bluuebunny/crossref_metadata_2025 huggingface dataset:
Pulse optimization for high-precision motional-mode characterization in trapped-ion quantum computers
Authors: Liang Qiyao , Kang Mingyu , Li Ming , Nam Yunseong
Published: April 2024

High-fidelity operation of quantum computers requires precise knowledge of the physical system through characterization. For motion-mediated entanglement generation in trapped ions, it is crucial to have precise knowledge of the motional-mode parameters such as the mode frequencies and the Lamb–Dicke parameters. Unfortunately, the state-of-the-art mode-characterization schemes do not easily render the mode parameters in a sufficiently accurate and efficient fashion for large-scale devices, due to the unwanted excitation of adjacent modes in the frequency space when targeting a single mode, an effect known as the cross-mode coupling. Here, we develop an alternative scheme that leverages the degrees of freedom in pulse design for the characterization experiment such that the effects of the cross-mode coupling is actively silenced. Further, we devise stabilization methods to accurately characterize the Lamb–Dicke parameters even when the mode frequencies are not precisely known due to experimental drifts or characterization inaccuracies. We extensively benchmark our scheme in simulations of a three-ion chain and discuss the parameter regimes in which the shaped pulses significantly outperform the traditional square pulses.
Temporal convolutional network for prediction of Li-ion batteries capacity fade knee
Authors: d’Apolito Luigi , Hong Hanchi
Published: April 2024

Lithium-ion batteries are widely used for electric vehicles for fast charging capabilities and driving range, but they are characterized by a deterioration dependent from their operational conditions. The process of battery degradation shows a first stage when the degradation proceeds at a slow pace, followed by a stage when the battery abruptly deteriorates. The transition between these two stages is known as capacity fade curve knee. Predicting the capacity fade curve knee can be used to improve the lifetime of the battery by modifying the charging strategies, planning the maintenance, deciding warranty conditions in more cost-effective way and is also important in second life (when the battery is used in a less-demanding application), by timely preventing an unreversible aging trend that could occur in the first life. The present study aims to develop a novel technique to predict the occurrence of the capacity fade curve knee, introducing an engineered state of health indicator and using a Temporal Convolutional Network (TNC) that combines dilations and residual connections with causal convolutions. The effect of the choice of different initial cycles on the prediction accuracy has been studied and a heuristic uncertainty quantification has been provided to obtain an approximate measure of the prediction quality. Moreover, the network has been trained using inputs with different sampling frequencies and results have been compared. The prediction metrics of the present method have been compared to other methods, showing the benefit of this method for the early forecast of the onset of the capacity fade curve knee.
Deep unsupervised learning using spike-timing-dependent plasticity
Authors: Lu Sen , Sengupta Abhronil
Published: April 2024

Spike-timing-dependent plasticity (STDP) is an unsupervised learning mechanism for spiking neural networks that has received significant attention from the neuromorphic hardware community. However, scaling such local learning techniques to deeper networks and large-scale tasks has remained elusive. In this work, we investigate a Deep-STDP framework where a rate-based convolutional network, that can be deployed in a neuromorphic setting, is trained in tandem with pseudo-labels generated by the STDP clustering process on the network outputs. We achieve 24.56% higher accuracy and 3.5 × faster convergence speed at iso-accuracy on a 10-class subset of the Tiny ImageNet dataset in contrast to a k-means clustering approach.
Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes
Authors: Zhao Weizhong , Wu Junze , Jiang Xingpeng , He Tingting , Hu Xiaohua
Published: April 2024

Motivation

The crisis of antibiotic resistance, which causes antibiotics used to treat bacterial infections to become less effective, has emerged as one of the foremost challenges to public health. Identifying the properties of antibiotic resistance genes (ARGs) is an essential way to mitigate this issue. Although numerous methods have been proposed for this task, most of these approaches concentrate solely on predicting antibiotic class, disregarding other important properties of ARGs. In addition, existing methods for simultaneously predicting multiple properties of ARGs fail to account for the causal relationships among these properties, limiting the predictive performance.

