bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular and MALDI‐ToF MS differentiation and antifungal susceptibility of prevalent clinical Fusarium species in China
Authors: Song Yinggai , Liu Xiao , Yang Zhining , Meng Xingye , Xue Ruoning , Yu Jin , Al‐Hatmi Abdullah M.S. , de Hoog G. Sybren , Li Ruoyu
Published: June 2021

Background

Fusarium species are emerging causative agents of superficial and disseminated human infections. Early diagnosis and treatment contribute to better prognosis of severe infection.

Objectives

To detect the effectiveness of matrix‐assisted laser desorption ionisation time of flight mass spectrometry (MALDI‐ToF MS) for Fusarium identification, and evaluate the susceptibility profiles to clinical available antifungals.

Methods

All 203 clinical Fusarium isolates and 25 environmental isolates were identified by using translation elongation factor 1‐alpha (TEF1) and RNA polymerase subunit II (RPB2) sequencing and MALDI‐ToF MS. Antifungal susceptibility testing was determined by a microdilution method following the CLSI approved standard M38‐A3 document.

Results

Correct identification rates at the species and genus levels were 89.04% (203/228) and 95.18% (217/228), respectively, using Bruker Filamentous Fungi Library 1.0 combined with the novel database. Seven species complexes with 19 Fusarium species were identified, including F. solani (59.21%, n = 135), F. verticillioides (17.54%, n = 40), F. proliferatum (6.58%, n = 15) and F. oxysporum (4.39%, n = 10). Four uncommon species complexes (F. incarnatum‐equiseti SC, F. dimerum SC, F. redolens SC and F. sporotrichioides SC) were also identified. A high degree of antifungal resistance was observed. Fusarium isolates exhibited lower MICs to luliconazole and terbinafine compared with amphotericin B and voriconazole, which in turn were significantly more active than amorolfine, fluconazole and itraconazole.

Conclusions

MALDI‐ToF MS showed good performance in Fusarium species with an adapted Bruker library and expanded database. Fusarium isolates exhibited lower MICs to luliconazole and terbinafine compared to amphotericin B and voriconazole.
The locoregional adiponectin and its synergistic antitumor effect with HIF‐1α blockade in TSCC
Authors: Guo Xiao‐Hong , Wu Ming‐Yu , Zhao Gang , Wu Feng‐Hua , Xu Yun‐Dan , Yin Ming‐Zhu , Xiang Lei
Published: June 2021

Adiponectin (APN) is a kind of endogenous anti‐tumor adipocytokine, which exerts its function by binding to its receptors (AdipoR1 and AdipoR2). However, hyperadiponectinemia is found in some pathophysiological processes without significant protective effect, which indicates the existence of APN resistance. Here, we aimed to investigate the locoregional expression of APN in tongue squamous cell carcinoma (TSCC) tissues, and to explore the potential regulatory mechanism of APN resistance under hypoxia. Consequently, we found that the protein expression of APN and AdipoR1, but not AdipoR2, was upregulated in the early stage of TSCC and after hypoxic treatment ex vivo and in vitro. Knockdown of HIF‐1α decreased the level of APN and AdipoR1, and simultaneously, HIF‐1α was identified as transcriptor of the APN. Intriguingly, a regenerative feedback of HIF‐1α was unexpectedly detected after application of recombinant globular APN (gAPN), which most likely contributed to the APN resistance. Furthermore, HIF‐1α blockade combined with gAPN has a prominent synergistic antitumor effect, which suggested an effective amelioration in APN resistance. In all, our study revealed the possible mechanism of APN resistance under hypoxia and provides a promising strategy of bi‐target treatment with APN and HIF‐1α for TSCC therapy.
Virological and immunological features of SARS‐COV‐2 infected children with distinct symptomatology
Authors: Cotugno Nicola , Ruggiero Alessandra , Pascucci Giuseppe Rubens , Bonfante Francesco , Petrara Maria Raffaella , Pighi Chiara , Cifaldi Loredana , Zangari Paola , Bernardi Stefania , Cursi Laura , Santilli Veronica , Manno Emma Concetta , Amodio Donato , Linardos Giulia , Piccioni Livia , Barbieri Maria Antonietta , Perrotta Daniela , Campana Andrea , Donà Daniele , Giaquinto Carlo ,   the CACTUS Study Team, Concato Carlo , Brodin Petter , Rossi Paolo , De Rossi Anita , Palma Paolo
Published: June 2021

Background

Although SARS‐CoV‐2 immunizations have started in most countries, children are not currently included in the vaccination programs; thus, it remains crucial to define their anti‐SARS‐CoV‐2 immune response in order to minimize the risk for other epidemic waves. This study sought to provide a description of the virology ad anti‐SARS‐CoV‐2 immunity in children with distinct symptomatology.

Methods

Between March and July 2020, we recruited 15 SARS‐CoV‐2 asymptomatic (AS) and 51 symptomatic (SY) children, stratified according to WHO clinical classification. We measured SARS‐CoV‐2 viral load using ddPCR and qPCR in longitudinally collected nasopharyngeal swab samples. To define anti‐SARS‐CoV‐2 antibodies, we measured neutralization activity and total IgG load (DiaSorin). We also evaluated antigen‐specific B and CD8+T cells, using a labeled S1+S2 protein and ICAM expression, respectively. Plasma protein profiling was performed with Olink.

