock Domains (MCD) opens the opportunity for fine-grain power management within theprocessor chip. When used with dynamic voltage scaling (DVS), we can control the voltage and power of each domain independently. A significant power and energy improvement has been shown when using MCD design in comparison to managing a single voltage domain for the whole chip, as in traditional chips with global DVS. In this paper, we propose PACSL a Power-Aware Compiler-based approach using Supervised Learning. PACSL automatically derives an integrated CPU-core and on-chip L2 cache DVS policy tailored to a specific system and workload. Our approach uses supervised machine learning to discover a policy, which relies on monitoring a few performance counters. We present our approach detailing the role of a compiler in constructing a custom power management policy. We also discuss some implementation issues associated with our technique. We show that PACSL improves on traditional power management techniques that are used in general MCD chips. Our technique saves 22% on average (up to 46%) in energy-delay product over a DVS technique that applies independent DVS decisions in each domain. Compared to no-power management, our technique improves energy-delay product by 26% on average (up to 64%).
Dilute Temperley-Lieb algebra

In this thesis the regular and dilute n-diagram algebra, with the variable β = q−1 + q are studied, the regular and dilute Temperley-Lieb algebra are introduced to give a more abstract representation of the corresponding n-diagram algebra and their equivalence is proven. In the case that q is not a root of unity a full set of irreducible modules is given and after proving the irreducibility of these modules it is shown that the algebras are semisimple using Wedderburn’s theorem. After that transfer matrices are introduced and shown how they relate with the Temperley-Lieb algebra, these transfer matrices are then used to show the relation between the Potts model on the square lattice and the Temperley-Lieb algebra. Then a O(n) model on the square lattice is examined and the corresponding phase diagram is explored further. Title: Dilute Temperley-Lieb algebra Authors: Michiel Lieftink, michiellieftink@gmail.com, 11044764 Supervisors: prof. dr. Bernard Nienhuis, prof. dr. Jasper Stokman Second grader: dr. Raf Bocklandt, prof. dr. Kareljan Schoutens End date: July 13, 2018 Institute of Physics University of Amsterdam Science Park 904, 1098 XH Amsterdam http://www.iop. uva.nl Korteweg-de Vries Institute for Mathematics University of Amsterdam Science Park 904, 1098 XH Amsterdam http://www.kdvi. uva.nl
Patients with Prior Fractures Have an Increased Risk of Future Fractures: A Summary of the Literature and Statistical Synthesis

Numerous studies have reported increased risks of hip, spine, and other fractures among people who had previous clinically diagnosed fractures, or who have radiographic evidence of vertebral fractures. However, there is some variability in the magnitudes of associations among studies. We summarized the literature and performed a statistical synthesis of the risk of future fracture, given a history of prior fracture. The strongest associations were observed between prior and subsequent vertebral fractures; women with preexisting vertebral fractures (identified at baseline by vertebral morphometry) had approximately 4 times greater risk of subsequent vertebral fractures than those without prior fractures. This risk increases with the number of prior vertebral fractures. Most studies reported relative risks of approximately 2 for other combinations of prior and future fracture sites (hip, spine, wrist, or any site). The confidence profile method was used to derive a single pooled estimate from the studies that provided sufficient data for other combinations of prior and subsequent fracture sites. Studies of peri‐ and postmenopausal women with prior fractures had 2.0 (95% CI = 1.8, 2.1) times the risk of subsequent fracture compared with women without prior fractures. For other studies (including men and women of all ages), the risk was increased by 2.2 (1.9, 2.6) times. We conclude that history of prior fracture at any site is an important risk factor for future fractures. Patients with a history of prior fracture, therefore, should receive further evaluation for osteoporosis and fracture risk
Implant-assisted magnetic targeting of gold drug carriers in capillary beds

The feasibility of targeting nanosizegold drug carriersby using a ferromagnetic wire implanted in capillary beds is studied theoretically. An external uniform magnetic field is applied transversely to the wire to produce high gradient magnetic field which produce magnetic force acting on the carriers in the vicinity of wire surface. The study of gold drug carriers' motion in capillary beds under the influences of magnetic force and blood flow is simplified by neglecting the effect of capillaries' walls. Equations of motion of the carriers are formulated and are solved numerically to obtain carriers' trajectories. By analyzing carriers' trajectories, the feasibility of capturing gold drug carriers near wire surface can be examined and the capture efficacy can be estimated for various parameters suchas the strength of applied uniform magnetic field, the radius of gold drug carrier and the radius of the wire. The results show the feasibility of targeting gold drug carriers in capillary beds by using the implant. Information from this study are useful for developing techniques for magnetic targeting of gold drug which are now used for cancer and tumor therapies.
Typing first-class continuations in ML

