Miracle-dz/UniFAR-FTUs huggingface dataset:
Frequency and type of medications and vaccines used during pregnancy

Providing safe pharmacotherapy for pregnant women is challenging. Nearly all pregnant women are prescribed or inadvertently receive medication during their pregnancy. We reviewed the scientific literature to identify the specific medications and vaccines that are most often used during pregnancy and described them by category and indication. Our interest was to update the research before the implementation of the recently released FDA labeling rule for pregnancy and lactation that eliminates the use of pregnancy categories in product labels. Our results confirm that most products taken during pregnancy are over-the-counter or in the former FDA pregnancy categories A or B. However, medications taken prior to pregnancy recognition (inadvertent exposures) and those prescribed for chronic illness such as allergies, depression, and pain are of concern. A better understanding of medication and vaccine utilization during pregnancy may help clinicians reduce inadvertent first trimester exposures and improve the safe and effective treatment of pregnant women.
Cache-Oblivious Buffer Heap and Cache-Efficient Computation of Shortest Paths in Graphs

We present the buffer heap, a cache-oblivious priority queue that supports Delete-Min, Delete, and a hybrid Insert/Decrease-Key operation in O(1/B log2 N/M) amortized block transfers from main memory, where M and B are the (unknown) cache size and block size, respectively, and N is the number of elements in the queue. We introduce the notion of a slim data structure that captures the situation when only a limited portion of the cache, which we call a slim cache, is available to the data structure to retain data between data structural operations. We show that a buffer heap automatically adapts to such an environment and supports all operations in O(1/λ + 1/B log2 N/λ) amortized block transfers each when the size of the slim cache is λ. Our results provide substantial improvements over known trivial cache performance bounds for cache-oblivious priority queues with Decrease-Keys. Using the buffer heap, we present cache-oblivious implementations of Dijkstra’s algorithm for undirected and directed single-source shortest path (SSSP) problems for graphs with non-negative real edge-weights. On a graph with n vertices and m edges, our algorithm for the undirected case performs O(n + m/B log2 n/M) block transfers and for the directed case performs O((n + m/B) ċ log2 n/B) block transfers. These results give the first non-trivial cache-oblivious bounds for the SSSP problem on general graphs. For the all-pairs shortest path (APSP) problem on weighted undirected graphs, we incorporate slim buffer heaps into multi-buffer-buffer-heaps and use these to improve the cache-aware cache complexity. We also present a simple cache-oblivious APSP algorithm for unweighted undirected graphs that performs O(mn/B logM/B n/B) block transfers. This matches the cache-aware bound and is a substantial improvement over the previous cache-oblivious bound for the problem.
Reversible Polygon that Faithfully Represents the Convex and Concave Parts of a Digital Curve

From results about digital convexity, we deﬁne a reversible polygon that faithfully represents the maximal convex and concave parts of a digital curve. Such a polygon always exists and is unique in the general case. It is computed from a given digital curve in linear-time using well-known routines: adding a point at the front of a digital straight segment and removing a point from the back of a digital straight segment. It may helps to extract perceptually meaningful parts of shape outlines or lines.
Kargus: a highly-scalable software-based intrusion detection system

As high-speed networks are becoming commonplace, it is increasingly challenging to prevent the attack attempts at the edge of the Internet. While many high-performance intrusion detection systems (IDSes) employ dedicated network processors or special memory to meet the demanding performance requirements, it often increases the cost and limits functional flexibility. In contrast, existing software-based IDS stacks fail to achieve a high throughput despite modern hardware innovations such as multicore CPUs, manycore GPUs, and 10 Gbps network cards that support multiple hardware queues. We present Kargus, a highly-scalable software-based IDS that exploits the full potential of commodity computing hardware. First, Kargus batch processes incoming packets at network cards and achieves up to 40 Gbps input rate even for minimum-sized packets. Second, it exploits high processing parallelism by balancing the pattern matching workloads with multicore CPUs and heterogeneous GPUs, and benefits from extensive batch processing of multiple packets per each IDS function call. Third, Kargus adapts its resource usage depending on the input rate, significantly saving the power in a normal situation. Our evaluation shows that Kargus on a 12-core machine with two GPUs handles up to 33 Gbps of normal traffic and achieves 9 to 10 Gbps even when all packets contain attack signatures, a factor of 1.9 to 4.3 performance improvements over the existing state-of-the-art software IDS. We design Kargus to be compatible with the most popular software IDS, Snort.
High-performance genomic analysis framework with in-memory computing

