Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust and efficient coding with grid cells

The neuronal code arising from the coordinated population activity of grid cells in the rodent entorhinal cortex can uniquely represent space across large distances but the precise conditions for efficient coding are unknown. Here we present a number-theoretic analysis of grid coding and derive an upper bound on the distance that a population of grid cells can represent without error. We show that in the absence of neuronal noise, the capacity of the system would be extremely sensitive to the choice of the grid periods. However, when the accuracy of the representation is limited by neuronal noise, the capacity becomes gradually more robust against the choice of grid scales as the number of modules increases and remains near optimal even for random scale choices. Our study reveals that robust and efficient coding can be achieved without parameter tuning in the case of grid cell representation.
Role of Candida albicans secreted aspartyl protease Sap9 in interkingdom biofilm formation.

The fungus Candida albicans colonizes oral cavity surfaces and is carried by up to 60% of human populations. Biofilm development by C. albicans may be modulated by oral streptococci, such as Streptococcus gordonii, S. oralis or S. mutans, so as to augment pathogenicity. In this study we sought to determine if the cell wall-associated secreted aspartyl proteinase Sap9 was necessary for hyphal adhesin functions associated with biofilm community development. A sap9Δ mutant of C. albicans SC5314 formed biofilms that were flatter, and contained fewer blastospores and more hyphal filaments than the parent strain. This phenotypic difference was accentuated under flow (shear) conditions and in the presence of S. gordonii. Dual-species biofilms of C. albicans sap9Δ with S. oralis, S. sanguinis, S. parasanguinis, S. mutans and Enterococcus faecalis all contained more matted hyphae and more bacteria bound to substratum compared to C. albicans wild type. sap9Δ mutant hyphae showed significantly increased cell surface hydrophobicity, ∼25% increased levels of binding C. albicans cell wall protein Als3, and reduced interaction with Eap1, implicating Sap9 in fungal cell-cell recognition. These observations suggest that Sap9 is associated with protein-receptor interactions between fungal cells, and with interkingdom communication in the formation of polymicrobial biofilm communities.
Application of Machine Learning for the Spatial Analysis of Binaural Room Impulse Responses

Spatial impulse response analysis techniques are commonly used in the field of acoustics, as they help to characterise the interaction of sound with an enclosed environment. This paper presents a novel approach for spatial analyses of binaural impulse responses, using a binaural model fronted neural network. The proposed method uses binaural cues utilised by the human auditory system, which are mapped by the neural network to the azimuth direction of arrival classes. A cascade-correlation neural network was trained using a multi-conditional training dataset of head-related impulse responses with added noise. The neural network is tested using a set of binaural impulse responses captured using two dummy head microphones in an anechoic chamber, with a reflective boundary positioned to produce a reflection with a known direction of arrival. Results showed that the neural network was generalisable for the direct sound of the binaural room impulse responses for both dummy head microphones. However, it was found to be less accurate at predicting the direction of arrival of the reflections. The work indicates the potential of using such an algorithm for the spatial analysis of binaural impulse responses, while indicating where the method applied needs to be made more robust for more general application.
Frequency and developmental timing of linear enamel hypoplasia defects in Early Archaic Texan hunter-gatherers

Digital photographs taken under controlled conditions were used to examine the incidence of linear enamel hypoplasia defects (LEHs) in burials from the Buckeye Knoll archaeological site (41VT98 Victoria county, Texas), which spans the Early to Late Archaic Period (ca. 2,500–6,500 BP uncorrected radiocarbon). The majority (68 of 74 burials) date to the Texas Early Archaic, including one extremely early burial dated to 8,500 BP. The photogrammetric data collection method also results in an archive for Buckeye Knoll, a significant rare Archaic period collection that has been repatriated and reinterred. We analyzed the incidence and developmental timing of LEHs in permanent canines. Fifty-nine percent of permanent canines (n = 54) had at least one defect. There were no significant differences in LEH frequency between the maxillary and mandibular canines (U = 640.5, n1 = 37, n2 = 43, p = .110). The sample studied (n = 92 permanent canines) had an overall mean of 0.93 LEH defect per tooth, with a median of one defect, and a mode of zero defects. Average age at first insult was 3.92 (median = 4.00, range = 2.5–5.4) and the mean age of all insults per individual was 4.18 years old (range = 2.5–5.67). Age at first insult is consistent with onset of weaning stress—the weaning age range for hunter-gatherer societies is 1–4.5. Having an earlier age of first insult was associated with having more LEHs (n = 54, rho = −0.381, p = 0.005).
Abdominal obesity adversely affects bone mass in children