Results

In this study, we propose a causality-guided framework for annotating properties of ARGs, in which causal inference is utilized for representation learning. More specifically, the hidden biological patterns determining the properties of ARGs are described by a Gaussian Mixture Model, and procedure of causal representation learning is used to derive the hidden features. In addition, a causal graph among different properties is constructed to capture the causal relationships among properties of ARGs, which is integrated into the task of annotating properties of ARGs. The experimental results on a real-world dataset demonstrate the effectiveness of the proposed framework on the task of annotating properties of ARGs.

Availability and implementation

The data and source codes are available in GitHub at https://github.com/David-WZhao/CausalARG.
VarChat: the generative AI assistant for the interpretation of human genomic variations
Authors: De Paoli Federica , Berardelli Silvia , Limongelli Ivan , Rizzo Ettore , Zucca Susanna
Published: April 2024

Motivation

In the modern era of genomic research, the scientific community is witnessing an explosive growth in the volume of published findings. While this abundance of data offers invaluable insights, it also places a pressing responsibility on genetic professionals and researchers to stay informed about the latest findings and their clinical significance. Genomic variant interpretation is currently facing a challenge in identifying the most up-to-date and relevant scientific papers, while also extracting meaningful information to accelerate the process from clinical assessment to reporting. Computer-aided literature search and summarization can play a pivotal role in this context. By synthesizing complex genomic findings into concise, interpretable summaries, this approach facilitates the translation of extensive genomic datasets into clinically relevant insights.

Results

To bridge this gap, we present VarChat (varchat.engenome.com), an innovative tool based on generative AI, developed to find and summarize the fragmented scientific literature associated with genomic variants into brief yet informative texts. VarChat provides users with a concise description of specific genetic variants, detailing their impact on related proteins and possible effects on human health. In addition, VarChat offers direct links to related scientific trustable sources, and encourages deeper research.

Availability and implementation

varchat.engenome.com.
Queer and trans community building in post-NALSA and post-377 India: a critical reflection
Authors: Kumar Pushpesh , Datta Sayantan , Mishra Neha
Published: April 2024

This article reflects on contestations that mark queer and trans community building in post- National Legal Services Authority (NALSA) and post-377 India. In the past decade, queer and trans communities in India have witnessed two landmark judgements: the NALSA v. Union of India judgement 2014 and the Navtej Singh Johar and Ors. v. Union of India judgement 2018. The former granted transgender persons legal recognition and a promise of civil and substantive rights. The latter read down the draconian Sec. 377 of the Indian Penal Code that criminalized consensual adult homosexual sex acts. In light of these two judgements, this article traces challenges faced by queer and trans communities and challenges to queer and trans community building in contemporary India by tracing recent developments in the contexts of health, public policy, jurisprudence, social institutions, education, popular culture, and the precarity of gender and sexually transgressive communities during the recent COVID-19 pandemic. Finally, the authors also trace narratives of hope that demonstrate how queer and trans people in post legal reform India continue to build enabling and affirmative communities in the face of an increasingly neoliberalizing country.
Skin dermatoses in the returning traveller: a practical guide
Authors: Efstathiadou Anthoula , Tsourouktsoglou Harilena , Shipman Alexa R
Published: April 2024

Skin problems are common in returning travellers, despite the fact that vaccination, insect repellent techniques, adequate clothing and footwear are all ways to prevent skin disease. When travelling to unusual areas, the traveller can still expect to pick up diseases that are common across the world, such as lice, scabies, and staphylococcal or streptococcal infections. What can differ are the different arthropods and the diseases they can spread. Given the plethora of dermatoses in returning travellers, a methodological approach is necessary. We attempted such an approach by creating a practical guide that includes a diagnostic flowchart alongside a world map presenting common skin problems by continent. Additional information regarding possible investigations, along with tables presenting common infectious skin diseases and their corresponding presentations, is also included in our study. Our aim is to help clinicians approach skin dermatosis in patients returning from holidays, acknowledging the diagnostic difficulties that this might entail.
Paediatrics and genetics
Authors: Sahadevan Geethanjali , Shaj Kiran
Published: April 2024

A 3-month-old child presented with cutaneous and mucosal erosions and blisters since birth. There was a history of the mother having similar lesions.
Primary hyperoxaluria in adults and children: a nationwide cohort highlights a persistent diagnostic delay
Authors: Pszczolinski Romain , Acquaviva Cécile , Berrahal Insaf , Biebuyck Nathalie , Burtey Stéphane , Clabault Karine , Dossier Claire , Guillet Matthieu , Hemery Floriane , Letavernier Emmanuel , Rousset-Rouvière Caroline , Bacchetta Justine , Moulin Bruno
Published: April 2024

Background

Primary hyperoxalurias (PH) are extremely rare genetic disorders characterized by clinical heterogeneity. Delay in diagnosing these conditions can have detrimental effects on patient outcomes. The primary objective of this study is to assess the current diagnostic delay for PH.