In this paper, we propose an in-memory computing framework (called GPF) that provides a set of genomic formats, APIs and a fast genomic engine for large-scale genomic data processing. Our GPF comprises two main components: (1) scalable genomic data formats and API. (2) an advanced execution engine that supports efficient compression of genomic data and eliminates redundancies in the execution engine of our GPF. We further present both system and algorithm-specific implementations for users to build genomic analysis pipeline without any acquaintance of Spark parallel programming. To test the performance of GPF, we built a WGS pipeline on top of our GPF as a test case. Our experimental data indicate that GPF completes Whole-Genome-Sequencing (WGS) analysis of 146.9G bases Human Platinum Genome in running time of 24 minutes, with over 50% parallel efficiency when used on 2048 CPU cores. Together, our GPF framework provides a fast and general engine for large-scale genomic data processing which supports in-memory computing.
Piscivorous fish exhibit temperature-influenced binge feeding during an annual prey pulse.

Understanding the limits of consumption is important for determining trophic influences on ecosystems and predator adaptations to inconsistent prey availability. Fishes have been observed to consume beyond what is sustainable (i.e. digested on a daily basis), but this phenomenon of hyperphagia (or binge-feeding) is largely overlooked. We expect hyperphagia to be a short-term (1-day) event that is facilitated by gut volume providing capacity to store consumed food during periods of high prey availability to be later digested. We define how temperature, body size and food availability influence the degree of binge-feeding by comparing field observations with laboratory experiments of bull trout (Salvelinus confluentus), a large freshwater piscivore that experiences highly variable prey pulses. We also simulated bull trout consumption and growth during salmon smolt outmigrations under two scenarios: 1) daily consumption being dependent upon bioenergetically sustainable rates and 2) daily consumption being dependent upon available gut volume (i.e. consumption is equal to gut volume when empty and otherwise 'topping off' based on sustainable digestion rates). One-day consumption by laboratory-held bull trout during the first day of feeding experiments after fasting exceeded bioenergetically sustainable rates by 12- to 87-fold at low temperatures (3 °C) and by ˜1·3-fold at 20 °C. The degree of binge-feeding by bull trout in the field was slightly reduced but largely in agreement with laboratory estimates, especially when prey availability was extremely high [during a sockeye salmon (Oncorhynchus nerka) smolt outmigration and at a counting fence where smolts are funnelled into high densities]. Consumption by bull trout at other settings were lower and more variable, but still regularly hyperphagic. Simulations demonstrated the ability to binge-feed increased cumulative consumption (16-32%) and cumulative growth (19-110%) relative to only feeding at bioenergetically sustainable rates during the ˜1-month smolt outmigration period. Our results indicate the ability for predators to maximize short-term consumption when prey are available can be extreme and is limited primarily by gut volume, then mediated by temperature; thus, predator-prey relationships may be more dependent upon prey availability than traditional bioenergetic models suggest. Binge-feeding has important implications for energy budgets of consumers as well as acute predation impacts on prey.
Changes in Excess Mortality from End Stage Renal Disease in the United States from 1995 to 2013.