Abstract An extension of ML with continuation primitives similar to those found in Scheme is considered. A number of alternative type systems are discussed, and several programming examples are given. A continuation-based operational semantics is defined for a small, purely functional language, and the soundness of the Damas–Milner polymorphic type assignment system with respect to this semantics is proved. The full Damas–Milner type system is shown to be unsound in the presence of first-class continuations. Restrictions on polymorphism similar to those introduced in connection with reference types are shown to suffice for soundness.
Cancer Biology and Signal Transduction Synuclein g Compromises Spindle Assembly Checkpoint and Renders Resistance to Antimicrotubule Drugs

Defects in the spindle assembly checkpoint (SAC) have been proposed to contribute to the chromosomal instability inhuman cancers.Oneof themajormechanismsunderlying antimicrotubule drug (AMD) resistance involves acquired inactivation of SAC. Synuclein g (SNCG), previously identified as a breast cancer–specific gene, is highly expressed in malignant cancer cells but not in normal epithelium. Here, we show that SNCG is sufficient to induce resistance to AMD-caused apoptosis in breast cancer cells and cancer xenografts. SNCG binds to spindle checkpoint kinase BubR1 and inhibits its kinase activity. Specifically, the C-terminal (Gln106Asp127) of SNCG binds to the N-terminal TPR (tetratricopeptidelike folds) motif of BubR1. SNCG–BubR1 interaction induces a structure changeof BubR1, attenuates its interactionwith other key checkpoint proteins of Cdc20, and thus compromises SAC function. SNCG expression in breast cancers from patients with a neoadjuvant clinical trial showed that SNCG-positive tumors are resistant to chemotherapy-induced apoptosis. These data show that SNCG renders AMD resistance by inhibiting BubR1 activity and attenuating SAC function. Mol Cancer Ther; 13(3); 699–713. 2014 AACR.
Restoration of retinal images with space-variant blur

Abstract. Retinal images are essential clinical resources for the diagnosis of retinopathy and many other ocular diseases. Because of improper acquisition conditions or inherent optical aberrations in the eye, the images are often degraded with blur. In many common cases, the blur varies across the field of view. Most image deblurring algorithms assume a space-invariant blur, which fails in the presence of space-variant (SV) blur. In this work, we propose an innovative strategy for the restoration of retinal images in which we consider the blur to be both unknown and SV. We model the blur by a linear operation interpreted as a convolution with a point-spread function (PSF) that changes with the position in the image. To achieve an artifact-free restoration, we propose a framework for a robust estimation of the SV PSF based on an eye-domain knowledge strategy. The restoration method was tested on artificially and naturally degraded retinal images. The results show an important enhancement, significant enough to leverage the images’ clinical use.
Ja n 20 00 QUIESCENT COSMOLOGICAL SINGULARITIES

The most detailed existing proposal for the structure of spacetime singularities originates in the work of Belinskii, Khalatnikov and Lifshitz. We show rigorously the correctness of this proposal in the case of analytic solutions of the Einstein equations coupled to a scalar field or stiff fluid. More specifically, we prove the existence of a family of spacetimes depending on the same number of free functions as the general solution which have the asymptotics suggested by the Belinskii-Khalatnikov-Lifshitz proposal near their singularities. In these spacetimes a neighbourhood of the singularity can be covered by a Gaussian coordinate system in which the singularity is simultaneous and the evolution at different spatial points decouples.
Distributed Data Association in Robotic Networks With Cameras and Limited Communications

We address the data association problem of features that are observed by a robotic network. Every robot in the network has limited communication capabilities and can only exchange local matches with its neighbors. We propose a distributed algorithm that takes these local matches and, by their propagation in the network, computes global correspondences. When the algorithm finishes, each robot knows the correspondences between its features and the features of all the other robots, even if they cannot directly communicate. The presence of spurious local correspondences may produce inconsistent global correspondences, which are association paths between features observed by the same robot. The contributions of this study are the propagation of the local matches and the detection and resolution of these inconsistencies. We formally prove that after executing the algorithm, all the robots finish with a data association that is free of inconsistencies. We provide a fully decentralized solution to the problem that is valid for any fixed communication topology and with bounded communications between the robots. Simulations and experimental results with real images show the performance of the method considering different features, matching functions, and robotic applications.
Laparoscopic "drilling" by diathermy or laser for ovulation induction in anovulatory polycystic ovary syndrome.