Methods

This nationwide, observational and retrospective study included patients who received a genetic diagnosis of PH types 1, 2 and 3 between 1 January 2015 and 31 December 2019. Diagnostic delay was defined as the duration between the onset of symptoms and the time of genetic diagnosis.

Results

A total of 52 patients (34 children and 18 adults) were included in the study, with 40 PH1 (77%), 3 PH2 (6%) and 9 PH3 (17%). At the time of diagnosis, 12 patients (23%) required dialysis. Among the PH1 patients, the predominant symptom at onset in adults was renal colic (79% of cases), whereas symptoms in children were more diverse (renal colic in 17% of cases). The diagnostic delay was significantly shorter in children compared with adults [median (interquartile range)]: 1.2 (0.1–3.0) versus 30 (17–36) years, respectively (P < .0001). RNA interference was utilized in 23 patients (58%). Five individuals (13%) underwent double liver–kidney transplantation, and five (13%) received isolated kidney transplantation, with lumasiran therapy in four patients. For PH2 and PH3 patients, the diagnostic delay ranges from 0 to 3 years, with renal colic as first symptom in 33% of cases.

Conclusion

This extensive and recent cohort of PH underscores the considerable delay in diagnosing PH, particularly in adults, even in a country with a dedicated organization for enhancing the overall management of rare diseases. These findings reinforce the imperative for increased awareness among relevant specialties regarding the evaluation of urolithiasis.
Dapagliflozin treatment of patients with chronic kidney disease without diabetes across different albuminuria levels (OPTIMISE-CKD)
Authors: Svensson Maria K , Tangri Navdeep , Bodegård Johan , Adamsson Eryd Samuel , Thuresson Marcus , Sofue Tadashi
Published: April 2024

Background

We compared kidney and cardiorenal protection in patients without type 2 diabetes across urine albumin–creatinine ratio (UACR) levels after initiation on dapagliflozin for the treatment of chronic kidney disease (CKD).

Methods

OPTIMISE-CKD is an observational study describing dapagliflozin treatment for CKD. Adult patients with CKD without type 2 diabetes were included in the primary analysis. Baseline UACR was grouped as normal/mildly elevated (0–29 mg/g), low (30–200 mg/g) and high (>200 mg/g). Outcomes were estimated glomerular filtration rate (eGFR) trajectories/slopes, cardiorenal complications and all-cause mortality.

Results

In total, 1480 patients had low (n = 796) and high (n = 684) UACR. The two groups were similar at baseline, aged 75 and 74 years, and 42% and 39% female, respectively. After dapagliflozin initiation, an acute eGFR dip of 3 mL/min/1.73 m2 was observed, followed by a flat development in both groups. The eGFR slope [95% confidence interval (CI)] for patients with low UACR was 0.79 mL/min/1.73 m2 per year (–0.59, 2.56), and similar to patients with high UACR [0.40 mL/min/1.73 m2 per year (–0.46, 1.38)]. Risks of cardiorenal complications and all-cause mortality were similar, with adjusted hazard ratios of 0.89 (95% CI 0.66, 1.19) and 1.10 (95% CI 0.63, 1.92), respectively. Analogous results were found in those with normal/mildly elevated UACR.

