Miracle-dz/UniFAR-FTUs huggingface dataset:
New Cytogenetic Photomap and Molecular Diagnostics for the Cryptic Species of the Malaria Mosquitoes Anopheles messeae and Anopheles daciae from Eurasia

Simple Summary The most dangerous vectors of malaria in the northern regions of the world belong to the Maculipennis group. Among the 22 species in this group, six are considered dominant vectors of malaria. Of these six, Anopheles messeae represents the most widely spread and genetically diverse species in Eurasia and Anopheles daciae, a cryptic species whose taxonomic status is still under debate, has been differentiated from An. messeae based on differences in their ribosomal DNA. However, genetic studies of these species are scarce. The availability of well-developed polytene chromosomes in malaria mosquitoes provides an opportunity to construct high-resolution cytogenetic photomaps that can be used to investigate the genetic divergence between these species. In this study, we created a standard universal cytogenetic map for the salivary gland polytene chromosomes of An. messeae and An. daciae and developed a simple and robust molecular approach for species diagnostics. The quality of the cytogenetic map was validated by studying inversion polymorphisms in populations of An. messeae and An. daciae from a location in the Asian part of Russia. The map will facilitate further investigation of the genetic diversity of these cryptic species. Abstract The Eurasian malaria vector Anopheles messeae is a widely spread and genetically diverse species. Five widespread polymorphic chromosomal inversions were found in natural populations of this mosquito. A cryptic species, Anopheles daciae, was differentiated from An. messeae by the presence of several nucleotide substitutions in the Internal Transcribed Spacer 2 (ITS2) region of ribosomal DNA. However, because of the absence of a high-quality reference cytogenetic map, the inversion polymorphisms in An. daciae and An. messeae remain poorly understood. Moreover, a recently determined heterogeneity in ITS2 in An. daciae questioned the accuracy of the previously used Restriction Fragment Length Polymorphism (RFLP) assay for species diagnostics. In this study, a standard-universal cytogenetic map was constructed based on orcein stained images of chromosomes from salivary glands for population studies of the chromosomal inversions that can be used for both An. messeae and An. daciae. In addition, a new ITS2-RFLP approach for species diagnostics was developed. Both methods were applied to characterize inversion polymorphism in populations of An. messeae and An. daciae from a single location in Western Siberia in Russia. The analysis demonstrates that cryptic species are remarkably different in their frequencies of chromosomal inversion variants. Our study supports previous observations that An. messeae has higher inversion polymorphism in all autosomes than the cryptic species An. daciae.
Fine-grained Co-Attentive Representation Learning for Semantic Code Search

Code search aims to find code snippets from large-scale code repositories based on the developer's query intent. A significant challenge for code search is the semantic gap between programming language and natural language. Recent works have indicated that deep learning (DL) techniques can perform well by automatically learning the relationships between query and code. Among these DL-based approaches, the state-of-the-art model is TabCS, a two-stage attention-based model for code search. However, TabCS still has two limitations: semantic loss and semantic confusion. TabCS breaks the structural information of code into token-level words of abstract syntax tree (AST), which loses the sequential semantics between words in programming statements, and it uses a co-attention mechanism to build the semantic correlation of code-query after fusing all features, which may confuse the correlations between individual code features and query. In this paper, we propose a code search model named FcarCS (Fine-grained Co-Attentive Representation Learning Model for Semantic Code Search). FcarCS extracts code textual features (i.e., method name, API sequence, and tokens) and structural features that introduce a statement-level code structure. Unlike TabCS, FcarCS splits AST into a series of subtrees corresponding to code statements and treats each subtree as a whole to preserve sequential semantics between words in code statements. FcarCS constructs a new fine-grained co-attention mechanism to learn interdependent representations for each code feature and query, respectively, instead of performing one co-attention process for the fused code features like TabCS. Generally, this mechanism leverages row/column-wise CNN to enable our model to focus on the strongly correlated local information between code feature and Query. We train and evaluate FcarCS on an open Java dataset with 475k and 10k code/query pairs, respectively. Experimental results show that FcarCS achieves an MRR of 0.613, outperforming three state-of-the-art models DeepCS, UNIF, and TabCS, by 117.38%, 16.76%, and 12.68%, respectively. We also performed a user study for each model with 50 real-world queries, and the results show that FcarCS returned code snippets that are more relevant than the baseline models.
ENRICHING PRINTED BOOK READING EXPERIENCE BY PROVIDING ADDITIONAL DIGITAL CONTENT THROUGH AR TECHNOLOGY