Results

Virological profiling showed that AS patients had lower viral load at diagnosis (p = .004) and faster virus clearance (p = .0002) compared with SY patients. Anti‐SARS‐CoV‐2 humoral and cellular response did not appear to be associated with the presence of symptoms. AS and SY patients showed similar titers of SARS‐CoV‐2 IgG, levels of neutralizing activity, and frequency of Ag‐specific B and CD8+ T cells, whereas pro‐inflammatory plasma protein profile was found to be associated with symptomatology.

Conclusion

We demonstrated the development of anti‐SARS‐CoV‐2 humoral and cellular response with any regard to symptomatology, suggesting the ability of both SY and AS patients to contribute toward herd immunity. The virological profiling of AS patients suggested that they have lower virus load associated with faster virus clearance.
Potential sex differences in human milk leptin and their association with asthma and wheeze phenotypes: Results of the Ulm Birth Cohorts
Authors: Siziba Linda P. , Brenner Hermann , Amitay Efrat L. , Koenig Wolfgang , Rothenbacher Dietrich , Genuneit Jon
Published: June 2021

Background

The hormone leptin has been suggested to play a role in the respiratory and immune systems. Evidence on sex‐specific concentrations of leptin in human milk and sex‐specific associations with the development of asthma and wheeze has been put forward but is still scarce.

Objective

To investigate whether male and female infants receive different levels of leptin through human milk and whether leptin is implicated in the development of asthma and wheeze in a sex‐dependent manner using data from the two Ulm Birth Cohort studies.

Methods

Leptin data were available from human milk samples collected at 6 weeks (Ulm Birth Cohort Study [UBCS, n = 678; Ulm SPATZ Health Study, n = 587]), and, in SPATZ only, at 6 months (n = 377) and 12 months (n = 66) of lactation. Sex‐specific associations with doctor‐diagnosed asthma and wheeze phenotypes were assessed in crude and adjusted models using logistic regression. Adjustments were made for maternal allergy, exclusive breastfeeding, infant age at the time of milk sampling, and child BMI z‐score.

Results

At 6 weeks, leptin levels (median [min, max], in ng/L) were higher in the milk for girls (197 [0.100, 4120]) than in milk for boys (159 [1.02, 3280], p = .045) in UBCS. No significant sex differences were observed in SPATZ (p = .152). There were no significant associations of leptin with asthma or wheeze in both studies, even in a sex‐dependent manner (p > .05).

Conclusion

It remains unclear whether male and female infants receive different levels of leptin through human milk. However, leptin in human milk may not be associated with history and development of asthma and wheeze in a sex‐specific manner.
HSP70‐16 and VDAC3 jointly inhibit seed germination under cold stress in Arabidopsis
Authors: Ashraf Muhammad , Mao Qionglei , Hong Jun , Shi Lei , Ran Xiaoruo , Liaquat Fiza , Uzair Muhammad , Liang Wanqi , Fernie Alisdair R. , Shi Jianxin
Published: June 2021

Abscisic acid (ABA) transport plays a crucial role in seed germination under unfavourable conditions such as cold stress. Both heat shock protein 70 (HSP70) and voltage‐dependent anion channel (VDAC) protein are involved in cold stress responses in Arabidopsis. However, their roles in seed germination with regard to ABA signaling remain unknown. Here we demonstrated that Arabidopsis HSP70‐16 and VDAC3 jointly suppress seed germination under cold stress conditions. At 4°C, both HSP70‐16 and VDAC3 facilitated the efflux of ABA from the endosperm to the embryo and thus inhibited seed germination. HSP70‐16 interacted with VDAC3 on the plasma membrane and in the nucleus, and the interplay between HSP70‐16 and VDAC3 activated the opening of the VDAC3 ion channel. Our work established a novel function of HSP70‐16 in seed germination under cold stress and a possible association of VDAC3 activity with ABA transportation from endosperm to embryo under cold stress conditions. This study reveals that HSP70‐16 interacts with VDAC3 and facilitates the opening of the VDAC3 ion channel, which influences ABA efflux from endosperm to embryo, thus negatively regulates seed germination under cold stress.
Taking Care of Each Other: How Can We Increase Compliance with Personal Protective Measures During the COVID‐19 Pandemic in Chile?
Authors: Gerber Monica M. , Cuadrado Cristóbal , Figueiredo Ana , Crispi Francisca , Jiménez‐Moya Gloria , Andrade Valentina
Published: June 2021

In the context of the COVID‐19 pandemic, personal protective measures (e.g., social distancing, handwashing, and mask wearing) have been adopted as a cornerstone to limit the spread of the disease. Yet, the effectiveness of these measures depends on people's levels of adherence. In this article, we apply social‐psychological research to the study of compliance with personal protective measures during the COVID‐19 pandemic in Chile. We consider three possible models underlying adherence: (1) sociodemographic and socioeconomic factors, (2) instrumental factors, and (3) normative factors. We draw on data from a longitudinal nonrepresentative panel study (Study 1, n = 32,304) and a cross‐sectional representative survey (Study 2, n = 1,078) to explore the impact of these different factors on personal protective measures compliance. Findings show the strongest support for the role of instrumental and normative factors, in that people who comply with protective measures report to a greater extent that relatives and friends comply too and tend to perceive high risk of COVID‐19. We finish by proposing policy recommendations to promote effective strategies to contain the spread of the virus.
Combined cryopreservation of canine ejaculates collected at a one‐hour interval increases semen doses for artificial insemination without negative effects on post‐thaw sperm characteristics
Authors: Lechner Dominik , Aurich Jörg , Schäfer‐Somi Sabine , Herbel Johannes , Aurich Christine
Published: June 2021

