Miracle-dz/UniFAR-FTUs huggingface dataset:
Regularization and Reparameterization Avoid Vanishing Gradients in Sigmoid-Type Networks

Deep learning requires several design choices, such as the nodes' activation functions and the widths, types, and arrangements of the layers. One consideration when making these choices is the vanishing-gradient problem, which is the phenomenon of algorithms getting stuck at suboptimal points due to small gradients. In this paper, we revisit the vanishing-gradient problem in the context of sigmoid-type activation. We use mathematical arguments to highlight two different sources of the phenomenon, namely large individual parameters and effects across layers, and to illustrate two simple remedies, namely regularization and rescaling. We then demonstrate the effectiveness of the two remedies in practice. In view of the vanishing-gradient problem being a main reason why tanh and other sigmoid-type activation has become much less popular than relu-type activation, our results bring sigmoid-type activation back to the table.
Cross-language Sentence Selection via Data Augmentation and Rationale Training

This paper proposes an approach to cross-language sentence selection in a low-resource setting. It uses data augmentation and negative sampling techniques on noisy parallel sentence data to directly learn a cross-lingual embedding-based query relevance model. Results show that this approach performs as well as or better than multiple state-of-the-art machine translation + monolingual retrieval systems trained on the same parallel data. Moreover, when a rationale training secondary objective is applied to encourage the model to match word alignment hints from a phrase-based statistical machine translation model, consistent improvements are seen across three language pairs (English-Somali, English-Swahili and English-Tagalog) over a variety of state-of-the-art baselines.
Natural inflation after Planck 2018

We calculate high-precision constraints on Natural Inflation relative to current observational constraints from Planck 2018 + BICEP/Keck(BK15) Polarization + BAO on r and n S, including post-inflationary history of the universe. We find that, for conventional post-inflationary dynamics, Natural Inflation with a cosine potential is disfavored at greater than 95% confidence out by current data. If we assume protracted reheating characterized by w̅>1/3, Natural Inflation can be brought into agreement with current observational constraints. However, bringing unmodified Natural Inflation into the 68% confidence region requires values of T re below the scale of electroweak symmetry breaking. The addition of a SHOES prior on the Hubble Constant H 0 only worsens the fit.
Comparison of Denaturing Gradient Gel Electrophoresis and Microarray Technology for Detection of Betaproteobacteria Ammonia-Oxidizing Communities

Abstract Methods linking environmental function and microbial community composition are limited by phylogenetic resolution and throughput time. Denaturing gradient gel electrophoresis (DGGE) allows for resolution of ammonia-oxidizing bacteria strains separated by as little as one base pair (bp) in 16S rRNA gene sequence but is low throughput. In contrast, microarrays are high throughput. We have designed a microarray platform to identify the majority of environmental strains of betaproteobacterial ammonia oxidizers using signature oligonucleotide sequences. Seventy-seven target sequences or single-nucleotide polymorphisms (SNP) were derived from 183 betaproteobacterial ammonia oxidizer 16S rRNA gene sequences representing the genera Nitrosospira and Nitrosomonas of the &bgr; sub-class of Proteobacteria and the cluster groups of strains within each genera identified using DNA homology values. These sequences were obtained from the National Center for Biotechnology Information database. Templates isolated from pure cultures of betaproteobacterial ammonia oxidizers and soil samples incubated with and without dairy slurry were amplified using primers CTO189f and CTO654r. Amplicons were analyzed via DGGE and microarray hybridization. Mixtures of pure culture strains of betaproteobacterial ammonia oxidizers were used to simulate environmental samples containing a known number of sequences and template concentrations. Our DNA oligonucleotide microarray demonstrated highly specific detection of individual betaproteobacterial ammonia oxidizer strains amplified from pure cultures, model communities, and soil samples and provided resolution of community composition comparable to that of DGGE. High-throughput analyses of betaproteobacterial ammonia oxidizer communities will further our knowledge of their ecology and link process level functions to management practices such as dairy slurry applications and specific strains of betaproteobacterial ammonia-oxidizing bacteria.
The Hydrostructure: a Universal Framework for Safe and Complete Algorithms for Genome Assembly

Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of an arc-covering walk of the graph. Since assembly graphs admit many solutions, the goal is to find what is definitely present in all solutions, or what is safe. Most practical assemblers are based on heuristics having at their core unitigs, namely paths whose internal nodes have unit in-degree and out-degree, and which are clearly safe. The long-standing open problem of finding all the safe parts of the solutions was recently solved [RECOMB 2016] yielding a 60% increase in contig length. This safe and complete genome assembly algorithm was followed by other works improving the time bounds, as well as extending the results for different notions of assembly solution. But it remained open whether one can be complete also for models of genome assembly of practical applicability. In this paper we present a universal framework for obtaining safe and complete algorithms which unify the previous results, while also allowing for easy generalisations to assembly problems including many practical aspects. This is based on a novel graph structure, called the hydrostructure of a walk, which highlights the reachability properties of the graph from the perspective of the walk. The hydrostructure allows for simple characterisations of the existing safe walks, and of their new practical versions. Almost all of our characterisations are directly adaptable to optimal verification algorithms, and simple enumeration algorithms. Most of these algorithms are also improved to optimality using an incremental computation procedure and a previous optimal algorithm of a specific model.
Mismatched Decoding Reliability Function at Zero Rate

We derive an upper bound on the reliability function of mismatched decoding for zero-rate codes. The bound is based on a result by Komlós that shows the existence of a subcode with certain symmetry properties. The bound is shown to coincide with the expurgated exponent at rate zero for a broad family of channel-decoding metric pairs.
Uniqueness theorems of meromorphic functions with their differential-difference operators in several complex variables

An example in the article shows that the first derivative of $f(z)=\frac{2}{1-e^{-2z}}$ sharing $0$ CM and $1,\infty$ IM with its shift $\pi i$ cannot obtain they are equal. In this paper, we study the uniqueness of meromorphic function sharing small functions with their shifts concerning its $k-th$ derivatives. We improves the author's result \cite{h} from entire function to meromorphic function, the first derivative to its differential-difference polynomial, and also finite values to small functions. As for $k=0$, we obtain: Let $f(z)$ be a transcendental meromorphic function of $\rho_{2}(f)<1$, let $c$ be a nonzero finite value, and let $a_{1}(z)\not\equiv\infty, a_{2}(z)\not\equiv\infty\in \hat{S}(f)$ be two distinct small functions of $f(z)$ such that $a(z)$ is a periodic function with period $c$ and $b(z)$ is any small function of $f(z)$. If $f(z)$ and $f(z+c)$ share $a_{1}(z),\infty$ CM, and share $a_{2}(z)$ IM, then either $f(z)\equiv f(z+c)$ or $$e^{p(z)}\equiv \frac{f(z+c)-a_{1}(z+c)}{f(z)-a_{1}(z)}\equiv \frac{a_{2}(z+c)-a_{1}(z+c)}{a_{2}(z)-a_{1}(z)},$$ where $p(z)$ is a non-constant entire function of $\rho(p)<1$ such that $e^{p(z+c)}\equiv e^{p(z)}$.
Field evaluation of specificity and sensitivity of a standard SARS-CoV-2 antigen rapid diagnostic test: A prospective study at a teaching hospital in Northern Ghana

Background: The testing capacity for SARS-CoV-2 in Africa is rather limited. Antigen-detection rapid diagnostic tests (Ag-RDTs) are a cheap and rapid alternative to reverse transcriptase-polymerase chain reaction (RT-PCR) tests, but there is little data about their performance under real life conditions in tropical countries. Objective: To evaluate the performance of a standard Ag-RDT in a population of a major hospital in northern Ghana. Methods: Prospective, cross-sectional, blinded verification of the performance of the SD Biosensor Standard Q SARS-CoV-2 Ag-RDT under real life conditions in 135 symptomatic patients and 58 contacts of RT-PCR positives at Tamale Teaching Hospital in February 2021. Nasopharyngeal samples were taken under standard conditions and tested against RT-PCR in the hospital laboratory. Results: 193 participants (median age 35 years, 109 male) were included into the study for which both RT-PCR test and Ag-RDT results were available. A total of 42 (22%) were RT-PCR-positive. Of the 42 RT-PCR-positives, 27 were Ag-RDT positive, resulting in a sensitivity of 64% (95% CI 49-79). Sensitivity among symptomatic patients was 58% (95% CI 38-78). 123 were identified Ag-RDT negatives of the 151 RT-PCR negatives, resulting in a specificity of 81% (95% CI 75-87). Conclusions: SARS-CoV-2 Ag-RDTs appear to have a rather low sensitivity and particularly a low specificity under real life conditions in Africa. The role of existing Ag-RDTs in countries with high-temperature climates and limited resources still needs more data and discussion.
Transvaginal ultrasound for diagnosis of deep endometriosis involving uterosacral ligaments, torus uterinus and posterior vaginal fornix: prospective study

To evaluate the accuracy of transvaginal ultrasound (TVS) in diagnosing deep endometriosis (DE) involving the uterosacral ligaments (USLs), torus uterinus (TU) or posterior vaginal fornix (PVF) in women with suspected endometriosis scheduled for laparoscopic surgery.
Impact of rotavirus vaccine introduction on rotavirus hospitalizations among children under 5 years of age - World Health Organization African Region, 2008-2018.

