Fast Program Research Articles

Fast and accurate short-read alignment with hybrid hash-tree data structure

Rapidly increasing the amount of short-read data generated by NGSs (new-generation sequencers) calls for the development of fast and accurate read alignment programs. The programs based on the hash table (BLAST) and Burrows-Wheeler transform (bwa-mem) are used, and the latter is known to give superior performance. We here present a new algorithm, a hybrid of hash table and suffix tree, which we designed to speed up the alignment of short reads against large reference sequences such as the human genome. The total turnaround time for processing one human genome sample (read depth of 30) is just 31 min with our system while that was more than 25 h with bwa-mem/gatk. The time for the aligner alone is 28 min for our system but around 2 h for bwa-mem. Our new algorithm is 4.4 times faster than bwa-mem while achieving similar accuracy. Variant calling and other downstream analyses after the alignment can be done with open-source tools such as SAMtools and Genome Analysis Toolkit (gatk) packages, as well as our own fast variant caller, which is well parallelized and much faster than gatk.

Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.

One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.

Perioperative management and fast track in knee arthroplasty

Knee arthroplasty is an established surgical treatment for advanced osteoarthritis of the knee. In view of the rising number of surgical procedures, increasing costs in the healthcare system with aparallel increase in patient age and comorbidities, an evidence-based perioperative management is gaining importance. Fast Recovery concepts comprise arange of evidence-based strategies for optimizing the perioperative course. By reducing perioperative risks and optimizing pre-, peri- and postoperative processes, complications can be reduced, as well as perioperative morbidity, while comprising faster convalescence. This review is based on asystematic literature search in the PubMed, Cochrane Library and Web of Science databases on the topic of perioperative optimization and evidence for Fast Recovery programs in knee resurfacing. In knee arthroplasty, Fast Recovery protocols lead to asignificant reduction in the length of stay in hospital without an increase in complication rates. Patients also benefit from afaster return to mobility and areduced level of postoperative pain. The involvement of multidisciplinary teams, the optimization of pain therapy, the minimization of blood loss and early mobilization are key elements of these protocols. The implementation of Fast Recovery protocols in the perioperative care of patients is an effective strategy to improve surgical outcomes. Essential for the success of such programs is individualized multidisciplinary patient care with preoperative risk assessment, optimized pain management and early physiotherapeutic mobilization. Future research should focus on the long-term effects of these approaches and their adaptation to different patient populations.

Optimal containment control for multi‐agent systems using fast adaptive dynamic programming

AbstractIn this paper, an innovative adaptive dynamic programming (ADP) algorithm with fast convergence speed is designed for the optimal containment control problem of discrete‐time linear multi‐agent systems. Precisely, a quadratic input energy cost function, including local containment error information and actuator information in the neighborhood, is designed for each follower. Solving the stationary condition of the cost function, the optimal containment controllers are obtained. Traditional ADP methods use actor–critic neural networks to approximate optimal costs and control strategies, it is time‐consuming to solve large‐scale multi‐agent problems due to the computational complexity of neural networks. In order to seek faster convergence speed of optimal containment control without knowing the model information, the fast ADP algorithm framework is designed, it is proved theoretically that the convergence speed is determined by some configurable parameters, and the whale optimization algorithm is employed to globally optimize the parameters of given spaces to derive the optimal configuration. Finally, numerical simulation results are given to verify the effectiveness of the designed algorithm.

A hybrid niching memetic algorithm for multi-modal optimization of double row layout problem

Double row layout problem (DRLP) involves identifying the exact locations of machines participating in a production task on two rows. There are typically multiple layouts with approximately optimal material handling cost for a DRLP. These layouts often exhibit significantly different layout configurations. Identifying multiple global or local optimal layouts can provide layout designers with a wide range of options, which is of great significance for enhancing the maintainability, scalability, and customisability of the facility. However, most existing studies on DRLPs typically focus on designing a single optimal layout. In this paper, we study a multi-modal optimization of double row layout problem (MDRLP). A hybrid approach combing a fast niching memetic algorithm and linear programming (FNMA-LP) is proposed for MDRLP to locate multiple global or local optimal layouts with a similar quality. First, a fast niching memetic algorithm is developed to find a set of approximate optimal machine sequences. Then, LP is employed to optimise the exact locations of machines for each machine sequence. To evaluate the performance of the proposed algorithm, FNMA-LP is compared against three popular multi-modal algorithms and a state-of-the-art single-modal algorithm developed for DRLP. Experiments show that our approach outperforms competing approaches on almost all problem instances.