AIM To determine the effect of childhood obesity and insulin resistance on bone health. METHODS We conducted a cross sectional study in pubertal adolescents and young adults 13-20 years old who were either overweight/obese or normal weight. Participants were Tanner 3 or above for pubertal stage, and had fasting blood work done to measure glucose, insulin, C-reactive protein and lipid levels. Homeostatic model of insulin resistance (HOMA-IR) was calculated using the formula (Fasting Blood Glucose *Insulin/405). Body composition and bone mineral density were measured using dual energy X-ray absorptiometry (DXA; Hologic QDR 4500, Waltham, MA, United Kingdom). RESULTS Percent trunk fat was associated inversely with whole body bone mineral content (BMC), whereas HOMA-IR was associated positively with whole body BMC. CONCLUSION Our results suggest that abdominal adiposity may have an adverse effect on whole body bone parameters and that this effect is not mediated by insulin resistance.
A discriminative model approach for accurate duplicate bug report retrieval

Bug repositories are usually maintained in software projects. Testers or users submit bug reports to identify various issues with systems. Sometimes two or more bug reports correspond to the same defect. To address the problem with duplicate bug reports, a person called a triager needs to manually label these bug reports as duplicates, and link them to their "master" reports for subsequent maintenance work. However, in practice there are considerable duplicate bug reports sent daily; requesting triagers to manually label these bugs could be highly time consuming. To address this issue, recently, several techniques have be proposed using various similarity based metrics to detect candidate duplicate bug reports for manual verification. Automating triaging has been proved challenging as two reports of the same bug could be written in various ways. There is still much room for improvement in terms of accuracy of duplicate detection process. In this paper, we leverage recent advances on using discriminative models for information retrieval to detect duplicate bug reports more accurately. We have validated our approach on three large software bug repositories from Firefox, Eclipse, and OpenOffice. We show that our technique could result in 17--31%, 22--26%, and 35--43% relative improvement over state-of-the-art techniques in OpenOffice, Firefox, and Eclipse datasets respectively using commonly available natural language information only.
LATTER M INIMA WITH SGD

It has been discussed that over-parameterized deep neural networks (DNNs) trained using stochastic gradient descent (SGD) with smaller batch sizes generalize better compared with those trained with larger batch sizes. Additionally, model parameters found by small batch size SGD tend to be in flatter regions. We extend these empirical observations and experimentally show that both large learning rate and small batch size contribute towards SGD finding flatter minima that generalize well. Conversely, we find that small learning rates and large batch sizes lead to sharper minima that correlate with poor generalization in DNNs.
Constructing Ebola transmission chains from West Africa and estimating model parameters using internet sources

SUMMARY During the recent Ebola crisis in West Africa, individual person-level details of disease onset, transmissions, and outcomes such as survival or death were reported in online news media. We set out to document disease transmission chains for Ebola, with the goal of generating a timely account that could be used for surveillance, mathematical modeling, and public health decision-making. By accessing public web pages only, such as locally produced newspapers and blogs, we created a transmission chain involving two Ebola clusters in West Africa that compared favorably with other published transmission chains, and derived parameters for a mathematical model of Ebola disease transmission that were not statistically different from those derived from published sources. We present a protocol for responsibly gleaning epidemiological facts, transmission model parameters, and useful details from affected communities using mostly indigenously produced sources. After comparing our transmission parameters to published parameters, we discuss additional benefits of our method, such as gaining practical information about the affected community, its infrastructure, politics, and culture. We also briefly compare our method to similar efforts that used mostly non-indigenous online sources to generate epidemiological information.
Location Privacy Protection for Smartphone Users

As smartphones are increasingly used to run apps that provide users with location-based services, the users' location privacy has become a major concern. Existing solutions to this concern are deficient in terms of practicality, efficiency, and effectiveness. To address this problem, we design, implement, and evaluate LP-Guardian, a novel and comprehensive framework for location privacy protection for Android smartphone users. LP-Guardian's overcomes the shortcomings of existing approaches by addressing the tracking, profiling, and identification threats while maintaining app functionality. We have implemented and evaluated LP-Guardian's on Android 4.3. 1. Our evaluation results show that LP-Guardian's effectively thwarts the privacy threats, without deteriorating the user's experience (less than 10% overhead in delay and energy). Also, LP-Guardian's privacy protection is shown to be achieved at a tolerable loss in app functionality.
Stearic Acid Accumulation in Macrophages Induces Toll-Like Receptor 4/2-Independent Inflammation Leading to Endoplasmic Reticulum Stress–Mediated Apoptosis