A limiting factor in canine artificial insemination (AI) is the low number of insemination doses obtained per ejaculate. In this study, semen was collected from dogs (n = 28) either once and frozen directly after collection or the same dogs were submitted to a dual semen collection with a 1‐hr interval and the two ejaculates were combined for cryopreservation. We hypothesized that combining two ejaculates increases semen doses per cryopreservation process without negative effects on semen characteristics. Total sperm count was lower in semen from a single semen collection in comparison with the combination of the first and second ejaculate of a dual semen collection (p < .001). The percentage of motile and membrane‐intact spermatozoa determined by computer‐assisted sperm analysis (CASA) in raw semen did not differ between single and combined dual ejaculates and was reduced (p < .001) by cryopreservation to the same extent in single (motility 73.7 ± 1.8%, membrane integrity 65.6 ± 2.2%) and combined dual ejaculates (motility 72.7 ± 2.3%, membrane integrity 64.6 ± 2.5%). The percentage of spermatozoa with morphological defects increased after cryopreservation (p < .001) but was similar in single and combined dual ejaculates. The CASA sperm velocity parameters decreased with cryopreservation (p < .001) but did not differ between single and combined dual ejaculates. The number of insemination doses increased from 2.7 ± 0.4 for single to 4.7 ± 0.8 for combined dual ejaculates (p < .01), based on 100 million motile spermatozoa per frozen‐thawed semen dose. In conclusion, combining two ejaculates collected at short interval for one cryopreservation process increases the number of AI doses without compromising semen quality.
Prediction of cow's fertility based on data recorded by automatic milking system during the periparturient period
Authors: Kliś Piotr , Sawa Anna , Piwczyński Dariusz , Sitkowska Beata , Bogucki Mariusz
Published: June 2021

The results of most studies show the beneficial effect of milking automation on production parameters of dairy cows, but its effect on fertility traits is debatable. Therefore, a study was undertaken to predict cow fertility – services per conception (SC) and calving interval (CI) – based on automatic milking system (AMS) data collected in the periparturient period subdivided into the second and first week before calving, 1–4, 5–7, 8–14, 15–21 and 22–28 days of lactation. SC and CI were predicted using daily indicators such as concentrate intake, number of milkings, cow box time, milking time, milking speed, colostrum and milk yield, composition, temperature and electrical conductivity. The study material was derived from the AMS management system and from the SYMLEK milk recording system. The analysis covered data for 16,329 milkings of 398 Polish Holstein‐Friesian (PHF) cows, which were used in three AMS herds. The collected numerical data were statistically analysed by correlation analysis in parallel with decision tree technique (SAS statistical package). The present study showed that due to the low, mostly non‐significant coefficients of correlation between AMS data collected between 2 weeks before and 4 weeks after calving, it is not possible to predict cow fertility based on single traits. It has been established that the decision tree method may help breeders, already during the postcalving period, to choose the level of factors associated with AMS milking, which will ensure good fertility of cows in a herd. The most favourable number of services per conception is to be expected from cows that were milked <1.6 times per day from 1 to 4 days of lactation and electrical conductivity of their colostrum did not exceed 69 mS during that time. In turn, shortest CI (366 days) will be characteristic of the cows whose average daily colostrum yield did not exceed 20.2 kg and their daily concentrate intake from 8 to 14 days of lactation was at least 5.0 kg.
The impact of trade with pure exporters
Authors: Gao Bo , Tvede Mich
Published: June 2021

We extend the Melitz model to include pure exporters and study how they influence economic performance. We find that the presence of pure exporters lowers the productivity premium of exporters. Moreover, if there is a large portion of pure exporters, then international trade lowers the average productivity, but not welfare. Moreover, we explore how trade liberalization in form of lower entry cost into foreign markets and lower variable export cost influences the distribution of firms between pure exporters, ordinary exporters and non‐exporters.
Pricing Wind Power Futures
Authors: Härdle Wolfgang Karl , López Cabrera Brenda , Melzer Awdesch
Published: June 2021

With increasing wind power (WP) penetration an extensive amount of volatile and weather dependent energy is fed into the German electricity system. To manage the volume risk of windless days and the transfer of revenue risk from wind turbine owners to investors, WP derivatives were introduced. These insurance-like securities allow the hedging of the volume risk of unstable WP production on exchanges such as NASDAQ and EEX. We present a modern and powerful methodology to model weather derivatives, with very skewed underlying assets, incorporating techniques from extreme event modelling to tune seasonal volatility. We compare transformed Gaussian and non-Gaussian CARMA(p, q) models. Our results indicate that the Gaussian CARMA(p, q) model is preferred over the non-Gaussian alternative. Out-of-sample backtesting results show good performance, with respect to benchmarks, employing smooth market price of risk (MPR) estimates based on NASDAQ weekly and monthly German WP futures prices. A seasonal MPR of a smile shape is observed, with slightly positive values in times of high volatility, for example, winter months, and negative values, in times of low volatility and production, for example, in summer months. We conclude that producers pay premiums to insure stable revenue steams, while investors pay premiums when weather risk is high.
Fixed costs, markups and concentration in Eswatini (Swaziland): A firm‐level analysis of panel data
Authors: Mhlanga Samuel Vika , Rankin Neil Andrew
Published: June 2021