Getting a colonoscopy at The Valley Hospital.

71 Background: Colorectal cancer (CRC) is the 3rd most common cancer in the U.S., yet it is preventable with evidence-based strategies such as early screening. The Valley Hospital (TVH) located in Bergen County NJ, is recognized for its high insured payer mix and median household income. According to the 2016 TVH Community Health Needs Assessment, only 71.4% of patients in TVH service area have had a CRC screening. The American Cancer Society National Colorectal Cancer Roundtable (NCCRT) campaigned to reach CRC screening rates of 80% and higher in communities across the nation. The Fast Track Screening Colonoscopy Program (FTSCP) at TVH was created to streamline the process of obtaining a screening colonoscopy and reach the NCCRT’s goal. Through the FTSCP, patients can omit the initial consultation with a gastroenterologist or colorectal surgeon. Patients are instead screened via a telephone call by a Physician Assistant (PA) or Advanced Practice Nurse (APN). The FTSCP is cost effective for patients as it potentially eliminates the initial consultation copayment and/or coinsurance. Methods: The purpose of the FTSCP is to achieve the NCCRT’s 80% goal of CRC screenings in TVH service area. An interdisciplinary team of gastroenterologists, colorectal surgeons, oncologists, anesthesiologists, and administration collaborated to create the FTSCP. A screening questionnaire was developed using the Lincoln Hospital in NYC’s existing criteria for patients who are eligible for a direct endoscopy referral. The questionnaire criteria ensures patients are safe to eliminate the initial consultation. A PA or APN determines the patients’ eligibility for the FTSCP over a screening telephone call. To qualify, patients cannot have significant medical comorbidities or exhibit signs or symptoms of CRC. If deemed eligible, the PA or APN sends a bowel preparation prescription to the patient’s pharmacy, reviews the instructions with them, and meets with them on the day of the procedure at TVH to perform a pre-procedural physical exam. To promote awareness and education of the FTSCP, multiple ongoing outreach events are held in the community. Patients also learn about the FTSCP through primary and specialty care referrals. Results: Since the inception of FTSCP in 2018, over 1300 patients have been screened for CRC. Additionally, adenocarcinomas, carcinoid tumors and tubular adenomas with high grade dysplasia have been detected. 394 tubular adenomas (30%) were identified and removed. In 2018, 59 patients were screened. The number of patients increased by 500% to 296 in 2023. The 2022 TVH Community Health Needs Assessment showed an increase to 79.6% of patients in TVH service area who have undergone CRC screening. Conclusions: The FTSCP at TVH is maximizing patient’s access to the prevention and timely screening for CRC. Additionally, TVH’s relocation from Ridgewood, NJ to Paramus, NJ offers further opportunities to educate a new community on CRC prevention.

Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis.

Observing a single biomolecule performing its function is fundamental in biophysics as it provides important information for elucidating the mechanism. High-speed atomic force microscopy (HS-AFM) is a unique and powerful technique that allows the observation of biomolecular motion in a near-native environment. However, the spatial resolution of HS-AFM is limited by the physical size of the cantilever tip, which restricts the ability to obtain atomic details of molecules. In this study, we propose a novel computational algorithm designed to derive atomistic models of conformational dynamics from AFM images. Our method uses normal-mode analysis to describe the expected motions of the molecule, allowing these motions to be represented with a limited number of coordinates. This approach mitigates the problem of overinterpretation inherent in the analysis of AFM images with limited resolution. We demonstrate the effectiveness of our algorithm, NMFF-AFM, using synthetic data sets for three proteins that undergo significant conformational changes. NMFF-AFM is a fast and user-friendly program that requires minimal setup and has the potential to be a valuable tool for biophysical studies using HS-AFM.