Conclusions

Dapagliflozin in patients without type 2 diabetes for the treatment of CKD demonstrated similar kidney protection, cardiorenal and all-cause mortality risk across UACR levels. This suggests that the efficacy of dapagliflozin found in clinical trials expands to real-world patients with CKD, regardless of albuminuria levels.
Disability and Superability: The Spectacle of Extra/Ordinary Bodies in Maxine Hong Kingston’sTripmaster Monkey: His Fake Book
Authors: Chen Fu-jen
Published: April 2024

This essay explores how Maxine Hong Kingston’s Tripmaster Monkey (1989) showcases and anticipates cultural imaginaries surrounding Asian bodies as repositories for fantasy and affect. From the fragmented body of the suicidal protagonist to the spectacle of the Siamese conjoined twins, Kingston stages diverse bodily tropes that reflect racist, sexist, and ableist perceptions throughout history. The protagonist Wittman Ah Sing, embodied as a postmodern “Monkey King,” represents a neoliberal subjectivity marked by adaptive resilience. In contrast, the Siamese twins enact intersubjective connections, catalyzing the protagonist’s communal theater production. The play’s communal vision challenges the ideological norms of the “Normate” and resists complicity with global capitalism. Ultimately, the acknowledgment of shared struggles amidst radical divisions and recognition of our participation in ideological fantasies fosters collective solidarity and a radical critique of the capitalist system.
‘William Fowler’, Sir William Garrard, Sir John Hawkins and the Sixteenth-Century Atlantic Slave Trade
Authors: Baker Gary Paul , Lambert Craig
Published: April 2024

This article sheds new light on English involvement in the sixteenth-century transatlantic slave trade, especially the voyages of John Hawkins in the 1560s. Its focus is on William Fowler, a merchant who in 1569 was brought in front of the English High Court of the Admiralty to provide expert evidence on behalf of Sir William Garrard and Sir John Hawkins. Fowler was an experienced slave trader who worked within the Spanish system, probably trading out of Seville to New Spain. His testimony in 1569 was of great importance to Hawkins, Garrard and the other investors who backed Hawkins’s ill-fated slaving voyage of 1567–9, for in his testimony Fowler provided independent and up-to-date information as to the value of slaves and other commodities which Hawkins lost in 1568 at San Juan de Ulúa. Hawkins and his backers would use these valuations to bolster their claim for compensation from the Spanish Crown for the goods they lost in 1568. Using previously unpublished sources, the article will investigate the origins of William Fowler and assess the social and economic connections that existed between Hawkins and his investors, and explain why these socio-economic networks brought Fowler to the Admiralty court in 1569. The article concludes with a transcription of Fowler’s testimony.
Bendopnea prevalence and prognostic value in older patients with heart failure: FRAGILE-HF–SONIC-HF post hoc analysis
Authors: Nakade Taisuke , Maeda Daichi , Matsue Yuya , Fujimoto Yudai , Kagiyama Nobuyuki , Sunayama Tsutomu , Dotare Taishi , Jujo Kentaro , Saito Kazuya , Kamiya Kentaro , Saito Hiroshi , Ogasahara Yuki , Maekawa Emi , Konishi Masaaki , Kitai Takeshi , Iwata Kentaro , Toki Misako , Yoshioka Kenji , Wada Hiroshi , Kasai Takatoshi , Nagamatsu Hirofumi , Momomura Shin-ichi , Minamino Tohru
Published: April 2024

Aims

This study aimed to investigate the prevalence, clinical characteristics, and prognostic value of bendopnea in older patients hospitalized for heart failure.

Methods and results

This post hoc analysis was performed using two prospective, multicentre, observational studies: the FRAGILE-HF (main cohort) and SONIC-HF (validation cohort) cohorts. Patients were categorized based on the presence of bendopnea, which was evaluated before discharge. The primary endpoint was 2-year all-cause mortality after discharge. Among the 1243 patients (median age, 81 years; 57.2% male) in the FRAGILE-HF cohort and 225 (median age, 79 years; 58.2% men) in the SONIC-HF cohort, bendopnea was observed in 31 (2.5%) and 10 (4.4%) patients, respectively. Over a 2-year follow-up period, all-cause death occurred in 20.8 and 21.9% of the patients in the FRAGILE-HF and SONIC-HF cohorts, respectively. Kaplan–Meier survival curves demonstrated significantly higher mortality rates in patients with bendopnea than in those without bendopnea in the FRAGILE-HF (log-rank P = 0.006) and SONIC-HF cohorts (log-rank P = 0.014). Cox proportional hazard analysis identified bendopnea as an independent prognostic factor for all-cause mortality in both the FRAGILE-HF [hazard ratio (HR) 2.11, 95% confidence interval (CI) 1.18–3.78, P = 0.012] and SONIC-HF cohorts (HR 4.20, 95% CI 1.63–10.79, P = 0.003), even after adjusting for conventional risk factors.