s on Human Factors in Computing Systems. Association for Computing Machinery, New York, NY, USA, 1953–1958 . DOI:https://doi.org/10.1145/1240866.1240931 [10] Son Do-Lenh, Frédéric Kaplan, Akshit Sharma, and Pierre Dillenbourg. 2009. Multi-finger interactions with papers on augmented tabletops. In Proceedings of the 3rd International Conference on Tangible and Embedded Interaction (TEI '09). Association for Computing Machinery, New York, NY, USA, 267–274. DOI:https://doi.org/10.1145/1517664.1517720 [11] Jiwon Kim, Steven M. Seitz, and Maneesh Agrawala. 2004. Video-based document tracking: unifying your physical and electronic desktops. In <i>Proceedings of the 17th annual ACM symposium on User interface software and technology</i> (<i>UIST '04</i>). Association for Computing Machinery, New York, NY, USA, 99–107. DOI:Video-based document tracking: unifying your physical and electronic desktops [12] Gombrich, Ernst Hans, and Ernst Hans Gombrich. The story of art . Vol. 12. London: Phaidon, 1995. https://www.phaidon. com/store/art/the-story-of-art-9780714832470/ [13] Rosling, Hans. Factfulness . Flammarion, 2019. [14] Few, Stephen. Now you see it: simple visualization techniques for quantitative analysis . No. Sirsi) i9780970601988. 2009. [15] Dix, Alan, and Geoffrey Ellis. "Starting simple: adding value to static visualization through simple interaction. " Proceedings of the working conference on Advanced visual interfaces . 1998. [16] Rosling, Hans. "Hans Rosling: The best stats you've ever seen. " Video file], Feb (2006). [17] Vuforia. Retrieved from: https://library.vuforia. com/ [18] Rosling, Hans, and Zhongxing Zhang. "Health advocacy with Gapminder animated statistics. " Journal of epidemiology and global health 1.1 (2011): 11. [19] Datawrapper. Retrieved from: https://www.datawrapper. de/ [20] Kano model. Retrieved from: https://en.wikipedia. org/wiki/Kano_model
Practical Bandits: An Industry Perspective

The bandit paradigm provides a unified modeling framework for problems that require decision-making under uncertainty. Because many business metrics can be viewed as rewards (a.k.a. utilities) that result from actions, bandit algorithms have seen a large and growing interest from industrial applications, such as search, recommendation and advertising. Indeed, with the bandit lens comes the promise of direct optimisation for the metrics we care about. Nevertheless, the road to successfully applying bandits in production is not an easy one. Even when the action space and rewards are well-defined, practitioners still need to make decisions regarding multi-arm or contextual approaches, on- or off-policy setups, delayed or immediate feedback, myopic or long-term optimisation, etc. To make matters worse, industrial platforms typically give rise to large action spaces in which existing approaches tend to break down. The research literature on these topics is broad and vast, but this can overwhelm practitioners, whose primary aim is to solve practical problems, and therefore need to decide on a specific instantiation or approach for each project. This tutorial will take a step towards filling that gap between the theory and practice of bandits. Our goal is to present a unified overview of the field and its existing terminology, concepts and algorithms -- with a focus on problems relevant to industry. We hope our industrial perspective will help future practitioners who wish to leverage the bandit paradigm for their application.
SURFACE ANTIGENS OF CELLS OF THE II ~