Keeping African women in social reproduction roles: a systematic qualitative review of literature on post-FTLRP Zimbabwe

ABSTRACT The capitalist sytem has been underwritten by unpaid social reproduction labour mostly provided by women. This article deploys social reproduction theory (SRT) to systematically review scholarly literature on Zimbabwe's fast track land reform programme (FTLRP) published since 2011. Research evidence indicates reasonable improvement on women's access to and control of land, but whether or not FTLPRP led to a more egalitarian division of social reproduction labour remains to be researched. The paper concludes by proposing a new research agenda on the shifting boundaries between workplace and home, paid and unpaid labour, for women on post-FTLRP farms.

Hope and trust in diagnostic imaging contexts – Constituting technology and liminal patients

IntroductionThis study investigates patients’ experience of selected imaging examinations and how human experiences are transformed through technological mediation. MethodA qualitative study of patients' experiences during selected imaging examinations, centering on human-technology relations, was conducted.Data was gathered in two Danish hospitals, through semi-structured interviews and participant observations. The study included fifteen diagnostic imaging examination cases, distributed over three Computed Tomography (CT)-guided lung biopsy interventions, seven conventional CT examinations, and five Positron Emission Tomography CT examinations. The participating patients were undergoing investigation for cancer within Fast Track Cancer Referral Programs (FTCRP).The study has a philosophical approach to practice grounded in Postphenomenology and draws on anthropological studies of healthcare practice as its theoretical and analytical framework. ResultsDiagnostic imaging technologies were found to have existential implications creating hope and trust in patients. Patients demonstrated technological readiness, in their willingness to comply with examination criteria and the professional's instructions. The patient's primary concern was achieving a good examination result, for which they were prepared to push themselves beyond their usual limits.Participating in diagnostic imaging examinations may be viewed as a life crisis ritual, wherein patients are constituted as liminal beings, existing between healthy and sick. ConclusionsThe existential implications of an imaging examination were clear in terms of hope and trust. Hope is related to life and death in two temporal perspectives: A future hope of surviving cancer and a present hope of being cancer-free. Hope was linked to avoiding despair and rested on trusting oneself to technology, thus, forming a circle of interrelated concepts. Implications for practiceProfessionals need to recognize the patients’ liminal passings yet, unnoticed transformative and existential implications, to perform better patient-centered care.

The French fast breeder program and the European nuclear integration

Pendant plus d’une décennie (1959-1969), la Commission Euratom (Communauté européenne de l’énergie atomique) a essayé de convaincre les États membres de réaliser une grande centrale à neutrons rapides, en créant une « entreprise commune » dans le cadre du traité Euratom. En 1974, les producteurs d’électricité français, italiens et ouest-allemands ont créé la multinationale NERSA (Centrale nucléaire européenne à neutrons rapides SA) pour construire une telle centrale, nommée Superphénix. Même si NERSA avait le droit de demander le statut d’entreprise commune, elle ne l’a jamais fait. S’appuyant sur des documents d’archives, cet article retrace l’approche ambiguë des acteurs français vis-à-vis d’Euratom et apporte un éclairage nouveau sur la relation entre les acteurs français du nucléaire et l’intégration nucléaire européenne. Il montre que le désir de la Commission Euratom de réaliser une centrale rapide dans le cadre communautaire a coïncidé avec une période cruciale de la stratégie nucléaire française, au cours de laquelle la technologie à neutrons rapides était considérée comme vitale pour le succès nucléaire de la France. En conséquence, les pouvoirs publics français ont éloigné le programme nucléaire français de la Commission Euratom afin d’éviter un contrôle communautaire sur Superphénix. L’article questionne également l’urgence du développement industriel de la technologie à neutrons rapides, en soutenant que les technocrates français ont construit un récit d’urgence qui a conduit la Commission Euratom à investir dans cette technologie.