BACKGROUND AND OBJECTIVES Individuals with ESRD have a very high risk of death. Although mortality rates have decreased over time in ESRD, it is unknown if improvements merely reflect parallel increases in general population survival. We, therefore, examined changes in the excess risk of all-cause mortality-over and above the risk in the general population-among people treated for ESRD in the United States from 1995 to 2013. We hypothesized that the magnitude of change in the excess risk of death would differ by age and RRT modality. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We used time-dependent relative survival models including data from persons with incident ESRD as recorded in the US Renal Data System and age-, sex-, race-, and calendar year-specific general population mortality rates from the Centers for Disease Control and Prevention. We calculated relative excess risks (analogous to hazard ratios) to examine the association between advancing calendar time and the primary outcome of all-cause mortality. RESULTS We included 1,938,148 children and adults with incident ESRD from 1995 to 2013. Adjusted relative excess risk per 5-year increment in calendar time ranged from 0.73 (95% confidence interval, 0.69 to 0.77) for 0-14 year olds to 0.88 (95% confidence interval, 0.88 to 0.88) for ≥65 year olds, meaning that the excess risk of ESRD-related death decreased by 12%-27% over any 5-year interval between 1995 and 2013. Decreases in excess mortality over time were observed for all ages and both during treatment with dialysis and during time with a functioning kidney transplant (year by age and year by renal replacement modality interactions were both P<0.001), with the largest relative improvements observed for the youngest persons with a functioning kidney transplant. Absolute decreases in excess ESRD-related mortality were greatest for the oldest persons. CONCLUSIONS The excess risk of all-cause mortality among people with ESRD, over and above the risk in the general population, decreased significantly between 1995 and 2013 in the United States.
A novel network construction via nodes mergence approach

In this paper, we start by reviewing two small-world networks. Next, we present a novel approach to construct a network based on the so-called nodes mergence in order to better describe special characteristics of nodes in a network. Analysis of what distribution and parameters to choose is discussed, through which we obtain the best strategy to build the network. Further more, coordinate expression of nodes' characteristics is proposed in convenience for depicting merged nodes in a way computer could recognize. By comparing several statistical indexes including the average path length, clustering coefficient, and connectivity distribution of the newly created network and actual social networks, we find it quite realistic. Lastly, we conduct error tolerance analysis, which demonstrates the network's structural robustness towards both random and target attacks extends up to a 40% fraction of all nodes.
Sculptured Thin Films: Nanoengineered Morphology and Optics

Sculptured thin films (STFs) are a class of nanoengineered materials with properties that can be designed and realized in a controllable manner using physical vapor deposition. This text, presented as a short course at the SPIE Optical Science and Technology Symposium, couples detailed knowledge of thin-film morphology with the optical response characteristics of STF devices. An accompanying CD contains Mathematica(TM) programs for use with the presented formalisms. Thus, readers will learn to design and engineer STF materials and devices for future applications, particularly with optical applications. Graduate students in optics and practicing optical engineers will find the text valuable, as well as those interested in emerging nanotechnologies for optical devices.
α1‐antitrypsin Pittsburgh and plasmin‐mediated proteolysis

Essentials Patients with α‐1‐antitrypsin (α1‐AT) Pittsburgh exhibit a mild bleeding tendency. A new case of α1‐AT Pittsburgh with suspected high antifibrinolytic potential was studied. We showed that α1‐AT Pittsburgh inhibits tissue plasminogen activator and plasmin. The antifibrinolytic potential of the variant contributes to explaining the mild bleeding phenotype.
Improving the Morphological Analysis of Classical Sanskrit

The paper describes a new tagset for the morphological disambiguation of Sanskrit, and compares the accuracy of two machine learning methods (Conditional Random Fields, deep recurrent neural networks) for this task, with a special focus on how to model the lexicographic information. It reports a significant improvement over previously published results.
Advanced Dynamic Modeling of Three-Phase Mutually Coupled Switched Reluctance Machine