I t is remarkable that of the six separate systems of surface antigens identified on thymocytes and lymphocytes of the mouse with cytotoxic antisera (1), all but one (H-2) are represented only, or mainly, on these cell types. Another antigen system with characteristically limited tissue representation has recently been recognized on plasma cells (2). We have referred to such discriminatory surface components as "differentiation antigens" (1). Thus the antigenic constitution of the surfaces of immunocompetent cells, and by inference also the spectrum of genes used by these cells to build their surface membranes (1), is characteristic of this pathway of differentiation. Continuing our study of the antigenic composition of cells belonging to the immune system, we have examined the question "What immunoglobulin components can be identified as surface elements of immunocompetent cells of different types? " There is already a variety of evidence from other laboratories that Ig components are in fact detectable on such cells (see review ref. 3). To do this we have studied the reactivity of a range of anti-Ig sera in tests with various immunocompetent cell populations, using the same cytotoxicity test system that has been used to identify all the other known surface antigens of immunocompetent cells referred to above. The Ig phenotypes of these cells were then further defined by testing the ability of various anti-Ig sera to interfere with their activity in a number of well-defined tests that measure functions of immunocompetent cells. In discussion, we shall at tempt to summarize present information on the surface phenotypes of different cells belonging to the various compartments of the immune system, including all the known differentiation antigens which serve to distinguish one such population from another, of which the Ig components represent one category.
WALKING AS AN INCOMPLETE EXERCISE FOR METABOLIC SYNDROME: PHYSIOLOGICAL AND BIOCHEMICAL OVERVIEW

Prasad MV 1 , Mohsina Hyder 1 , Smilty Benny 1 and Dinesh Roy D 2 . 1. Dr. Prasad’s DCRC, Kenichira, Wayanad, Kerala, India. 2. Genetika, Centre for Advanced Genetic Studies, Trivandrum-695024, Kerala, India. Manuscript Info Abstract . Manuscript History
Late-Stage Tumor Regression after PD-L1 Blockade Plus a Concurrent OX40 Agonist

PD-L1 blockade with concurrent OX40 agonism enhanced frequency and functionality of antigen-specific CD8+ T cells in mouse models of large tumors. Th1 skewing, CD8+ T cell metabolism, and antitumor immunity were augmented, and tumor regression was promoted. The protective capability of tumor antigen–specific T cells is regulated by costimulatory and inhibitory signals. Current approaches in cancer immunotherapy seek to restore the function of unresponsive T cells by blocking inhibitory pathways. In contrast, providing exogenous costimulatory signals to T cells also enhances antitumor functionality. By combining these two clinical approaches, we demonstrate the synergy of targeting PD-L1 together with the costimulatory molecule OX40, to enhance antitumor immunity. Concurrently blocking PD-L1 and providing a costimulatory agonist to OX40 increased the presence and functionality of tumor antigen–specific CD8+ T cells with simultaneous enhancement of T-helper type 1 (Th1)-skewed CD4+ T cells. This shift was functionally supported by increased glucose metabolism of antigen-specific CD8+ T cells and the acquisition of granzyme B by regulatory T cells. Together, this mechanism promoted tumor regression of late-stage tumors beyond that achieved by either blockade as monotherapy. These findings indicate that targeting both T-cell intrinsic (OX40) and extrinsic (PD-L1) regulatory molecules increases the bioenergetic potential of T cells, thereby expanding functional and tumor antigen–specific T cells.
Asynchronous Data-dependent Jitter Compensation

Certified by . Vladimir M. Stojanovic Assistant Professor Thesis Supervisor Certified by . Michael St. Germain Design Engineer, Analog Devices Inc. Thesis Supervisor
Trends in the Incidence and Mortality of Diabetes in China from 1990 to 2017: A Joinpoint and Age-Period-Cohort Analysis