Objective—Elevated serum free fatty acid levels are associated with an increased risk of cardiovascular disease and type 2 diabetes mellitus. Macrophages are recruited to atherosclerotic plaques and metabolic tissues during obesity and accumulate lipids, including free fatty acids. We investigated the molecular consequences of intracellular saturated free fatty acid accumulation in macrophages. Methods and Results—Previously, we demonstrated that cotreatment of mouse peritoneal macrophages (MPMs) with stearic acid and triacsin C (an inhibitor of long-chain acyl coenzyme A synthetases) results in intracellular free fatty acid accumulation and apoptosis. Here, we used Western blotting analysis, real-time reverse transcription polymerase chain reaction, and terminal deoxynucleotidyl transferase dUTP nick-end labeling staining to assess endoplasmic reticulum (ER) stress, inflammation, and apoptosis in MPMs. Intracellular stearic acid accumulation induces Toll-like receptor 4/2-independent inflammation that results in ER stress–mediated apoptosis of MPMs. Polarization of MPMs to a proinflammatory M1 phenotype increases their susceptibility to inflammation and ER stress, but not apoptosis, in response to cotreatment with stearic acid and triacsin C. Conclusion—Intracellular accumulation of stearic acid in MPMs activates inflammatory signaling, leading to ER stress–mediated apoptosis. M1 macrophages are more prone to stearic acid–induced inflammation and ER stress. These same pathways may be activated in macrophages residing in atherosclerotic plaques and metabolic tissues during conditions of obesity and hyperlipidemia.
An integrated EHR at Northern California Kaiser Permanente

Summary As legacy information systems age, transition to newer systems is inevitable, but at times fraught with challenge. This brief article addresses some of the pitfalls, challenges, and benefits we experienced at Kaiser Permanente as we transitioned several key clinical information systems to Epic Systems for our integrated comprehensive Electronic Health Record (EHR).
Consolidation Differentially Modulates Schema Effects on Memory for Items and Associations

Newly learned information that is congruent with a preexisting schema is often better remembered than information that is incongruent. This schema effect on memory has previously been associated to more efficient encoding and consolidation mechanisms. However, this effect is not always consistently supported in the literature, with differential schema effects reported for different types of memory, different retrieval cues, and the possibility of time-dependent effects related to consolidation processes. To examine these effects more directly, we tested participants on two different types of memory (item recognition and associative memory) for newly encoded visuo-tactile associations at different study-test intervals, thus probing memory retrieval accuracy for schema-congruent and schema-incongruent items and associations at different time points (t = 0, t = 20, and t = 48 hours) after encoding. Results show that the schema effect on visual item recognition only arises after consolidation, while the schema effect on associative memory is already apparent immediately after encoding, persisting, but getting smaller over time. These findings give further insight into different factors influencing the schema effect on memory, and can inform future schema experiments by illustrating the value of considering effects of memory type and consolidation on schema-modulated retrieval.
Virus-like particle vaccines containing F or F and G proteins confer protection against respiratory syncytial virus without pulmonary inflammation in cotton rats

ABSTRACT Vaccine-enhanced disease has been a major obstacle in developing a safe vaccine against respiratory syncytial virus (RSV). This study demonstrates the immunogenicity, efficacy, and safety of virus-like particle (VLP) vaccines containing RSV F (F VLP), G (G VLP), or F and G proteins (FG VLP) in cotton rats. RSV specific antibodies were effectively induced by vaccination of cotton rats with F VLP or FG VLP vaccines. After challenge, lung RSV clearance was observed with RSV F, G, FG VLP, and formalin inactivated RSV (FI-RSV) vaccines. Upon RSV infection, cotton rats with RSV VLP vaccines were protected against airway hyper-responsiveness and weight loss, which are different from FI-RSV vaccination exhibiting vaccine-enhanced disease of airway obstruction, weight loss, and severe histopathology with eosinophilia and mucus production. FG VLP and F VLP vaccines did not cause pulmonary inflammation whereas G VLP induced moderate lung inflammation with eosinophilia and mucus production. In particular, F VLP and FG VLP vaccines were found to be effective in inducing antibody secreting cell responses in bone marrow and lymphoid organs as well as avoiding the induction of T helper type 2 cytokines. These results provide further evidence to develop a safe RSV vaccine based on VLP platforms.
Demonstration of Resistant or Wild-Type Virus in Recurrent Viremia After Ganciclovir-Resistant Cytomegaloviral Infection

Background: Ganciclovir-resistant cytomegalovirus (GR-CMV) is a serious complication of transplantation. Recurrence after primary infection is common. Little is known about CMV drug resistance and latency. Objective: Review CMV genotype during episodes of recurrent CMV viremia after prior documentation of ganciclovir resistance to evaluate if resistance is redemonstrated. Methods: All adult transplant recipients with history of GR-CMV viremia from January 1, 2011, to December 31, 2015, were screened; those with subsequent laboratory evidence of recurrent CMV viremia and genotyping were included. Results: A total of 23 patients had genetically confirmed GR-CMV within the study time period; 14 were excluded due to lack of repeat resistance testing at recurrence and 4 due to of lack of negativity between testing, leaving 5 patients with 7 episodes of recurrent viremia to evaluate. At first recurrent viremia, 4 patients (80%) demonstrated resistant genotype; 1 patient had wild type. Two patients went on to have a second viremia recurrence; both demonstrated wild-type genotype, despite the fact that the first recurrence in these patients was resistant genotype. Conclusion: In transplant recipients with history of GR-CMV, it appears that there is strain variability in latency: repeat genetic testing in patients with recurrent viremia after GR-CMV should be conducted. In the setting of wild-type repopulation, use of GCV should be considered.
Arrhythmia classification from the abductive interpretation of short single-lead ECG records