Synthesis of an electronic control module for a selected technological node with a focus on its automation

The article presents problems related to the design of sequential control systems using algorithmic design method. Based on a graph describing the functions of signal processing, the method of fast programming of sequential electro-pneumatic systems and systems with logic elements is presented. The developed sequential system was verified through simulation using the FluidSim computer-aided design software from Festo.

A fast-cadenced search for gamma-ray burst orphan afterglows with the Deeper, Wider, Faster programme

ABSTRACT The relativistic outflows that produce long gamma-ray bursts (LGRBs) can be described by a structured jet model where prompt $\gamma$-ray emission is restricted to a narrow region in the jet’s core. Viewing the jet off-axis from the core, a population of afterglows without an associated GRB detection can be predicted. In this work, we conduct an archival search for these ‘orphan’ afterglows (OAs) with minute-cadence, deep ($g\sim 23$) data from the Dark Energy Camera (DECam) taken as part of the Deeper, Wider, Faster programme (DWF). We introduce a method to select fast-evolving OA candidates within DWF data that comprises a machine learning model, based on a realistic synthetic population of OAs. Using this classifier, we recover 51 OA candidates. Of these candidates, 42 are likely flare events from M-class stars. The remaining nine possess quiescent, coincident sources in archival data with angular profiles consistent with a star and are inconsistent with the expected population of LGRB host galaxies. We therefore conclude that these are likely Galactic events. We calculate an upper limit on the rate of OAs down to $g\lt 22$ AB mag of 7.46 deg$^{-2}$yr$^{-1}$ using our criteria and constrain possible jet structures. We also place an upper limit of the characteristic angle between the $\gamma$-ray-emitting region and the jet’s half-opening angle. For a smooth power law and a power law with core jet model, respectively, these values are $58.3^{\circ }$ and $56.6^{\circ }$, for a power-law index of 0.8 and $75.3^{\circ }$ and $76.8^{\circ }$ for a power-law index of 1.2.

Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation.

The increasing number and volume of genomic and metagenomic data necessitates scalable and robust computational models for precise analysis. Sketching techniques utilizing -mers from a biological sample have proven to be useful for large-scale analyses. In recent years, FracMinHash has emerged as a popular sketching technique and has been used in several useful applications. Recent studies on FracMinHash proved unbiased estimators for the containment and Jaccard indices. However, theoretical investigations for other metrics, such as the cosine similarity, are still lacking. In this paper, we present a theoretical framework for estimating cosine similarity from FracMinHash sketches. We establish conditions under which this estimation is sound, and recommend a minimum scale factor for accurate results. Experimental evidence supports our theoretical findings. We also present frac-kmc, a fast and efficient FracMinHash sketch generator program. frac-kmc is the fastest known FracMinHash sketch generator, delivering accurate and precise results for cosine similarity estimation on real data. We show that by computing FracMinHash sketches using frac-kmc, we can estimate pairwise cosine similarity speedily and accurately on real data. frac-kmc is freely available here: https://github.com/KoslickiLab/frac-kmc/.

Monolayer Vacancy-Induced MXene Memory for Write-Verify-Free Programming.

The fundamental logic states of 1 and 0 in Complementary Metal-Oxide-Semiconductor (CMOS) are essential for modern high-speed non-volatile solid-state memories. However, the accumulated storage signal in conventional physical components often leads to data distortion after multiple write operations. This necessitates a write-verify operation to ensure proper values within the 0/1 threshold ranges. In this work, a non-gradual switching memory with two distinct stable resistance levels is introduced, enabled by the asymmetric vertical structure of monolayer vacancy-induced oxidized Ti3C2Tx MXene for efficient carrier trapping and releasing. This non-cumulative resistance effect allows non-volatile memories to attain valid 0/1 logic levels through direct reprogramming, eliminating the need for a write-verify operation. The device exhibits superior performance characteristics, including short write/erase times (100ns), a large switching ratio (≈3×104), long cyclic endurance (>104 cycles), extended retention (>4×106s), and highly resistive stability (>104 continuous write operations). These findings present promising avenues for next-generation resistive memories, offering faster programming speed, exceptional write performance, and streamlined algorithms.