Background: The prevalence of diabetes mellitus is rapidly increasing in China, but the secular trends in incidence and mortality remain unknown. This study aims to examine time trends from 1990 to 2017 and the net age, period, and cohort effects on diabetes incidence and mortality. Methods: Incidence and mortality rates of diabetes (1990–2017) were collected for each 5-year age group (from 5–9 to 80–84 age group) stratified by gender from the Global Burden of Disease 2017 Study. The average annual percentage changes in incidence and mortality were analyzed by joinpoint regression analysis; the net age, period, and cohort effects on the incidence and mortality were estimated by age-period-cohort analysis. Results: The joinpoint regression analysis showed that age-standardized incidence significantly rose by 0.92% (95% CI: 0.6%, 1.3%) in men and 0.69% in women (95% CI: 0.3%, 1.0%) from 1990 to 2017; age-standardized mortality rates rose by 0.78% (95% CI: 0.6%, 1.0%) in men and decreased by 0.12% (95% CI: −0.4%, 0.1%) in women. For age-specific rates, incidence increased in most age groups, with exception of 30–34, 60–64, 65–69 and 70–74 age groups in men and 25–29, 30–34, 35–39 and 70–74 age groups in women; mortality in men decreased in the younger age groups (from 20–24 to 45–49 age group) while increased in the older age groups (from 50–54 to 80–84 age group), and mortality in women decreased for all age groups with exception of the age group 75–79 and 80–84. The age effect on incidence showed no obvious changes with advancing age while mortality significantly increased with advancing age; period effect showed that both incidence and mortality increased with advancing time period while the period trend on incidence began to decrease since 2007; cohort effect on incidence and mortality decreased from earlier birth cohorts to more recent birth cohorts while incidence showed no material changes from 1982–1986 to 2012–2016 birth cohort. Conclusions: Mortality decreased in younger age groups but increased in older age groups. Incidence increased in most age groups. The net age or period effect showed an unfavorable trend while the net cohort effect presented a favorable trend. Aging likely drives a continued increase in the mortality of diabetes. Timely population-level interventions aiming for obesity prevention, healthy diet and regular physical activity should be conducted, especially for men and earlier birth cohorts at high risk of diabetes.
GATE and FENCE: Geo-Blocking Protocols for Named Data Networking

Named Data Networking (NDN) is a novel Internet architecture which focuses on content distribution by exploiting in-network caching and name-based forwarding. Contrary to today’s Internet, NDN has been designed from the ground up to be secure. From a content provider perspective (e.g., YouTube, Netflix), NDN offers appealing advantages in terms of network load and traffic reduction at producer side through in-network requests aggregation and content caching. As a side effect, content providers lose control on content dissemination when consumers’ requests are aggregated or satisfied by the network. This hinders the correct application of copyright and licensing agreements: only specific regions are allowed to consume a subset of the distributed contents. In attempt to address this problem, the existing TCP/IP approaches exploit requests’ source addresses (at server side) to identify the geographic origin of each request. In NDN these solutions are unfeasible for two reasons: consumers’ requests do not carry any source address, and a request will never reach content providers when aggregated or satisfied in the network. We solve this problem by proposing two lightweight and distributed geo-blocking protocols (GATE and FENCE) which use packet marking to identify and validate network regions at network edges. We perform experiments both on a network simulator and by extending the NDN implementation. Through our results we prove the proposed protocols are feasible, i.e., all the regions blacklisted by content providers are blocked and their network costs, in terms of space and router processing overhead, are negligible.
Accounting Data and Value: The Basic Results*

Subsequent to Feltham and Ohlson 1995 and Ohlson 1995, the accounting literature has published a large numbers of papers on accounting data and value.1 A review of this literature reveals that many themes and insights recur across the papers. With the advantage of hindsight, the repetitions seem inefficient. A student who takes a stab at familiarizing herself with subject matter naturally tends to view such a state of affairs as less than ideal. Questions like “What is it that I really need to understand? ” or “Taken in its totality, what ideas and results make the literature tick? ” arise. This paper addresses the essence of such questions. It states the central results as eight simple formal propositions. Because all the propositions are freestanding, they can, at least in principle, be internalized independently of each other. But the sequencing is in fact relevant because it introduces step-by-step increasingly sophisticated concepts. The concepts build upon each other; the propositions’ analytical simplicity should, therefore, not be taken as a sign that they are conceptually simplistic. Much discussion follows the propositions to spell out their broader significance. And the paper approaches this task always maintaining the texture of accounting: the central variables are earnings, book values, and dividends. The paper does not digress on proofs and finer analytical points. These aspects are of little interest, which is another way of saying that the paper focuses squarely on analytical constructs/representations and how these fit together. Nor does this paper elaborate on the extent to which the literature has already dealt with the results or insights. There is no question that most, if not all, results have had some kind of presence and thus lack novelty. That said, such cataloguing and related discussion would have been long and tedious without facilitating a better understanding of the insights I wish to convey. Aside from trying to systemize the literature, and thereby making it more accessible to the average reader, the paper also has a more ambitious objective. It goes to the heart of subject matter: the exposition should give the reader the sense that all pieces and insights interrelate logically and conceptually. In other words, the task at hand is to go beyond a listing of useful results (though this should hopefully be the case, too), and instead give a sense of how the various pieces coalesce into a whole. The development of such a coherent mental map allows the reader to think of the broad literature in an integrated fashion, rather than as consisting of loosely connected, or even competing, models that primarily differ in their empirical
Supplementary Information for “Growth patterns for shape-shifting elastic bilayers”