BACKGROUND Rotavirus is the leading cause of acute gastroenteritis (AGE) among children worldwide. Prior to rotavirus vaccine introduction, over one third of AGE hospitalizations in Africa were due to rotavirus. We describe the impact of rotavirus vaccines using data from the African Rotavirus Surveillance Network (ARSN). METHODS For descriptive analysis, we included all sites reporting to ARSN for any length of time between 2008-2018. For vaccine impact analysis, continuous surveillance throughout the year was required to minimize potential bias due to enrollment of partial seasons and sites had to report a minimum of 100 AGE cases per year. We report the proportion of rotavirus AGE cases by year relative to vaccine introduction, and the relative reduction in the proportion of rotavirus AGE cases reported following vaccine introduction. RESULTS From 2008-2018, 97,366 prospectively enrolled hospitalized children <5 years of age met the case definition for AGE, and 34.1% tested positive for rotavirus. Among countries that had introduced rotavirus vaccine, the proportion of hospitalized AGE cases positive for rotavirus declined from 39.2% in the pre-vaccine period to 25.3% in the post-vaccine period, a 35.5% (95% CI: 33.7-37.3) decline. No declines were observed among countries that had not introduced the vaccine over the 11-year period. CONCLUSION Rotavirus vaccine introduction led to large and consistent declines in the proportion of hospitalized AGE cases that are positive for rotavirus. To maximize the public health benefit of these vaccines, efforts to introduce rotavirus vaccines to the remaining countries in the region and improve coverage should continue.
Pediatric Staphylococcus aureus bacteremia: clinical spectrum and predictors of poor outcome.

BACKGROUND Staphylococcus aureus is a common cause of bacteremia, yet the epidemiology, and predictors of poor outcome remain inadequately defined in childhood. METHODS ISAIAH is a prospective, cross-sectional study of S. aureus bacteremia (SAB), in children hospitalized in Australia and New Zealand, over 24-months (2017-2018). RESULTS Overall, 552 SABs were identified, (incidence 4.4/100,000/yr [95% confidence interval (CI) 2.2-8.8]), with methicillin-susceptible (84%), community onset (78%) infection predominating. Indigenous children (8.1/100,000/yr [CI 4.8-14.4]), those from lower-socioeconomic areas (5.5/100,000/yr [CI 2.8-10.2]) and neonates (6.6/100,000/yr (CI 3.4-11.7) were over-represented. Although 90-day mortality was infrequent, one-third experienced the composite of: length of stay >30 days (26%), ICU admission (20%), relapse (4%), or death (3%). Predictors of mortality included prematurity (aOR 16.8 [CI 1.6-296.9]), multifocal infection (aOR 22.6 [CI 1.4-498.5]), necrotizing pneumonia (aOR 38.9 [CI 1.7 - 1754.6]), multiorgan dysfunction (aOR 26.5 [CI 4.1-268.8]) and empiric-vancomycin (aOR 15.7 [CI 1.6-434.4]); whilst Infectious Diseases (ID) consultation (aOR 0.07 [CI 0.004-0.9]) was protective. Neither MRSA nor vancomycin trough-targets impacted survival; however, empiric-vancomycin was associated with significant nephrotoxicity (OR 3.1 [CI 1.3-8.1]). CONCLUSIONS High SAB incidence was demonstrated, with at-risk populations identified for future prioritized care. For the first time in a pediatric setting, necrotizing pneumonia and multifocal infection were predictors of mortality, whilst ID consultation was protective. The need to re-evaluate pediatric vancomycin trough-targets and limit unnecessary empiric-vancomycin exposure, to reduce poor outcomes and nephrotoxicity is highlighted. One in three children experienced considerable SAB morbidity, therefore pediatric inclusion in future SAB comparator trials is paramount to improve outcomes.
Printing ionic polymer metal composite actuators by fused deposition modeling technology