Engineering Improvement of the Core Layers of Charge Trapping Flash Memory Based on Doped HfO2 and Segmented Fabrication

An engineering approach was applied to modify the core layers of charge-trapping flash (CTF) memory—the blocking layer, charge-trapping layer, and tunneling layer. The doping of Ti in the charge-trapping layer and the use of Si-doped HfO2 for the tunneling layer could optimize charge capture and leakage control. This design enhances programming and erasing speeds and increases overall device stability by creating more corner fields and using the Coulomb blockade effect. Experimental results demonstrate a larger memory window and better charge retention for the new device at the same charge-trapping layer thickness. These findings signify the advancement of the new CTF memory in balancing fast programming and long-term charge retention. The long-standing contradiction between charge capturing and retention could be partially resolved by using this engineering method.

Effects of intermittent fasting on periodontal inflammation and subgingival microbiota.

Studies on the impact of intermittent fasting on periodontal health are still scarce. Thus, this study evaluated the effects of long-term intermittent fasting on periodontal health and the subgingival microbiota. This pilot study was part of a nonrandomized controlled trial. Overweight/obese participants (n=14) entered an intermittent fasting program, specifically the 5:2 diet, in which they restricted caloric intake to about a quarter of the normal total daily caloric expenditure for two nonconsecutive days/week. Subjects underwent a thorough clinical and laboratory examination, including an assessment of their periodontal condition, at baseline and 6months after starting the diet. Additionally, subgingival microbiota was assessed by 16S rRNA gene sequencing. After 6months of intermittent fasting, weight, body mass index, C-reactive protein, hemoglobin A1c (HbA1c), and the cholesterol profile improved significantly (p<0.05). Moreover, significant reductions were observed in bleeding on probing (p=0.01) and the presence of shallow periodontal pockets after fasting (p<0.001), while no significant change was seen in plaque index (p=0.14). While we did not observe significant changes in α- or β-diversity of the subgingival microbiota related to dietary intervention (p>0.05), significant differences were seen in the abundances of several taxa among individuals exhibiting ≥60% reduction (good responders) in probing pocket depth of 4-5mm compared to those with <60% reduction (bad responders). Intermittent fasting decreased systemic and periodontal inflammation. Although the subgingival microbiota was unaltered by this intervention, apparent taxonomic variability was observed between good and bad responders.

A perturbed-Alexander invariant

In this note, we give concise formulas, which lead to a simple and fast computer program that computes a powerful knot invariant. This invariant \rho_{1} is not new; yet our formulas are by far the simplest and fastest. Given a knot, we write one of the standard matrices, A , whose determinant is its Alexander polynomial; yet instead of computing the determinant, we consider a certain quadratic expression in the entries of A^{-1} . The proximity of our formulas to the Alexander polynomial suggests that they should have a topological explanation, which we do not have yet.

Optimal sizing and placement of capacitors in the isolated microgrid throughout the day considering the demand response program

Reactive power compensation (RPC) is a big problem during power system operation. Parenthetically, capacitor allocation and sizing may be the only convenient solution for RPC of power systems. The loss sensitivity factor (LSF) is applied here for finding the optimum capacitor position. This paper presents quasi-oppositional fast convergence evolutionary programming (QOFCEP), fast convergence evolutionary programming (FCEP), and evolutionary programming (EP) for the optimum location and sizing of shunt capacitors in the isolated microgrid (MG) for minimizing total real power loss throughout the day with and without the demand response program (DRP). The 33-node, 69-node, and 118-node isolated MGs have been studied to authenticate the efficacy of the suggested approach. Each MG includes small hydro power plants (SHPPs), solar PV plants (SPVPs), wind turbine generators (WTGs), diesel generators (DGs), and plug-in electric vehicles (PEVs).