In this work we propose a new method for the rhythm classification of short single-lead ECG records, using a set of high-level and clinically meaningful features provided by the abductive interpretation of the records. These features include morphological and rhythm-related features that are used to build two classifiers: one that evaluates the record globally, using aggregated values for each feature; and another one that evaluates the record as a sequence, using a Recurrent Neural Network fed with the individual features for each detected heartbeat. The two classifiers are finally combined using the stacking technique, providing an answer by means of four target classes: Normal sinus rhythm (N), Atrial fibrillation (A), Other anomaly (O) and Noisy (∼). The approach has been validated against the 2017 Physionet/CinC Challenge dataset, obtaining a final score of 0.83 and ranking first in the competition.
Analysis of the three United States Food and Drug Administration investigational device exemption cervical arthroplasty trials.

OBJECT There are now 3 randomized, multicenter, US FDA investigational device exemption, industry-sponsored studies comparing arthroplasty with anterior cervical discectomy and fusion (ACDF) for single-level cervical disease with 2 years of follow-up. These 3 studies evaluated the Prestige ST, Bryan, and ProDisc-C artificial discs. The authors analyzed the combined results of these trials. METHODS A total of 1213 patients with symptomatic, single-level cervical disc disease were randomized into 2 treatment arms in the 3 randomized trials. Six hundred twenty-one patients received an artificial cervical disc, and 592 patients were treated with ACDF. In the three trials, 94% of the arthroplasty group and 87% of the ACDF group have completed 2 years of follow-up. The authors analyzed the 2-year data from these 3 trials including previously unpublished source data. Statistical analysis was performed with fixed and random effects models. RESULTS The authors' analysis revealed that segmental sagittal motion was preserved with arthroplasty (preoperatively 7.26° and postoperatively 8.14°) at the 2-year time point. The fusion rate for ACDF at 2 years was 95%. The Neck Disability Index, 36-Item Short Form Health Survey Mental, and Physical Component Summaries, neck pain, and arm pain scores were not statistically different between the groups at the 24-month follow-up. The arthroplasty group demonstrated superior results at 24 months in neurological success (RR 0.595, I(2) = 0%, p = 0.006). The arthroplasty group had a lower rate of secondary surgeries at the 2-year time point (RR 0.44, I(2) = 0%, p = 0.004). At the 2-year time point, the reoperation rate for adjacent-level disease was lower for the arthroplasty group when the authors analyzed the combined data set using a fixed effects model (RR 0.460, I(2) = 2.9%, p = 0.030), but this finding was not significant using a random effects model. Adverse event reporting was too heterogeneous between the 3 trials to combine for analysis. CONCLUSIONS Both anterior cervical discectomy and fusion as well as arthroplasty demonstrate excellent 2-year surgical results for the treatment of 1-level cervical disc disease with radiculopathy. Arthroplasty is associated with a lower rate of secondary surgery and a higher rate of neurological success at 2 years. Arthroplasty may be associated with a lower rate of adjacent-level disease at 2 years, but further follow-up and analysis are needed to confirm this finding.
Worsening Clinical Outcome with Increasing Number of So-Called Off-Label or Unapproved Indications for Use of Drug Eluting Stents

Objective: We explored the impact of increasing number of off-label patient and lesion character-istics on 5-year clinical outcome following implantation of first generation drug eluting stents. Furthermore we tried to assess if stent performance might be improved if the off-label character-istics present were taken into account to guide the stent brand selection. Design: A total of 2888 coronary lesions treated with first generation drug eluting stents were classified for eventual presence of 18 different off-label characteristics and correlated to the 5-year clinical outcome by multiple stepwise Cox regression analysis. Results: The composite of cardiac death, myocardial infarction and target vessel revascularization (major adverse cardiac event, MACE) was 16.7% in cases with zero off-label characteristics and showed a stepwise increased rate up to 32.7% in cases with 5 off-label characteristics. The MACE rate for the sirolimus eluting stent appears to be 10% lower than the paclitaxel stent group and it may be further reduced by 10% - 18% if the off-label characteristics present in each case were taken into account to guide the stent brand selection. Conclusion: With increasing number of concomitantly appearing off-label characteristics there is a stepwise increase in MACE rate. The MACE rate may be reduced if the off-label characteristics were used to guide the stent brand selection.