Miracle-dz/UniFAR-FTUs huggingface dataset:
Non-parallel changes in songbird migration timing are not explained by changes in stopover duration

Shifts in the timing of animal migration are widespread and well-documented; however, the mechanism underlying these changes is largely unknown. In this study, we test the hypothesis that systematic changes in stopover duration—the time that individuals spend resting and refueling at a site—are driving shifts in songbird migration timing. Specifically, we predicted that increases in stopover duration at our study site could generate increases in passage duration—the number of days that a study site is occupied by a particular species—by changing the temporal breadth of observations and vise versa. We analyzed an uninterrupted 46-year bird banding dataset from Massachusetts, USA using quantile regression, which allowed us to detect changes in early-and late-arriving birds, as well as changes in passage duration. We found that median spring migration had advanced by 1.04 days per decade; that these advances had strengthened over the last 13 years; and that early-and late-arriving birds were advancing in parallel, leading to negligible changes in the duration of spring passage at our site (+0.07 days per decade). In contrast, changes in fall migration were less consistent. Across species, we found that median fall migration had delayed by 0.80 days per decade, and that changes were stronger in late-arriving birds, leading to an average increase in passage duration of 0.45 days per decade. Trends in stopover duration, however, were weak and negative and, as a result, could not explain any changes in passage duration. We discuss, and provide some evidence, that changes in population age-structure, cryptic geographic variation, or shifts in resource availability are consistent with increases in fall passage duration. Moreover, we demonstrate the importance of evaluating changes across the entire phenological distribution, rather than just the mean, and stress this as an important consideration for future studies.
Clinical significance of different periampullary diverticulum classifications for endoscopic retrograde cholangiopancreatography cannulation

BACKGROUND Different types of periampullary diverticulum (PAD) may differentially affect the success of endoscopic retrograde cholangiopancreatography (ERCP) cannulation, but the clinical significance of the two current PAD classifications for cannulation is limited. AIM To verify the clinical value of our newly proposed PAD classification. METHODS A new PAD classification (Li-Tanaka classification) was proposed at our center. All PAD patients with native papillae who underwent ERCP from January 2012 to December 2017 were classified according to three classification systems, and the effects of various types of PAD on ERCP cannulation were compared. RESULTS A total of 3564 patients with native papillae were enrolled, including 967 (27.13%) PAD patients and 2597 (72.87%) non-PAD patients. In the Li-Tanaka classification, type I PAD patients exhibited the highest difficult cannulation rate (23.1%, P = 0.01), and type II and IV patients had the highest cannulation success rates (99.4% in type II and 99.3% in type IV, P < 0.001). In a multivariable-adjusted logistic model, the overall successful cannulation rate in PAD patients was higher than that in non-PAD patients [odds ratio (OR) = 1.87, 95% confidence interval (CI): 1.04-3037, P = 0.037]. In addition, compared to the non-PAD group, the difficulty of cannulation in the type I PAD group according to the Li-Tanaka classification was greater (OR = 2.04, 95%CI: 1.13-3.68, P = 0.004), and the successful cannulation rate was lower (OR = 0.27, 95%CI: 0.11-0.66, P < 0.001), while it was higher in the type II PAD group (OR = 4.44, 95%CI: 1.61-12.29, P < 0.01). CONCLUSION Among the three PAD classifications, the Li-Tanaka classification has an obvious clinical advantage for ERCP cannulation, and it is helpful for evaluating potentially difficult and successful cannulation cases among different types of PAD patients.
The association of EGF rs2237051 variant, serum EGF levels and generalized aggressive periodontitis: a preliminary study

Background Epidermal growth factor (EGF) is a pro-inflammatory small peptide that stimulates cell growth, proliferation and differentiation through binding to its receptor. EGF rs2237051 and serum EGF levels have been demonstrated to be related with a variety of diseases, including several tumors and inflammatory diseases. Therefore, this study aims to investigate the association of the EGF rs2237051 variant and serum EGF levels in Chinese patients with generalized aggressive periodontitis (GAgP). Material and Methods A case-control study was conducted among 216 patients with GAgP and 138 healthy controls. The clinical parameters of plaque index, probing depth, attachment loss and bleeding index were recorded. The EGF rs2237051 polymorphism was genotyped using time-of-flight mass spectrometry, and serum EGF levels were determined. Logistic and linear regression models were used to investigate the association between the genotypes of EGF rs2237051, serum EGF levels and GAgP risk. Results The AA genotype of EGF rs2237051 showed higher risk for GAgP than the combined genotypes GG and AG (adjusted OR = 1.65, 95% CI [1.06–2.57]). Increased serum EGF levels were associated with GAgP (adjusted OR = 1.18, 95% CI [1.14–1.22]). Moreover, the serum EGF level for the AA genotype was significantly higher than that for the AG/GG genotypes in patients with GAgP (adjusted β = 4.70, 95% CI [2.09–7.31]). Conclusion We demonstrated that EGF rs2237051 variant and the increased level of serum EGF were associated with the risk of GAgP, the serum EGF was up-regulated in patients with GAgP. It was indicated that serum EGF might be a biomarker of GAgP and EGF rs2237051 may be related to the genetic background of GAgP.
Optimization of cassava fermentation for fufu production: effects of single starter cultures