Conclusion

Bendopnea was observed in a relatively small proportion of older patients hospitalized for heart failure before discharge. However, its presence was significantly associated with an increased risk of all-cause mortality.
Ferriphaselus amnicola strain GF-20, a new iron- and thiosulfate-oxidizing bacterium isolated from a hard rock aquifer
Authors: Garry Mélissa , Farasin Julien , Drevillon Laetitia , Quaiser Achim , Bouchez Camille , Le Borgne Tanguy , Coffinet Sarah , Dufresne Alexis
Published: April 2024

Ferriphaselus amnicola GF-20 is the first Fe-oxidizing bacterium isolated from the continental subsurface. It was isolated from groundwater circulating at 20 m depth in the fractured-rock catchment observatory of Guidel-Ploemeur (France). Strain GF-20 is a neutrophilic, iron- and thiosulfate-oxidizer and grows autotrophically. The strain shows a preference for low oxygen concentrations, which suggests an adaptation to the limiting oxygen conditions of the subsurface. It produces extracellular stalks and dreads when grown with Fe(II) but does not secrete any structure when grown with thiosulfate. Phylogenetic analyses and genome comparisons revealed that strain GF-20 is affiliated with the species F. amnicola and is strikingly similar to F. amnicola strain OYT1, which was isolated from a groundwater seep in Japan. Based on the phenotypic and phylogenetic characteristics, we propose that GF-20 represents a new strain within the species F. amnicola.
Code-Switching, Queering Food and Narrative Construction in Monica Meneghetti’s Memoir What the Mouth Wants
Authors: Baldo Michela
Published: April 2024

This article examines the extent to which the Italian-Canadian queer writer Monica Meneghetti, in her memoir What the Mouth Wants, challenges and disrupts heteronormative notions of gender and sexuality through the code-switching of food terms in Italian or in a Northern Italian dialect. Code-switching is used primarily to evoke memories of Meneghetti’s late mother through the author’s favourite dishes, and of the homophobia (or rather biphobia) directed at her by her father, with whom she used to make fresh pasta and cook Italian meals. The memories and flashbacks, interspersed with present-day accounts of the preparation of Italian childhood meals with her polyamorous family, allow the memoir’s protagonist to build a new sense of family: a queer Italian-Canadian family. Drawing on feminist and queer food studies, the article reveals that Meneghetti uses code-switching to signal point of view and to construct the memoir’s characters and plot, as code-switched food items are also linked to the notion of memory and to what it means to write the memoir.
Parthenogenetic Stick Insects Exhibit Signatures of Preservation in the Molecular Architecture of Male Reproduction
Authors: Forni Giobbe , Mantovani Barbara , Mikheyev Alexander S , Luchetti Andrea
Published: April 2024

After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (i) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (ii) that gene co-expression network architecture could constrain individual gene expression. Our testing ground has been the Bacillus stick insect species complex, which contains close relatives that are either bisexual or parthenogenetic. After the identification of genes expressed in male reproductive tissues in a bisexual species, we investigated their gene co-expression network structure in two parthenogenetic species. We found that gene co-expression within the male gonads was partially preserved in parthenogens. Furthermore, parthenogens did not show relaxed selection on genes upregulated in male gonads in the bisexual species. As these genes were mostly expressed in female gonads, this preservation could be driven by pleiotropic interactions and an ongoing role in female reproduction. Connectivity within the network also played a key role, with highly connected—and more pleiotropic—genes within male gonad also having a gonad-biased expression in parthenogens. Our findings provide novel insight into the mechanisms which could underlie the production of rare males in parthenogenetic lineages; more generally, they provide an example of the cryptic persistence of a lost trait molecular architecture, driven by gene pleiotropy on other traits and within their co-expression network.
WormBase 2024: status and transitioning to Alliance infrastructure
Authors: Sternberg Paul W , Van Auken Kimberly , Wang Qinghua , Wright Adam , Yook Karen , Zarowiecki Magdalena , Arnaboldi Valerio , Becerra Andrés , Brown Stephanie , Cain Scott , Chan Juancarlos , Chen Wen J , Cho Jaehyoung , Davis Paul , Diamantakis Stavros , Dyer Sarah , Grigoriadis Dionysis , Grove Christian A , Harris Todd , Howe Kevin , Kishore Ranjana , Lee Raymond , Longden Ian , Luypaert Manuel , Müller Hans-Michael , Nuin Paulo , Quinton-Tulloch Mark , Raciti Daniela , Schedl Tim , Schindelman Gary , Stein Lincoln
Published: April 2024

WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.
Repair of the complete atrioventricular septal defect—impact of postoperative moderate or more regurgitation
Authors: Ozturk Mahmut , Tongut Aybala , Sterzbecher Vanessa , Desai Manan , Esmailian Gabriel , Henmi Soichiro , Spurney Christopher , Staffa Steven J , d’Udekem Yves , Yerebakan Can
Published: April 2024

OBJECTIVES

To study the risk factors for mortality, moderate or more left atrioventricular valve regurgitation (LAVVR) and reoperation after the surgical repair of complete atrioventricular septal defect (cAVSD) in a single centre.

METHODS

The current study is a retrospective review of patients who underwent surgical repair of cAVSD between 2000 and 2021. Patients with unbalanced ventricles not amenable to biventricular repair, double outlet right ventricle and malpositioned great arteries were excluded. The clinical predictors of outcome for end points were analysed with univariate and multivariable Cox regression analysis or Fine–Gray modelling for competing risks. Time-dependent end points were estimated using the Kaplan–Meier curve analysis and cumulative incidence curves.

RESULTS

The median follow-up time was 2.3 years. Among 220 consecutive patients were 10 (4.6%) operative and 21 late mortalities (9.6%). A total of 26 patients were identified to have immediate postoperative moderate or more regurgitation and 10 of them ultimately died. By multivariable analysis prematurity and having more than moderate regurgitation immediately after the operation were identified as predictors of overall mortality (P = 0.003, P = 0.012). Five- and ten-year survival rates were lower for patients with immediate postoperative moderate or more LAVVR {51.9% [confidence interval (CI): 27.5–71.7%]} when compared to patients without moderate or more regurgitation [93.2% (CI: 87.1–96.4%) and 91.3% (CI: 83.6–95.5%)].

CONCLUSIONS

The patients who undergo cAVSD repair remain subjected to a heavy burden of disease related to postoperative residual LAVVR. Immediate postoperative moderate or more LAVVR contributes significantly to overall mortality. Whether a second run of bypass can decrease this observed mortality should be investigated.
Repeated endovascular approaches achieve successful complete remodelling for type IIIb acute aortic dissection
Authors: Matsuura Makoto , Kuroyanagi Satoshi , Kobayashi Masaaki , Komooka Masatoshi
Published: April 2024

Thoracic endovascular repair for type IIIb aortic dissection results in the disappearance of false lumen perfusion in the abdominal aorta in only about 20% of cases, with concern for expansion in the long term. Staged endovascular therapy with intervention on all re-entries can lead to complete false lumen thrombosis and remodelling of the entire aorta. This approach could be an option in cases in which long-term expansion is anticipated.
Evaluating energy, exergy and economic aspects of a CO
2
-free Kalina cycle cogeneration system with various solar collectors
Authors: Rad Hima Nikafshan , Ghasemi Amir , Akrami Mohammad , Golizadeh Farid
Published: April 2024

This study meticulously evaluates a Kalina cycle system, adeptly designed for the simultaneous generation of heat, power and cooling. Examining the system from energy, exergy and economic perspectives, the research analyzes the performance of various solar thermal collectors: parabolic trough collectors (PTCs), linear Fresnel reflector, dish-based systems and vacuum tubes (VTs). Among these, the PTC stands out, excelling in energy and exergy efficiency while ensuring cost-effectiveness and minimal system losses. The research also explores the impact of component adjustments on heat, power and cooling production rates. Notably, it identifies the VT collector as the most prominent in terms of exergy destruction and associated costs, with figures reaching 11.07 MW and 159 100 $/year, respectively, offering valuable insights for enhancing the system’s efficiency and economic viability.
Temporal dynamics of genetic parameters and SNP effects for performance and disorder traits in poultry undergoing genomic selection
Authors: Richter Jennifer , Hidalgo Jorge , Bussiman Fernando , Breen Vivian , Misztal Ignacy , Lourenco Daniela
Published: April 2024