This paper documents the evolution of markups and concentration, detects causality between firm churning and markups/concentration, and determines the impact of fixed costs on markups. It relies on production data of Eswatini during 1994–2007 to estimate markups using the production approach. It finds elasticities, markups and concentration to be comparable with other findings elsewhere. Although no causality is found from a regression of markups/concentration to entry/exit dynamics an increase in productivity within high capital stock industries and in fixed costs raises average markups. Further research will focus on markup state dependence, unobserved heterogeneity, and endogenous regime switching to enhance understanding of markup pricing.
When does a wedding mark the beginning of a new chapter in one’s life?
Authors: Kirkegaard Thomsen Dorthe , Talarico Jennifer M. , Steiner Kristina L.
Published: June 2021

Life story chapters may be formed in relation to substantial and enduring changes in material circumstances, and we explored this idea by capitalizing on naturally occurring variations in the change of material circumstances associated with marriage. In two studies, we asked participants to report whether they cohabitated before marriage and whether they relocated in connection with marriage, using these as proxies for material change. Participants described their wedding and rated it on memory characteristics along with scales measuring material change, psychological change, and centrality to identity. Next, they identified chapters within the romantic domain of their lives. Finally, they placed the wedding memory in a chapter and marked the temporal location of the memory on a timeline representing the chapter. In study 2, not cohabitating before marriage was associated with greater likelihood of locating the wedding memory as a starting point for a chapter. The results provide some support for the role of material change in shaping the formation of chapters.
Intergenerational relations of older immigrants in the United States
Authors: Cao Xuemei
Published: June 2021

The rapid aging of the immigrant population in the United States has drawn increasing scholarly attention to studying the kinship support networks of older immigrants. Despite the common stereotype of older immigrants as passive dependents of their families and the receiving society, this review highlights their active negotiations of ties to adult children as they manage family relations and secure old‐age support. After a brief description of the demographic profiles of the older immigrant population in contemporary United States, this article shows how international migration challenges the patterns and power dynamics of two major aspects of intergenerational relationships in adulthood—intergenerational exchanges and intergenerational conflicts. By presenting the diversity and variations of intergenerational relations in aging immigrant families, the author argues that research on older immigrants' family relations holds great potentials to contribute to the literature on immigration, family, and aging studies.
Arabidopsis thaliana 2,3‐bisphosphoglycerate‐independent phosphoglycerate mutase 2 activity requires serine 82 phosphorylation
Authors: Duminil Pauline , Davanture Marlène , Oury Céline , Boex‐Fontvieille Edouard , Tcherkez Guillaume , Zivy Michel , Hodges Michael , Glab Nathalie
Published: June 2021

Phosphoglycerate mutases (PGAMs) catalyse the reversible isomerisation of 3‐phosphoglycerate and 2‐phosphoglycerate, a step of glycolysis. PGAMs can be sub‐divided into 2,3‐bisphosphoglycerate‐dependent (dPGAM) and ‐independent (iPGAM) enzymes. In plants, phosphoglycerate isomerisation is carried out by cytosolic iPGAM. Despite its crucial role in catabolism, little is known about post‐translational modifications of plant iPGAM. In Arabidopsis thaliana, phosphoproteomics analyses have previously identified an iPGAM phosphopeptide where serine 82 is phosphorylated. Here, we show that this phosphopeptide is less abundant in dark‐adapted compared to illuminated Arabidopsis leaves. In silico comparison of iPGAM protein sequences and 3D structural modelling of AtiPGAM2 based on non‐plant iPGAM enzymes suggest a role for phosphorylated serine in the catalytic reaction mechanism. This is confirmed by the activity (or the lack thereof) of mutated recombinant Arabidopsis iPGAM2 forms, affected in different steps of the reaction mechanism. We thus propose that the occurrence of the S82‐phosphopeptide reflects iPGAM2 steady‐state catalysis. Based on this assumption, the metabolic consequences of a higher iPGAM activity in illuminated versus darkened leaves are discussed.
An assessment of hepatitis B virus prevalence in South African young blood donors born after the implementation of the infant hepatitis B virus immunization program: Implications for transfusion safety
Authors: Vermeulen Marion , Swanevelder Ronel , Van Zyl Gert , Lelie Nico , Murphy Edward L.
Published: June 2021

Background

The prevalence of hepatitis B surface antigen is estimated to be 6.7% in the South African population and in April 1995 the nation introduced universal hepatitis B virus (HBV) vaccination for newborns and infants. We studied the temporal association of this program with HBV prevalence in young blood donors and the contemporary HBV incidence and residual risk of transfusion‐transmitted HBV infection (TT‐HBV).

Methods

We used blood donation data from January 2011 to December 2019. Estimation of HBV prevalence donations made by first‐time blood donors were analyzed by birth cohort and covariates. To estimate the incidence and residual risk of TT‐HBV, mathematical models used data from both first time and repeat donors.

Results

HBV prevalence in first‐time donors decreased from 0.84% (95% confidence interval [CI] 0.78–0.90) in 2011 to 0.66% (95% CI 0.61–0.70) in 2019. The post‐1995 birth cohort had a significantly lower HBV prevalence of 0.14% (95% CI 0.13–0.15) than the pre‐1985 birth cohort of 1.29% (95% CI 1.25–1.33) and the odds of HBV infection were reduced in a multivariable model (odds ratio [OR] = 0.28, 95% CI 0.24–0.34). The residual risk of TT‐HBV occurring from window‐period, occult, and possible vaccine breakthrough infections were estimated at 36.9, 5.8, and 2.2 per million red blood cell transfusions, respectively.