Single starter cultures were used to ferment cassava for fufu production in a process which involved steeping seeded cassava tubers in water for 96 h. The cultures used include Bacillus subtilis, Klebsiella sp. , Lactobacillus plantarum and Candida krusei. Lactobacillus plantarum exhibited the highest acid producing ability, decreasing the pH of the cassava tubers from 6.0 to 3.62, with a corresponding increase in total titratable acidity (TTA) from 0.072% to 0.250% during the 96 h fermentation period. The effected changes in pH and TTA by other organisms ranged respectively from 5.03 and 0.125% for Klebsiella sp. , 5.07 and 0.126% for C. krusei, to 5.20 and 0.128% for B. subtilis within the period. Lactobacillus plantarum grew better than other cultures singly inoculated. While all the cultures were found to contribute to the characteristic odour of fufu, C. krusei effected the highest perceived characteristic odour. Also, the cultures variably caused softening of the tubers, with B. subtilis showing the highest softening capability.
Molecular interactions between the importin α/β heterodimer and proteins involved in vertebrate nuclear protein import

We have used in vitro binding assays to examine specific interactions between a number of cytoplasmic and nuclear pore proteins involved in nuclear protein import in vertebrates. We demonstrate that nuclear transport factor 2 (NTF2), nucleoporin p62 and the Ras-like GTPase Ran bind to the importin heterodimer via its β subunit. The binding behaviour of p62 truncation mutants indicated that importin-β interacts primarily with the α-helical coiled-coil rod domain of nucleoporin p62 and not with the N-terminal domain that contains a number of degenerate repeats based on the xFxFG sequence motif. The binding of Ran to importin-β was sensitive to its nucleotide state, with RanGTP binding strongly, whereas RanGDP binding could not be detected using our assay conditions. RanGTP, but not RanGDP, was able to displace p62 bound to the importin α/β complex, suggesting that the binding sites for p62 and RanGTP on importin-β overlap. Moreover, RanGTP, but not RanGDP, weakened the interaction between importin-α and importin-β in a concentration-dependent manner. NTF2 bound to the importin heterodimer but did not displace p62, suggesting that the NTF2 and p62 binding sites on importin-β do not overlap. The set of interactions we observed was not altered by the binding of NLS-containing substrates such as transcription factor IIIA to the importin heterodimer. Our results are consistent with models for nuclear protein import in which Ran nucleotide exchange modulates the binding of the importin-substrate complexes during translocation through nuclear pore complexes.
Using real-world contact networks to quantify theeffectiveness of digital contact tracing and isolation strategies for Covid-19 pandemic

Contact tracing, both manual and potentially with digital apps, is considered a key ingredient in the control of infectious disease outbreaks, and in the strategies making it possible to alleviate the lock-down and to return to a quasi-normal functioning of society in the COVID-19 crisis. However, the current leading modeling framework for evaluating contact tracing is highly stylized, lacking important features and heterogeneities present in real-world contact patterns that are relevant for epidemic dynamics. Here, we fill this gap by considering a modeling framework extensively informed by real-world, high-resolution contact data to analyze the impact of digital (app-based) containment strategies for the COVID-19 pandemic. More specifically, we investigate how well contact tracing apps, coupled with the quarantine of identified contacts, can mitigate a spread in realistic scenarios such as a university campus, a workplace, or a high school. We find that restrictive policies are more effective in confining the epidemics but come at the cost of quarantining a large part of the population with a consequent social cost. It is possible to design less limiting policies, considering at risk only contacts with longer exposure and at shorter distance, in order to avoid this effect. Our results also show that isolation and tracing alone are unlikely to be sufficient to keep an outbreak under control, and additional measures need to be implemented simultaneously. Moreover, we confirm that a high level of app adoption is crucial to make digital contact tracing an effective measure. Finally, given the currently implemented infectiousness, we find that strategies focusing on long exposure times, even for weak links, perform better than approaches that emphasize close-range contacts for shorter time-periods. Our results have implications for the app-based contact tracing efforts currently being implemented across several countries worldwide.
Investigation of subsequent and co-infections associated with SARS-CoV-2 (COVID-19) in hospitalized patients