ABSTRACT In this work, we printed a Nafion precursor membrane by fused deposition modeling (FDM) rapid prototyping technology and further fabricated IPMCs by electroless plating. The ion-exchange capacity of the Nafion membrane was tested, and the morphology of IPMCs was observed. The electro-mechanical properties of IPMCs under AC voltage inputs were studied, and grasping experiments were performed. The results show that the Nafion membrane after hydrolysis has a good ion-exchange ability and water-holding capacity. SEM observed that the thickness of the IPMC’s electrode layer was about 400 nm, and the platinum layer was tightly combined with the substrate membrane. When using a square wave input of 3.5 V and 0.1 Hz, the maximum current of IPMCs reached 0.30 A, and the displacement and blocking force were 7.57 mm and 10.5 mN, respectively. The new fabrication process ensures the good driving performance of the printed IPMC. And two pieces of IPMCs can capture the irregular objects successfully, indicating the feasibility of printing IPMCs by FDM technology. This paper provides a new and simple method for the fabrication of three-dimensional IPMCs, which can be further applied in flexible grippers and soft robotics. GRAPHICAL ABSTRACT
Highly sensitive scent-detection of COVID-19 patients in vivo by trained dogs

Timely and accurate diagnostics are essential to fight the COVID-19 pandemic, but no test satisfies both conditions. Dogs can scent-identify the unique odors of the volatile organic compounds generated during infection by interrogating specimens or, ideally, the body of a patient. After training 6 dogs to detect SARS-CoV-2 in human respiratory secretions (in vitro scent-detection), we retrained 5 of them to diagnose the infection by scenting the patient directly (in vivo scent-detection). Then, efficacy trials were designed to compare the diagnostic performance of the dogs against that of the rRT-PCR in 848 human subjects: 269 hospitalized patients (COVID-19 prevalence 30.1%), 259 hospital staff (prevalence 2.7%), and 320 government employees (prevalence 1.25%). The limit of detection in vitro was lower than 10-12 copies ssRNA/mL. In vivo, all dogs detected 92 COVID-19 patients present among the 848 study subjects. Detection was immediate, and independent of prevalence, time post-exposure, or presence of symptoms, with 95.2% accuracy and high sensitivity (95.9%; 95% C.I. 93.6-97.4), specificity (95.1%; 94.4-95.8), positive predictive value (69.7%; 65.9-73.2), and negative predictive value (99.5%; 99.2-99.7). To determine real-life performance, we waited 75 days to carry out an effectiveness assay among the riders of the Metro System of Medellin, deploying the human-canine teams without previous training or announcement. Three dogs (one of each breed) scent-interrogated 550 citizens who volunteered for simultaneous canine and rRT-PCR testing. Negative predictive value remained at 99.0% (95% C.I. 98.3-99.4), but positive predictive value dropped to 28.2% (95% C.I. 21.1-36.7). Canine scent-detection in vivo is a highly accurate screening test for COVID-19, and it detects more than 99% of infected individuals independently of the key variables. However, real-life conditions increased substantially the number of false positives, indicating the necessity of training a threshold for the limit of detection to discriminate environmental odoriferous contamination from infection.
Early epidemiological signatures of novel SARS-CoV-2 variants: establishment of B.1.617.2 in England

The rapid emergence of SARS-CoV-2 mutants with new phenotypic properties is a critical challenge to the control of the ongoing pandemic. B.1. 1.7 was monitored in the UK through routine testing and S-gene target failures (SGTF), comprising over 90% of cases by March 2021. Now, the reverse is occurring: SGTF cases are being replaced by an S-gene positive variant, which we associate with B.1. 617.2. Evidence from the characteristics of S-gene positive cases demonstrates that, following importation, B.1. 617.2 is transmitted locally, growing at a rate higher than B.1. 1.7 and a doubling time between 5-14 days. S-gene positive cases should be prioritised for sequencing and aggressive control in any countries in which this variant is newly detected.
Type 2 Diabetes and Risk of Early-Onset Colorectal Cancer