Conclusion

Donors born after the start of routine HBV immunization had significantly lower prevalence of HBV infection, supporting the effectiveness of the vaccination program. The contemporary residual risk of TT‐HBV has decreased and should decline further as more vaccinated young people join the donor pool.
COVID‐19 convalescent plasma cohort study: Evaluation of the association between both donor and recipient neutralizing antibody titers and patient outcomes
Authors: Yokoyama Ana Paula H. , Wendel Silvano , Bonet‐Bub Carolina , Fachini Roberta M. , Dametto Ana Paula F. , Blumm Fernando , Dutra Valeria F. , Candelaria Gabriela T. P. , Sakashita Araci M. , Machado Rafael Rahal Guaragna , Fontão‐Wendel Rita , Hamerschlak Nelson , Achkar Ruth , Assunção Murillo Santucci Cesar , Scuracchio Patrícia , Nudelman Victor , Pastore Laerte , Pinho João R. R. , Ben Mirian Dal , Filho Roberto Kalil , Marra Alexandre R. , Amano Mariane T. , Kallás Esper G. , Helito Alfredo Salim , de Carvalho Carlos Roberto Ribeiro , Araujo Danielle Bastos , Durigon Edison Luiz , Camargo Anamaria A. , Rizzo Luiz V. , Reis Luiz F. L. , Kutner Jose M.
Published: June 2021

Background

Current evidence regarding COVID‐19 convalescent plasma (CCP) transfusion practices is limited and heterogeneous. We aimed to determine the impact of the use of CCP transfusion in patients with previous circulating neutralizing antibodies (nAbs) in COVID‐19.

Methods

Prospective cohort including 102 patients with COVID‐19 transfused with ABO compatible CCP on days 0–2 after enrollment. Clinical status of patients was assessed using the adapted World Health Organization (WHO) ordinal scale on days 0, 5, and 14. The nAbs titration was performed using the cytopathic effect‐based virus neutralization test with SARS‐CoV‐2 (GenBank MT126808.1). The primary outcome was clinical improvement on day 14, defined as a reduction of at least two points on the adapted WHO ordinal scale. Secondary outcomes were the number of intensive care unit (ICU)‐free days and the number of invasive mechanical ventilation‐free days.

Results

Both nAbs of CCP units transfused (p < 0.001) and nAbs of patients before CCP transfusions (p = 0.028) were associated with clinical improvements by day 14. No significant associations between nAbs of patients or CCP units transfused were observed in the number of ICU or mechanical ventilation‐free days. Administration of CCP units after 10 days of symptom onset resulted in a decrease in ICU‐free days (p < 0.001) and mechanical ventilation‐free days (p < 0.001).

Conclusion

Transfusion of high titer nAbs CCP units may be a determinant in clinical strategies against COVID‐19. We consider these data as useful parameters to guide future CCP transfusion practices.
Post‐operative complications following apocrine gland anal sac adenocarcinoma resection in dogs
Authors: Sterman Allyson , Butler J. Ryan , Chambers Aidan , Dickson Rachel , Dornbusch Josephine , Mickelson Megan , Selmic Laura , Scharf Valerie , Schlag Ariel , Skinner Owen , Vinayak Arathi , Janssens Brandan Wustefeld
Published: June 2021

Describe the complications associated with surgical resection of primary apocrine gland anal sac adenocarcinoma (AGASACA) tumours study design multi‐institutional retrospective cross‐sectional cohort study Animals Client owned dogs with spontaneous disease using the Clavien‐Dindo classification system, post‐operative events were assigned and described. Logistic regression analysis was used to analyse for risk factors for a significant association with complications. One hundred sixty‐one dogs were included in the analysis. The post‐operative sequelae, complication, and failure to cure rates specific to the anal sac site was 14%, 17% and 1%, respectively. The majority (68%) of complications were grade II or higher, therefore requiring some form of intervention. Intra‐operative complications were identified in 11 cases (7%) with anorectal wall perforation being most common. An intra‐operative complication was significantly associated with post‐operative complications (p < 0.001; OR 7.4) while anorectal wall perforation was the only significant risk factor on regression analysis (p < 0.001; OR 19). Surgical site infection was identified in 20 of 161 (12%) of cases. Local recurrence (LR) occurred in 18% of cases at a median of 374 days (95% CI: 318–430). The only risk factor significantly associated with LR was the presence of vascular or lymphatic invasion (p = 0.008; OR 3). Post‐operative complications were relatively infrequent but the risk was significantly increased when there was an intraoperative complication during resection of a primary AGASACA tumour. This study provides information for the clinician regarding risk factors for post‐operative complications.
Axonal GABAA stabilizes excitability in unmyelinated sensory axons secondary to NKCC1 activity
Authors: Bonalume Veronica , Caffino Lucia , Castelnovo Luca F. , Faroni Alessandro , Liu Sheng , Hu Jing , Milanese Marco , Bonanno Giambattista , Sohns Kyra , Hoffmann Tal , De Col Roberto , Schmelz Martin , Fumagalli Fabio , Magnaghi Valerio , Carr Richard
Published: June 2021

Key points

GABA depolarized sural nerve axons and increased the electrical excitability of C‐fibres via GABAA receptor.

Axonal excitability responses to GABA increased monotonically with the rate of action potential firing.

Action potential activity in unmyelinated C‐fibres is coupled to Na‐K‐Cl cotransporter type 1 (NKCC1) loading of axonal chloride.

Activation of axonal GABAA receptor stabilized C‐fibre excitability during prolonged low frequency (2.5 Hz) firing.

NKCC1 maintains intra‐axonal chloride to provide feed‐forward stabilization of C‐fibre excitability and thus support sustained firing.