S1 Geometry and elasticity 2 S1.1 Elastic energy of a curved monolayer . 3 S1.1. 1 Energy derivation . 4 S1.1. 2 Föppl-Von Karman energy for elastic plates . 5 S1.2 Elastic energy of a bilayer . 7 S1.3 Energy equivalence between monoand bilayers . 8 S1.3. 1 Equal layer thicknesses . 8 S1.3. 2 Unequal layer thicknesses . 11 S1.3. 3 Unequal layer thicknesses and Young’s moduli . 14
Assessing connectivity despite high diversity in island populations of a malaria mosquito

Documenting isolation is notoriously difficult for species with vast polymorphic populations. High proportions of shared variation impede estimation of connectivity, even despite leveraging information from many genetic markers. We overcome these impediments by combining classical analysis of neutral variation with assays of the structure of selected variation, demonstrated using populations of the principal African malaria vector Anopheles gambiae. Accurate estimation of mosquito migration is crucial for efforts to combat malaria. Modeling and cage experiments suggest that mosquito gene drive systems will enable malaria eradication, but establishing safety and efficacy requires identification of isolated populations in which to conduct field testing. We assess Lake Victoria islands as candidate sites, finding one island 30 km offshore is as differentiated from mainland samples as populations from across the continent. Collectively, our results suggest sufficient contemporary isolation of these islands to warrant consideration as field‐testing locations and illustrate shared adaptive variation as a useful proxy for connectivity in highly polymorphic species.
Standardization of PSA Measures: A Reappraisal and an Experience with WHO Calibration of Beckman Coulter Access Hybritech Total and Free PSA

Prostate-specific antigen (PSA) is the serum biomarker most widely used in prostate diseases. Since there is significant variation in PSA results among non-equimolar assays, the 90:10 ratio of complexed PSA to free PSA (the Stanford standard) was proposed as standardization; this became the basis for the PSA mass standards WHO 96/670 for tPSA and 96/668 for fPSA. Nevertheless, recent publications underlined the lack of interchangeability between different commercial assays, all claimed to be equimolar and calibrated to the WHO standard. Importantly, the WHO calibration yields about 16-20% lower PSA results. Manufacturers that have chosen to calibrate existing assays to the mass value of WHO 96/760 have introduced a significant negative bias compared to the Hybritech assay calibration; this bias is transferred to clinical evaluation if the cutoff of 4 ng/mL, clinically validated for the Hybritech assay, is maintained with the WHO calibration. Beckman Coulter recently provided the option of calibrating the Access Hybritech PSA and free PSA assays to the WHO standard introducing a different clinical cutoff. Using two different reagent lots, we tested about 200 routine patients for tPSA and fPSA with both calibrations; we also calculated the f/tPSA ratio with both calibrated methods. Moreover, we verified the analytical sensitivity and interand intra-assay variability. In accordance with the claim of the manufacturer, the results obtained with the WHO calibration showed a negative bias of about 25% and, as expected, no significant difference was found for % f/tPSA. The same bias was found when retesting samples of the External Quality Assessment Scheme of the Institute of Clinical Physiology of the National Research Council in Pisa. Based on this experience we decided for the moment to keep the Hybritech calibration, in order to avoid cutoff changes during patient follow-up. Moreover, we have started to provide information to clinicians aimed at the alignment of our results with the WHO standardization. (Int J Biol Markers 2007; 22: 295-301)