This paper proposes an advanced dynamic modelling approach of the mutually coupled switched reluctance motor (MCSRM) in the <inline-formula><tex-math notation="LaTeX">$dq$</tex-math></inline-formula> reference system that can consider saturation, cross-coupling, and spatial harmonics. Different topologies and their operating principles are investigated and an idealized <inline-formula><tex-math notation="LaTeX">$dq$</tex-math></inline-formula>-model considering the inductance harmonics is derived. A dynamic model is built based on flux-current lookup tables (LUTs) obtained from finite element analysis (FEA). A simplified method to inverse the two-dimensional LUTs is proposed. A fast computation approach is used to reduce the number of FEA simulations and calculation time to obtain the LUTs. Motor dynamic performances at different speeds are simulated by using the proposed dynamic model and the results are investigated and verified by FEA. The motor dynamic behavior can be accurately obtained in a short simulation time by using the proposed approach. Experiments are carried out on a 12/8 MCSRM, showing good accuracy of the proposed model.
Integrating HIV Preexposure Prophylaxis (PrEP) Into Routine Preventive Health Care to Avoid Exacerbating Disparities

More than 3 decades since its emergence in the United States, HIV continues to spread and disproportionately affect socially marginalized groups. Preexposure prophylaxis (PrEP), a highly effective prevention strategy federally approved since 2012, could fundamentally alter the course of the epidemic. However, PrEP’s potential has not been fully realized, in part because health care providers have been slow to adopt PrEP in clinical practice and have been selective in their discussion of PrEP with patients. This nonstandardized approach has constrained PrEP access. PrEP access has not only been inadequate but also inequitable, with several groups in high need showing lower rates of uptake than do their socially privileged counterparts. Recognizing these early warning signs that current approaches to PrEP implementation could exacerbate existing HIV disparities, we call on health professionals to integrate PrEP into routine preventive health care for adult patients-particularly in primary care, reproductive health, and behavioral health settings. Drawing on the empirical literature, we present 4 arguments for why doing so would improve access and access equity, and we conclude that the benefits clearly outweigh the challenges.
ViSlang: A System for Interpreted Domain-Specific Languages for Scientific Visualization

Researchers from many domains use scientific visualization in their daily practice. Existing implementations of algorithms usually come with a graphical user interface (high-level interface), or as software library or source code (low-level interface). In this paper we present a system that integrates domain-specific languages (DSLs) and facilitates the creation of new DSLs. DSLs provide an effective interface for domain scientists avoiding the difficulties involved with low-level interfaces and at the same time offering more flexibility than high-level interfaces. We describe the design and implementation of ViSlang, an interpreted language specifically tailored for scientific visualization. A major contribution of our design is the extensibility of the ViSlang language. Novel DSLs that are tailored to the problems of the domain can be created and integrated into ViSlang. We show that our approach can be added to existing user interfaces to increase the flexibility for expert users on demand, but at the same time does not interfere with the user experience of novice users. To demonstrate the flexibility of our approach we present new DSLs for volume processing, querying and visualization. We report the implementation effort for new DSLs and compare our approach with Matlab and Python implementations in terms of run-time performance.
Prevention of Infection in Orthopaedic Joint Replacement

Infection of a prosthetic joint is a significant adverse event, affecting the patient, the surgical team, and consuming hospital resources. The patient faces multiple operations, a prolonged hospital stay and a more challenging period of rehabilitation. The surgeon must perform longer and more technically demanding revision operations in order to remove the infected prosthesis, increasing the burden on hospital resources. It has been estimated that that the cost of managing an infected total hip replacement (THR) is four times greater than for a primary procedure (Dreghorn & Hamblen 1989). The personal cost to the patient must also be emphasised.
A phase 1 study of bortezomib and romidepsin in patients with chronic lymphocytic leukemia/small lymphocytic lymphoma, indolent B-cell lymphoma, peripheral T-cell lymphoma, or cutaneous T-cell lymphoma