GABAA receptor (GABAAR)‐mediated depolarization of dorsal root ganglia (DRG) axonal projections in the spinal dorsal horn is implicated in pre‐synaptic inhibition. Inhibition, in this case, is predicated on an elevated intra‐axonal chloride concentration and a depolarizing GABA response. In the present study, we report that the peripheral axons of DRG neurons are also depolarized by GABA and this results in an increase in the electrical excitability of unmyelinated C‐fibre axons. GABAAR agonists increased axonal excitability, whereas GABA excitability responses were blocked by GABAAR antagonists and were absent in mice lacking the GABAAR β3 subunit selectively in DRG neurons (AdvillinCre or snsCre). Under control conditions, excitability responses to GABA became larger at higher rates of electrical stimulation (0.5–2.5 Hz). However, during Na‐K‐Cl cotransporter type 1 (NKCC1) blockade, the electrical stimulation rate did not affect GABA response size, suggesting that NKCC1 regulation of axonal chloride is coupled to action potential firing. To examine this, activity‐dependent conduction velocity slowing (activity‐dependent slowing; ADS) was used to quantify C‐fibre excitability loss during a 2.5 Hz challenge. ADS was reduced by GABAAR agonists and exacerbated by either GABAAR antagonists, β3 deletion or NKCC1 blockade. This illustrates that activation of GABAAR stabilizes C‐fibre excitability during sustained firing. We posit that NKCC1 acts in a feed‐forward manner to maintain an elevated intra‐axonal chloride in C‐fibres during ongoing firing. The resulting chloride gradient can be utilized by GABAAR to stabilize axonal excitability. The data imply that therapeutic strategies targeting axonal chloride regulation at peripheral loci of pain and itch may curtail aberrant firing in C‐fibres.
World Championship and Olympic Games Experience Influences Future Medal Performance in Track-and-Field Athletes
Authors: Fulton Timothy J. , Baranauskas Marissa N. , Chapman Robert F.
Published: June 2021

Some track-and-field national governing bodies send athletes to World Championship and Olympic Games (WC/OG) to gain experience that may positively impact future success, even though athletes may not be expected to place high or medal. However, it is unclear if this strategy is advantageous for future medal attainment. Purpose: To determine if participation and/or advancement at a track-and-field athlete’s first WC/OG influences the odds of future medaling. Methods: Performances of US track-and-field athletes who made their first WC/OG team during 2000–2013 were tracked through 2016 to stratify athletes into categories. Athletes who medaled on their first team or never made a subsequent team (ie, no experience) were compared with athletes who did not medal on their first team but made subsequent teams (ie, experience). The experience group was further divided into athletes who advanced or did not advance out of the initial round at their first competition for a secondary analysis. Odds ratios (ORs) were calculated using logistic regression to measure the association between experience level and medaling. Results: A significant OR was obtained for advanced versus did not advance (OR = 2.29, 95% confidence interval, 1.07–4.89, P = .03), but not for experience versus no experience (OR = 1.04, 95% confidence interval, 0.60–1.78, P = .91) group. Conclusions: Advancing out of the initial round of competition during an athlete’s first WC/OG competition is associated with increased odds of future medaling. National governing bodies should consider this “experience threshold” during team selection processes.
Single $$\pi ^0$$ production off neutrons bound in deuteron with linearly polarized photons
Authors: Mullen C. , Gardner S. , Glazier D. I. , Kay S. J. D. , Livingston K. , Strakovsky I. I. , Workman R. L. , Abt S. , Achenbach P. , Afzal F. , Ahmed Z. , Akondi C. S. , Annand J. R. M. , Bashkanov M. , Beck R. , Biroth M. , Borisov N. S. , Braghieri A. , Briscoe W. J. , Cividini F. , Collicott C. , Costanza S. , Denig A. , Dieterle M. , Downie E. J. , Drexler P. , Fegan S. , Ferretti-Bondy M. I. , Ghosal D. , Gorodnov I. , Gradl W. , Günther M. , Gurevic G. , Heijkenskjöld L. , Hornidge D. , Huber G. M. , Jermann N. , Kaeser A. , Korolija M. , Kashevarov V. L. , Krusche B. , Kulikov V. V. , Lazarev A. , Lutterer S. , MacGregor I. J. D. , Manley D. M. , Martel P. P. , Martemianov M. A. , Meier C. , Miskimen R. , Mocanu M. , Mornacchi E. , Neganov A. , Oberle M. , Ostrick M. , Otte P. , Paudyal D. , Pedroni P. , Powell A. , Prakhov S. N. , Reicherz G. , Ron G. , Rostomyan T. , Sfienti C. , Sokhoyan V. , Spieker K. , Steffen O. , Strub Th. , Supek I. , Thiel A. , Thiel M. , Thomas A. , Unverzagt M. , Usov Yu. A. , Wagner S. , Walford N. K. , Watts D. P. , Werthmüller D. , Wettig J. , Witthauer L. , Wolfes M. , Zachariou N. ,   (A2 Collaboration at MAMI)
Published: June 2021