Objective: Early-onset colorectal cancer (CRC) is increasing in many developed countries. Type 2 diabetes mellitus has increased substantially in younger adults; however, its role in early-onset CRC remains unidentified. Design: We conducted a claims-based nested case-control study using IBM MarketScan Commercial Database (2006-2015). Incident early-onset CRC diagnosed at ages 18-49 were identified by ICD-9-CM diagnosis code, and the first coded diagnostic pathology date was assigned as the index date. Controls were frequency matched with cases. Type 2 diabetes, stratified by severity, was identified through ICD-9-CM using the Klabunde algorithm. Multivariate logistic regressions were used to estimate odds ratios (ORs) and 95% confidence intervals (Cls). Results: A total of 6001 early-onset CRC and 52104 controls were included. Type 2 diabetes was associated with an increased risk of early-onset CRC (5.0% in cases vs. 3.7% in controls; OR 1.24; 95% CI 1.09 to 1.41). The positive association was more pronounced for uncontrolled (OR 1.37; 95% CI 1.12 to 1.67) or complicated (OR 1.59; 95% CI 1.08-2.35) type 2 diabetes compared to controlled diabetes (OR 1.13; 95% CI 0.94 to 1.36). The positive association was driven by proximal (OR 1.35; 95% CI 1.03 to 1.77) and distal (OR 1.67; 95% CI 1.30 to 2.15) colon cancer but not rectal cancer. Conclusions: Individuals with type 2 diabetes have a higher risk of early-onset CRC, with stronger associations for uncontrolled/complicated diabetes. The rising prevalence of type 2 diabetes among younger adults in the US may partially contribute to the increasing incidence of early-onset CRC.
Carbon and nitrogen metabolism in rice cultivars affected by salt-alkaline stress

Abstract. Salt-alkaline stress generally leads to soil compaction and fertility decline. It also restricts rice growth and nutrient acquisition, so reduces rice yield. However, little is known about the effect of salt-alkaline stress on the carbon and nitrogen metabolism of rice. In this study, two relatively salt-alkaline tolerant (Changbai 9 and Dongdao 12) and sensitive (Jinongda 138 and Tongyu 315) rice cultivars were grown in a field experiment conducted with two soil types including black soil and salt-alkaline soil to evaluate the characteristics of yield, carbon and nitrogen metabolism in rice. Results showed that yield and nitrogen use efficiency (NUE) in rice greatly decreased under salt-alkaline stress. Changbai 9 (CB9) and Dongdao 12 (DD12) showed higher NUE than Jinongda 138 (JND138) and Tongyu 315 (TY315) under the salt-alkaline stress. Additionally, carbon and nitrogen metabolism enzyme activity and compound content were significantly affected by salt-alkali stress; different performances were observed between cultivars under salt-alkaline stress. In conclusion, our results indicate that salt-alkaline tolerant rice cultivars may have more stable carbon and nitrogen metabolism than sensitive genotypes under salt-alkaline conditions.
Postpartum mental illness during the COVID-19 pandemic: a population-based, repeated cross-sectional study

BACKGROUND: It is unclear whether the clinical burden of postpartum mental illness has increased during the COVID-19 pandemic. We sought to compare physician visit rates for postpartum mental illness in Ontario, Canada, during the pandemic with rates expected based on prepandemic patterns. METHODS: In this population-based, repeated cross-sectional study using linked health administrative databases in Ontario, Canada, we used negative binomial regression to model expected visit rates per 1000 postpartum people for March–November 2020 based on prepandemic data (January 2016–February 2020). We compared observed visit rates to expected visit rates for each month of the pandemic period, generating absolute rate differences, incidence rate ratios (IRRs) and their 95% confidence intervals (CIs). The primary outcome was a visit to a primary care physician or a psychiatrist for any mental disorder. We stratified analyses by maternal sociodemographic characteristics. RESULTS: In March 2020, the visit rate was 43.5/1000, with a rate difference of 3.11/1000 (95% CI 1.25–4.89) and an IRR of 1.08 (95% CI 1.03–1.13) compared with the expected rate. In April, the rate difference (10.9/1000, 95% CI 9.14–12.6) and IRR (1.30, 95% CI 1.24–1.36) were higher; this level was generally sustained through November 2020. From April–November, we observed elevated visit rates across provider types and for diagnoses of anxiety, depressive and alcohol or substance use disorders. Observed increases from expected visit rates were greater for people 0–90 days postpartum compared with 91–365 days postpartum; increases were small among people living in low-income neighbourhoods. Public health units in the northern areas of the province did not see sustained elevations in visit rates after July; southern health units had elevated rates through to November. INTERPRETATION: Increased visits for mental health conditions among postpartum people during the first 9 months of the COVID-19 pandemic suggest an increased need for effective and accessible mental health care for this population as the pandemic progresses.