Abstract A phase 1 study was conducted to determine the dose-limiting toxicities and maximum-tolerated dose (MTD) for bortezomib followed by romidepsin on days 1, 8, and 15 in patients with relapsed/refractory CLL/SLL or B- or T-cell lymphoma. Eighteen treated patients were evaluable for response. The MTD was 1.3 mg/m2 bortezomib and 10 mg/m2 romidepsin; median treatment duration was 3 cycles at this dose. The dose-limiting toxicities were grade 3 fatigue, vomiting, and chills. Two patients had partial responses, one lasting >2 years, 8 had stable disease, and 8 had progressive disease. The median duration of stable disease was 3.5 cycles. Correlative studies examining expression of NF-кB, XIAP, Bcl-xL, and Bim yielded variable results. The safety profile was consistent with that reported for single-agent bortezomib and romidepsin. This regimen has modest activity in heavily pretreated patients with relapsed/refractory CLL or B- or T-cell lymphoma. NCT00963274.
Molecular characterization of ‘Candidatus Borrelia tachyglossi’ (family Spirochaetaceae) in echidna ticks, Bothriocroton concolor

Recently, a novel species of the genus Borreliawas identified in Bothriocroton concolor and Ixodes holocyclus ticks from echidnas. Analyses of 16S rRNA and flaB genes identified three closely related genotypes of this bacterium (Borrelia sp. Aus A-C) that were unique and distinct from previously described borreliae. Phylogenetic analyses of flaB (763 bp), groEL (1537 bp), gyrB (1702 bp) and glpQ (874 bp) gene sequences and concatenated sequences (3585 bp) of three gene loci (16S rRNA, flaB and gyrB) were consistent with previous findings and confirm that this novel species of the genus Borrelia is more closely related to, yet distinct from, the Reptile-associated (REP) and Relapsing Fever (RF) groups. At the flaB locus, genotypes A, B and C shared the highest percentage sequence similarities (87.9, 88 and 87.9 %, respectively) with B.orrelia turcica (REP), whereas at the groEL and gyrB loci, these genotypes were most similar (88.2–89.4 %) to B.orrelia hermsii (RF). At the glpQ locus, genotypes A and B were most similar (85.7 and 85.4 % respectively) to Borrelia sp. Tortoise14H1 (REP). The presence of the glpQ gene, which is absent in the Lyme Borreliosis group spirochaetes, further emphasises that the novel species of the genus Borrelia characterized in the present study does not belong to this group. Phylogenetic analyses at multiple loci produced consistent topographies revealing the monophyletic grouping of this bacterium, therefore providing strong support for its species status. We propose the name ‘Candidatus Borrelia tachyglossi’, and hypothesize that this species of the genus Borrelia may be endemic to Australia. The pathogenic potential of this bacterium is not yet known.
Bacterial attachment on sub-nanometrically smooth titanium substrata

Despite the volume of work that has been conducted on the topic, the role of surface topography in mediating bacterial cell adhesion is not well understood. The primary reason for this lack of understanding is the relatively limited extent of topographical characterisation employed in many studies. In the present study, the topographies of three sub-nanometrically smooth titanium (Ti) surfaces were comprehensively characterised, using nine individual parameters that together describe the height, shape and distribution of their surface features. This topographical analysis was then correlated with the adhesion behaviour of the pathogenic bacteria Staphylococcus aureus and Pseudomonas aeruginosa, in an effort to understand the role played by each aspect of surface architecture in influencing bacterial attachment. While P. aeruginosa was largely unable to adhere to any of the three sub-nanometrically smooth Ti surfaces, the extent of S. aureus cell attachment was found to be greater on surfaces with higher average, RMS and maximum roughness and higher surface areas. The cells also attached in greater numbers to surfaces that had shorter autocorrelation lengths and skewness values that approached zero, indicating a preference for less ordered surfaces with peak heights and valley depths evenly distributed around the mean plane. Across the sub-nanometrically smooth range of surfaces tested, it was shown that S. aureus more easily attached to surfaces with larger features that were evenly distributed between peaks and valleys, with higher levels of randomness. This study demonstrated that the traditionally employed amplitudinal roughness parameters are not the only determinants of bacterial adhesion, and that spatial parameters can also be used to predict the extent of attachment.