The quasifree$$\overrightarrow{\gamma } d\rightarrow \pi ^0n(p)$$γ→d→π0n(p)photon beam asymmetry,$$\varSigma $$Σ, has been measured at photon energies,$$E_\gamma $$Eγ, from 390 to 610 MeV, corresponding to center of mass energy from 1.271 to 1.424 GeV, for the first time. The data were collected in the A2 hall of the MAMI electron beam facility with the Crystal Ball and TAPS calorimeters covering pion center-of-mass angles from 49$$^\circ $$∘to 148$$^\circ $$∘. In this kinematic region, polarization observables are sensitive to contributions from the$$\varDelta (1232)$$Δ(1232)andN(1440) resonances. The extracted values of$$\varSigma $$Σhave been compared to predictions based on partial-wave analyses (PWAs) of the existing pion photoproduction database. Our comparison includes the SAID, MAID and Bonn–Gatchina analyses; while a revised SAID fit, including the new$$\varSigma $$Σmeasurements, has also been performed. In addition, isospin symmetry is examined as a way to predict$$\pi ^0n$$π0nphotoproduction observables, based on fits to published data in the channels$$\pi ^0p$$π0p,$$\pi ^+n$$π+nand$$\pi ^-p$$π-p.
A Set of Batched Basic Linear Algebra Subprograms and LAPACK Routines
Authors: Abdelfattah Ahmad , Costa Timothy , Dongarra Jack , Gates Mark , Haidar Azzam , Hammarling Sven , Higham Nicholas J. , Kurzak Jakub , Luszczek Piotr , Tomov Stanimire , Zounon Mawussi
Published: June 2021

This article describes a standard API for a set of Batched Basic Linear Algebra Subprograms (Batched BLAS or BBLAS). The focus is on many independent BLAS operations on small matrices that are grouped together and processed by a single routine, called a Batched BLAS routine. The matrices are grouped together in uniformly sized groups, with just one group if all the matrices are of equal size. The aim is to provide more efficient, but portable, implementations of algorithms on high-performance many-core platforms. These include multicore and many-core CPU processors, GPUs and coprocessors, and other hardware accelerators with floating-point compute facility. As well as the standard types of single and double precision, we also include half and quadruple precision in the standard. In particular, half precision is used in many very large scale applications, such as those associated with machine learning.
PLANC
Authors: Eswar Srinivas , Hayashi Koby , Ballard Grey , Kannan Ramakrishnan , Matheson Michael A. , Park Haesun
Published: June 2021

We consider the problem of low-rank approximation of massive dense nonnegative tensor data, for example, to discover latent patterns in video and imaging applications. As the size of data sets grows, single workstations are hitting bottlenecks in both computation time and available memory. We propose a distributed-memory parallel computing solution to handle massive data sets, loading the input data across the memories of multiple nodes, and performing efficient and scalable parallel algorithms to compute the low-rank approximation. We present a software package called Parallel Low-rank Approximation with Nonnegativity Constraints, which implements our solution and allows for extension in terms of data (dense or sparse, matrices or tensors of any order), algorithm (e.g., from multiplicative updating techniques to alternating direction method of multipliers), and architecture (we exploit GPUs to accelerate the computation in this work). We describe our parallel distributions and algorithms, which are careful to avoid unnecessary communication and computation, show how to extend the software to include new algorithms and/or constraints, and report efficiency and scalability results for both synthetic and real-world data sets.
PCPATCH
Authors: Farrell Patrick E. , Knepley Matthew G. , Mitchell Lawrence , Wechsung Florian
Published: June 2021

Effective relaxation methods are necessary for good multigrid convergence. For many equations, standard Jacobi and Gauß–Seidel are inadequate, and more sophisticated space decompositions are required; examples include problems with semidefinite terms or saddle point structure. In this article, we present a unifying software abstraction, PCPATCH, for the topological construction of space decompositions for multigrid relaxation methods. Space decompositions are specified by collecting topological entities in a mesh (such as all vertices or faces) and applying a construction rule (such as taking all degrees of freedom in the cells around each entity). The software is implemented in PETSc and facilitates the elegant expression of a wide range of schemes merely by varying solver options at runtime. In turn, this allows for the very rapid development of fast solvers for difficult problems.
FAME
Authors: Lyu Xing-long , Li Tiexiang , Huang Tsung-ming , Lin Jia-wei , Lin Wen-wei , Wang Sheng
Published: June 2021

In this article, we propose the Fast Algorithms for Maxwell’s Equations (FAME) package for solving Maxwell’s equations for modeling three-dimensional photonic crystals. FAME combines the null-space free method with fast Fourier transform (FFT)-based matrix-vector multiplications to solve the generalized eigenvalue problems (GEPs) arising from Yee’s discretization. The GEPs are transformed into a null-space free standard eigenvalue problem with a Hermitian positive-definite coefficient matrix. The computation times for FFT-based matrix-vector multiplications with matrices of dimension 7 million are only 0.33 and 3.6 × 10
− 3
seconds using MATLAB with an Intel Xeon CPU and CUDA C++ programming with a single NVIDIA Tesla P100 GPU, respectively. Such multiplications significantly reduce the computational costs of the conjugate gradient method for solving linear systems. We successfully use FAME on a single P100 GPU to solve a set of GEPs with matrices of dimension more than 19 million, in 127 to 191 seconds per problem. These results demonstrate the potential of our proposed package to enable large-scale numerical simulations for novel physical discoveries and engineering applications of photonic crystals.
Linnea
Authors: Barthels Henrik , Psarras Christos , Bientinesi Paolo
Published: June 2021