Long-Term Effects of a 6-Week Power-Based Resistance Training and Fast Walking Interval Training Program on Physical Function, Muscle Power, Disability, and Frailty in Pre-Frail and Frail Older Adults

Introduction: Concurrent training has been shown to be a beneficial approach to improve overall health status in older adults. However, little is known about the adaptations of this type of training in the long term (i.e., after cessation of exercise), even less in older people affected by frailty syndrome. Therefore, this study aimed (i) to assess the effects of a 6-week concurrent training program composed of power-oriented resistance training and fast walking interval training on physical function, muscle power, disability in activities of daily living and frailty in pre-frail and frail older people, and (ii) to assess the effects of a 6-month detraining period on these outcomes. Methods: A total of 59 pre-frail and frail older adults (>75 years old; Frailty Phenotype >1) were allocated into intervention (INT; n = 32; 81.8 years; 21 women) or control (CON; n = 27; 82.5 years; 19 women) groups. Primary outcomes of this study were Short Physical Performance Battery (SPPB), relative sit-to-stand (STS) power, Barthel index, Lawton scale and Frailty Phenotype. Assessments were performed at baseline (PRE), after the concurrent training programme (POST) and after 6 months of follow-up (DET) in both groups. Mixed model repeated measures ANOVA with Bonferroni’s post hoc tests was used. Results: Immediately after the intervention (∆ = POST-PRE), INT improved SPPB (∆ = 3.0 points; p < 0.001), relative STS power (∆ = 0.87 W·kg−1; p < 0.001) and reduced their frailty levels (∆ = −1.42 criteria; p < 0.001), while no changes were observed in CON. After 6 months of detraining (∆ = DET-PRE), INT showed higher SPPB (∆ = 2.2 points; p < 0.001), higher relative STS power (∆ = 0.73 W·kg−1; p < 0.001) and lower frailty (∆ = −1.24 criteria; p < 0.001) values than those reported at baseline, which were significantly different than those reported by CON. Both, Barthel index and Lawton scale values were not modified during the study in either group. Conclusions: The 6-week concurrent training program improved physical function, muscle power and reduced frailty in pre-frail and frail older people and these improvements were maintained above baseline levels after 6 months of detraining. However, due to the individual variability found, future studies of long-term responders versus non-responders in frail populations are required.

Effect of treatment with carteolol and latanoprost in newly diagnosed primary open-angle glaucoma on peripapillary vessel density.

In a previous follow-up of glaucoma patients taking carteolol or latanoprost, we found a greater progression of visual field changes with the prostaglandin than the betablocker. In the present study we compared the impact of carteolol and latanoprost on peripapillary vessel density in newly diagnosed primary open-angle glaucoma (POAG) patients. The study consisted of two groups of POAG patients. There were 46 patient eyes treated with carteolol (Carteol LP 2%) in the first group and 52 eyes treated with latanoprost (Xalatan 0.005%) in the second. Intraocular pressure (IOP), vessel density (VD) and visual field were assessed in all patients. VD was measured peripapillary by optical coherence tomography angiography (OCTA) with the Avanti RTVue XR in eight segments: Inferior Temporal - IT (1); Temporal Inferior -TI (2); Temporal Superior - TS (3); Superior Temporal - ST (4); Superior Nasal - SN (5); Nasal Superior - NS (6); Nasal Inferior - NI (7) and Inferior Nasal - IN (8). The measurements were compared before and after three months of treatment. The visual field was examined with a fast threshold glaucoma program using a Medmont M 700 instrument from Medmont International Pty Ltd. and only when a diagnosis of POAG was done. The overall defect (OD) was assessed. Before treatment, there was no difference between groups in either OD or VD. After treatment, there was a decrease in IOP in both groups. In the carteolol-treated group, the mean decrease was 5.8 mmHg and in the latanoprost-treated eyes, the mean decrease was 7 mmHg. The difference was not statistically significant (P=0.133). After treatment with carteolol, there was a statistically significant increase in VD in segments 4, 5 and 6. After latanoprost treatment, VD was statistically significantly improved only in segment 5. A greater increase in VD values was found in eyes treated with carteolol than in eyes treated with latanoprost. Carteolol had a better effect on vessel density than latanoprost.