BACKGROUND Problems in inducing ovulation in women with polycystic ovary syndrome (PCOS) and anovulation (failure to ovulate) are well recognised. Surgical ovarian wedge resection was the first established treatment for anovulatory PCOS patients but was largely abandoned due to the risk of post-surgical adhesions and the introduction of medical ovulation induction with clomiphene and gonadotrophins. However patients with PCOS treated with gonadotrophins often have an over-production of follicles and are exposed to the risks of ovarian hyperstimulation syndrome (OHSS) and multiple pregnancy. Moreover ovulation induction with gonadotrophins, though effective, is an expensive, inconvenient and time-consuming treatment requiring intensive monitoring. Surgical therapy with laparoscopic ovarian "drilling" (LOD) may avoid or reduce the need for gonadotrophins or may facilitate their use. The procedure can be done on an outpatient basis with less trauma and fewer postoperative adhesions. Many uncontrolled observational studies have claimed that ovarian drilling is followed, at least temporarily, by a high rate of spontaneous ovulation and conception, and/or that subsequent medical ovulation induction becomes easier. OBJECTIVES To determine the effectiveness and safety of laparoscopic ovarian drilling compared with ovulation induction for subfertile women with clomiphene-resistant PCOS. SEARCH STRATEGY We used the search strategy of the Menstrual Disorders and Subfertility Group. SELECTION CRITERIA We included randomised controlled trials of subfertile women with clomiphene-resistant PCOS that undertook laparoscopic ovarian drilling in order to induce ovulation. DATA COLLECTION AND ANALYSIS Fifteen trials were identified and six were included in the review. All trials were assessed for quality criteria. The primary outcomes were live birth, ovulation and pregnancy rates and the secondary outcomes were rates of miscarriage, multiple pregnancy, ovarian hyperstimulation syndrome and cost. MAIN RESULTS There was no evidence of a difference in live births or ongoing pregnancies between LOD and gonadotrophins and the pooled Odds Ratio (OR) (all studies) was 1.04 (95% CI 0.74, 1.99) and 1.16 (95% CI 0.72, 1.86) respectively. Multiple pregnancy rates were lower with ovarian drilling than with gonadotrophins (1% vs 16%, OR: 0.13, 95% CI: 0.03 to 0.59). There was no evidence of a difference in miscarriage rates between the two groups (OR 0.81, 955% 0.36, 1.86). AUTHORS' CONCLUSIONS There was no evidence of a difference in the live birth rate and miscarriage rate in women with clomiphene resistant PCOS undergoing LOD compared to gonadotrophin treatment. The reduction in multiple pregnancy rates in women undergoing LOD makes this option attractive. However, there are ongoing concerns about long term effects of LOD on ovarian function.
Microtubule +TIPs at a glance

Microtubules are highly dynamic hollow tubes that are involved in many vital cellular activities, including maintenance of cell shape, division, migration and intracellular transport. They are assembled from heterodimers of α- and β-tubulin that align in a head-to-tail fashion. Microtubules are,
A series-capacitor tapped buck (SC-TaB) converter for regulated high voltage conversion ratio DC-DC applications

This paper explores a Series-Capacitor Tapped Buck (SC-TaB) converter for regulated high voltage conversion ratio dc-dc applications targeting high efficiency and high power density. By adding one series capacitor and one auxiliary switch to the conventional tapped inductor buck converter, the proposed converter features many advantages including: (1) full soft switching; (2) reduced parasitic ringing; (3) capacitive energy buffering; (4) extended duty ratio; (5) reduced switch stress and (6) high efficiency over wide operating ranges. Experimental results of a 48V/5V, 750kHz, 100W, two-phase-interleaved dc-dc converter shows 91% peak efficiency, and above 88% efficiency over 38-58V input voltage range and 25-75W power range.