Background SARS-CoV-2 has drastically affected healthcare globally and causes COVID-19, a disease that is associated with substantial morbidity and mortality. We aim to describe rates and pathogens involved in co-infection or subsequent infections and their impact on clinical outcomes among hospitalized patients with COVID-19. Methods Incidence of and pathogens associated with co-infections, or subsequent infections, were analyzed in a multicenter observational cohort. Clinical outcomes were compared between patients with a bacterial respiratory co-infection (BRC) and those without. A multivariable Cox regression analysis was performed evaluating survival. Results A total of 289 patients were included, 48 (16.6%) had any co-infection and 25 (8.7%) had a BRC. No significant differences in comorbidities were observed between patients with co-infection and those without. Compared to those without, patients with a BRC had significantly higher white blood cell counts, lactate dehydrogenase, C-reactive protein, procalcitonin and interleukin-6 levels. ICU admission (84.0 vs 31.8%), mechanical ventilation (72.0 vs 23.9%) and in-hospital mortality (45.0 vs 9.8%) were more common in patients with BRC compared to those without a co-infection. In Cox proportional hazards regression, following adjustment for age, ICU admission, mechanical ventilation, corticosteroid administration, and pre-existing comorbidities, patients with BRC had an increased risk for in-hospital mortality (adjusted HR, 3.37; 95% CI, 1.39 to 8.16; P = 0.007). Subsequent infections were uncommon, with 21 infections occurring in 16 (5.5%) patients. Conclusions Co-infections are uncommon among hospitalized patients with COVID-19, however, when BRC occurs it is associated with worse clinical outcomes including higher mortality.
Soil exploration and resource acquisition by plant roots: an architectural and modelling point of view

We provide a brief overview on soil exploration and resource extraction by roots during the course of plant development. First, we examine how roots explore the soil volume in relation with the heterogeneity of soil conditions. We then consider resource acquisition by roots and root systems, taking into account the root system’s heterogeneous functioning and its variable degree of plasticity. In extensive, complex and dynamic systems such as root systems, processes of soil exploration and resource acquisition can be analysed through the unifying point of view of root system architecture. We exemplify how a modelling approach based on the concepts of functional architecture has potential to provide sharper insight into the soil exploration/utilization processes.
A serological assay to detect SARS-CoV-2 antibodies in at-home collected finger-prick dried blood spots

Accurate surveillance of coronavirus disease 2019 (COVID-19) incidence requires large-scale testing of the population. Current testing methods require in-person collection of biospecimens by a healthcare worker, limiting access of individuals who do not have access to testing facilities while placing both the patient and healthcare worker at risk of exposure to infection. We report the development and validation of a at-home finger-prick dried blood spot collection kit and an analysis method. We demonstrated 100% sensitivity and specificity using at-home collected specimens across the US. Such methods may facilitate the conduct of unbiased serosurveys within hard to reach populations and help reduce the sample collection burden of serological testing on both health care systems and individuals alike.
Mutational analysis of the class I β‐tubulin gene in human breast cancer

Non‐small cell lung cancers have a high incidence of somatic mutations of the β‐tubulin (class I) gene, suggesting involvement in the acquisition of resistance to taxanes, which exert their effects through binding to β‐tubulin. Since taxanes are often used in the treatment of breast cancer, we carried out a mutational analysis of the class I β‐tubulin (GenBank accession AF070600) gene in breast cancer. We paid special attention to the primer design so as not to amplify the pseudogenes. We identified 1 somatic mutation, codon 306 [Arg (CGC) to Cys (TGC)], and 2 genetic polymorphisms, codon 217 [Leu (CTG) to Leu (CTA)] and (C to T) at 57 bases downstream from exon 4. Our results suggest that acquisition of resistance to taxanes is unlikely to be explained by somatic mutations of the class I β‐tubulin gene in most breast cancers. In addition, the overestimation of the incidence of somatic mutations of the class I β‐tubulin gene due to the pseudogenes is discussed. © 2002 Wiley‐Liss, Inc.
Rotavirus cell entry

The initial steps of viral infection involve the specific attachment of the viral particle to receptor(s) on the cell surface, followed by internalization of the virus into the cell and the subsequent uncoating of the virion to release the transcriptionally active particle. These events are essential for the successful initiation of a virus replication cycle and play an important role in tissue tropism and pathogenesis of viruses. Rotaviruses, the leading cause of severe childhood diarrhea, principally infect the mature enterocytes of the villi of the small intestine. Several cell-surface molecules have been implicated in the early interactions of rotavirus with its host cell, including sialic acid, various integrins, heat shock protein 70 and gangliosides. However, the mechanism by which rotaviruses enter cells is controversial, and both direct membrane penetration and endocytosis have been proposed. Recently developed molecular and biochemical tools have allowed the characterization of new endocytic pat.
Slash burning - its implications for 20-year height growth of eucalypt regeneration in Tasmania.