The translation of linear algebra computations into efficient sequences of library calls is a non-trivial task that requires expertise in both linear algebra and high-performance computing. Almost all high-level languages and libraries for matrix computations (e.g., Matlab, Eigen) internally use optimized kernels such as those provided by BLAS and LAPACK; however, their translation algorithms are often too simplistic and thus lead to a suboptimal use of said kernels, resulting in significant performance losses. To combine the productivity offered by high-level languages, and the performance of low-level kernels, we are developing Linnea, a code generator for linear algebra problems. As input, Linnea takes a high-level description of a linear algebra problem; as output, it returns an efficient sequence of calls to high-performance kernels. Linnea uses a custom best-first search algorithm to find a first solution in less than a second, and increasingly better solutions when given more time. In 125 test problems, the code generated by Linnea almost always outperforms Matlab, Julia, Eigen, and Armadillo, with speedups up to and exceeding 10×.
NEP
Authors: Campos Carmen , Roman Jose E.
Published: June 2021

SLEPc is a parallel library for the solution of various types of large-scale eigenvalue problems. Over the past few years, we have been developing a module within SLEPc, called NEP, that is intended for solving nonlinear eigenvalue problems. These problems can be defined by means of a matrix-valued function that depends nonlinearly on a single scalar parameter. We do not consider the particular case of polynomial eigenvalue problems (which are implemented in a different module in SLEPc) and focus here on rational eigenvalue problems and other general nonlinear eigenproblems involving square roots or any other nonlinear function. The article discusses how the NEP module has been designed to fit the needs of applications and provides a description of the available solvers, including some implementation details such as parallelization. Several test problems coming from real applications are used to evaluate the performance and reliability of the solvers.
Fast Matching Pursuit with Multi-Gabor Dictionaries
Authors: Průša Zdeněk , Holighaus Nicki , Balazs Peter
Published: June 2021

Finding the best
K
-sparse approximation of a signal in a redundant dictionary is an NP-hard problem. Suboptimal greedy matching pursuit algorithms are generally used for this task. In this work, we present an acceleration technique and an implementation of the matching pursuit algorithm acting on a multi-Gabor dictionary, i.e., a concatenation of several Gabor-type time-frequency dictionaries, each of which consists of translations and modulations of a possibly different window and time and frequency shift parameters. The technique is based on pre-computing and thresholding inner products between atoms and on updating the residual directly in the coefficient domain, i.e., without the round-trip to the signal domain. Since the proposed acceleration technique involves an approximate update step, we provide theoretical and experimental results illustrating the convergence of the resulting algorithm. The implementation is written in C (compatible with C99 and C++11), and we also provide Matlab and GNU Octave interfaces. For some settings, the implementation is up to 70 times faster than the standard Matching Pursuit Toolkit.
Medusa
Authors: Slak Jure , Kosec Gregor
Published: June 2021

Medusa, a novel library for implementation of non-particle strong form mesh-free methods, such as GFDM or RBF-FD, is described. We identify and present common parts and patterns among many such methods reported in the literature, such as node positioning, stencil selection, and stencil weight computation. Many different algorithms exist for each part and the possible combinations offer a plethora of possibilities for improvements of solution procedures that are far from fully understood. As a consequence there are still many unanswered questions in the mesh-free community resulting in vivid ongoing research in the field. Medusa implements the core mesh-free elements as independent blocks, which offers users great flexibility in experimenting with the method they are developing, as well as easily comparing it with other existing methods. The article describes the chosen abstractions and their usage, illustrates aspects of the philosophy and design, offers some executions time benchmarks and demonstrates the application of the library on cases from linear elasticity and fluid flow in irregular 2D and 3D domains.
HyperNOMAD
Authors: Lakhmiri Dounia , Digabel Sébastien Le , Tribes Christophe
Published: June 2021

The performance of deep neural networks is highly sensitive to the choice of the hyperparameters that define the structure of the network and the learning process. When facing a new application, tuning a deep neural network is a tedious and time-consuming process that is often described as a “dark art.” This explains the necessity of automating the calibration of these hyperparameters. Derivative-free optimization is a field that develops methods designed to optimize time-consuming functions without relying on derivatives. This work introduces the HyperNOMAD package, an extension of the NOMAD software that applies the MADS algorithm [7] to simultaneously tune the hyperparameters responsible for both the architecture and the learning process of a deep neural network (DNN). This generic approach allows for an important flexibility in the exploration of the search space by taking advantage of categorical variables. HyperNOMAD is tested on the MNIST, Fashion-MNIST, and CIFAR-10 datasets and achieves results comparable to the current state of the art.
Algorithm 1017
Authors: Škrabánek Pavel , Martínková Natália
Published: June 2021

Fuzzy regression provides an alternative to statistical regression when the model is indefinite, the relationships between model parameters are vague, the sample size is low, or the data are hierarchically structured. Such cases allow to consider the choice of a regression model based on the fuzzy set theory. In fuzzyreg, we implement fuzzy linear regression methods that differ in the expectations of observational data types, outlier handling, and parameter estimation method. We provide a wrapper function that prepares data for fitting fuzzy linear models with the respective methods from a syntax established in R for fitting regression models. The function fuzzylm thus provides a novel functionality for R through standardized operations with fuzzy numbers. Additional functions allow for conversion of real-value variables to be fuzzy numbers, printing, summarizing, model plotting, and calculation of model predictions from new data using supporting functions that perform arithmetic operations with triangular fuzzy numbers. Goodness of fit and total error of the fit measures allow model comparisons. The package contains a dataset named bats with measurements of temperatures of hibernating bats and the mean annual surface temperature reflecting the climate at the sampling sites. The predictions from fuzzy linear models fitted to this dataset correspond well to the observed biological phenomenon. Fuzzy linear regression has great potential in predictive modeling where the data structure prevents statistical analysis and the modeled process exhibits inherent fuzziness.