Summary Height data to 20 years are presented for a study previously reported by Lockett and Candy (1984) on the effects of slash-burning on growth rates of eucalypt regeneration established following clear-falling. The study covers a range of forest types on five sites throughout Tasmania with rainfalls ranging from 800mm to 1800mm. On the two driest sites, the initial conclusion that slash burning had no significant impact on height growth has been confirmed by subsequent measurements. On the three wetter sites, there was a consistent trend which suggests that slash-burning caused growth rates to be more than doubled in the third year post-burn. This effect progressively declined and finally disappeared between years ten and fifteen. The net result of burning would be a shortening of the rotation by a maximum of five years, or less where natural regeneration is already established, or can be established earlier in the absence of a slash-burn. Operationally, the decision whether to burn or not will invol.
The total number of glomeruli in the normal human kidney

Previous estimations of the total number of glomeruli in the kidney have been based on three methods : first, an estimation of the number of pyramids, lobes, lobules, tubules, or any combination of these and transfer of this value to a glomerular count, on the assumption that each arched collecting tubule is connected to one glomerulus; secondly, a count of the glomeruli in serial sections with the employment of some method to avoid duplication ; and, thirdly, a direct count of macerated kidney tissue with or without a preliminary injection to render the glomeruli more clearly visible. It is apparent that the first method is an estimate at the best. It has been employed by Huschke(l), Sappey(2), Peter (3 ) , and Traut (4). The avoidance of duplication in the serial-section method may be accomplished by the employment of an average factor, based on the mean number of sections through which any one glomerulus may appear, or by the use of the carbonpaper method. Miller and Carlton(5), Boycott(G), Brodie (7), and O'Connor and Conway(8) used the average factor on counts of serial sections, while Kittelson(9) and Arataki (10, 11, 12) placed the serial-section method 011 an accurate basis by the use of a carbon-paper method, the details of which may be secured from the original papers.
Trilobite larvae and larval ecology

Silicified trilobite faunas yield a well preserved and abundant record of early development in many taxa. Although their morphologies are well known, protaspid larvae are poorly understood in terms of trilobite life history and developmental biology. Two distinct morphologic types are recognized among the great diversity of protaspides studied; these are termed adult‐like and nonadult‐tike according to gross similarity to later developmental stages. Transitions between nonadult‐like and adult‐like morphologies are abrupt, occurring between successsive instars, and, thereby, constitute metamorphoses. By analogy with developmental patterns among modern marine arthropod taxa, metamorphoses during early trilobite ontogeny correspond to radical modifications in life mode and ecology. Adult‐like trilobite protaspides possess a dorso‐ventrally flattened tergum which displays a coarsely featured prosopon and surface‐parallel spines; these are interpreted as benthic larvae. In contrast, nonadult‐like protaspid lar.
Automatic Core Specialization for AVX-512 Applications

Advanced Vector Extension (AVX) instructions operate on wide SIMD vectors. Due to the resulting high power consumption, recent Intel processors reduce their frequency when executing complex AVX2 and AVX-512 instructions. Following non-AVX code is slowed down by this frequency reduction in two situations: When it executes on the sibling hyperthread of the same core in parallel or - as restoring the non-AVX frequency is delayed - when it directly follows the AVX2/AVX-512 code. As a result, heterogeneous workloads consisting of AVX-512 and non-AVX code are frequently slowed down by 10% on average. In this work, we describe a method to mitigate the frequency reduction slowdown for workloads involving AVX-512 instructions in both situations. Our approach employs core specialization and partitions the CPU cores into AVX-512 cores and non-AVX-512 cores, and only the former execute AVX-512 instructions so that the impact of potential frequency reductions is limited to those cores. To migrate threads to AVX-512 cores, we configure the non-AVX-512 cores to raise an exception when executing AVX-512 instructions. We use a heuristic to determine when to migrate threads back to non-AVX-512 cores. Our approach is able to reduce the frequency reduction overhead by 70% for an assortment of common benchmarks.
Exigência de energia metabolizável de codornas de corte no período de 1 a 14 dias de idade

This experiment was carried out to estimate the metabolizable energy (ME) requirements for meat quails from 1 to 14 days of age. A total of 1,140 1-day old meat quails were distributed in a completely randomized design, with five treatments (2,750; 2,850; 2,950; 3,050 and 3,150 kcal of ME/kg), six replications and 38 quails per experimental unit. There was linear reduction of energy levels in body weight, feed intake and weight gain of birds. The feed conversion ratio showed a quadratic effect, with the best estimate obtained with 2,997 kcal of ME/kg. Whereas crude protein content did not differ, water content decreased and ether extract increased linearly with the increasing levels of ME. The ME levels showed a quadratic effect on daily protein accretion rate and daily protein accretion efficiency. The ME requirements for meat quail in the initial growing stage is 2,997 kcal/kg, corresponding to a metabolizable energy/crude protein relation of 108.9.