Accurate genetic parameters are crucial for predicting breeding values and selection responses in breeding programs. Genetic parameters change with selection, reducing additive genetic variance and changing genetic correlations. This study investigates the dynamic changes in genetic parameters for residual feed intake (RFI), gain (GAIN), breast percentage (BP), and femoral head necrosis (FHN) in a broiler population that undergoes selection, both with and without the use of genomic information. Changes in single nucleotide polymorphism (SNP) effects were also investigated when including genomic information. The dataset containing 200,093 phenotypes for RFI, 42,895 for BP, 203,060 for GAIN, and 63,349 for FHN was obtained from 55 mating groups. The pedigree included 1,252,619 purebred broilers, of which 154,318 were genotyped with a 60K Illumina Chicken SNP BeadChip. A Bayesian approach within the GIBBSF90 + software was applied to estimate the genetic parameters for single-, two-, and four-trait models with sliding time intervals. For all models, we used genomic-based (GEN) and pedigree-based approaches (PED), meaning with or without genotypes. For GEN (PED), heritability varied from 0.19 to 0.2 (0.31 to 0.21) for RFI, 0.18 to 0.11 (0.25 to 0.14) for GAIN, 0.45 to 0.38 (0.61 to 0.47) for BP, and 0.35 to 0.24 (0.53 to 0.28) for FHN, across the intervals. Changes in genetic correlations estimated by GEN (PED) were 0.32 to 0.33 (0.12 to 0.25) for RFI–GAIN, −0.04 to −0.27 (−0.18 to −0.27) for RFI–BP, −0.04 to −0.07 (−0.02 to −0.08) for RFI–FHN, −0.04 to 0.04 (0.06 to 0.2) for GAIN–BP, −0.17 to −0.06 (−0.02 to −0.01) for GAIN–FHN, and 0.02 to 0.07 (0.06 to 0.07) for BP–FHN. Heritabilities tended to decrease over time while genetic correlations showed both increases and decreases depending on the traits. Similar to heritabilities, correlations between SNP effects declined from 0.78 to 0.2 for RFI, 0.8 to 0.2 for GAIN, 0.73 to 0.16 for BP, and 0.71 to 0.14 for FHN over the eight intervals with genomic information, suggesting potential epistatic interactions affecting genetic trait architecture. Given rapid genetic architecture changes and differing estimates between genomic and pedigree-based approaches, using more recent data and genomic information to estimate variance components is recommended for populations undergoing genomic selection to avoid potential biases in genetic parameters.
Timing of nanocrystalline silver-based dressing application: a retrospective single-center pediatric cohort study
Authors: Thibedeau Marshall , Fish Joel , Kelly Charis , Wenskus Julia , Zuccaro Jennifer , Gus Eduardo
Published: April 2024

Recent evidence has demonstrated that silver has anti-inflammatory properties that are independent of the known antimicrobial ones. In our current model of care, nonadherent, nonsilver dressings are applied for acute presentations of pediatric partial-thickness burn injuries. The wounds are re-assessed after the progression phase (48-72 hours after injury), and silver dressings are applied. However, when logistical obstacles prevent re-assessment within the 48- to 72-hour window, nanocrystalline silver-based dressings are applied on presentation. The objective of this study was to test our model of care. We hypothesized that immediate application (<24 hours after injury) of nanocrystalline silver-based dressings would reduce surgical interventions. This was a retrospective single-center cohort study. All patients <18 years old treated at a pediatric burn center for acute partial-thickness burn injuries between January 1, 2020, and December 31, 2021, were included. Multivariable logistic regression was used to compare surgical treatment rates between patients with different timing of nanocrystalline silver-based dressing application. Four hundred and seventy-six patients were included for analysis. One hundred and four patients (21.8%) had nanocrystalline silver-based dressings and 372 (78.2%) had non-silver, non-adherent dressings applied within 24 hours of injury. Multivariable logistic regression identified 3 statistically significant variables as predictors for surgical treatment: age (odds ratio [OR] = 1.14, 95% CI [1.06-1.23]), TBSA (OR = 1.15, 95% CI [1.06-1.25]), and burns to buttocks/lower extremity (OR = 2.39, 95% CI [1.26-4.53]). Immediate (<24 hours after injury) application of nanocrystalline silver-based dressings does not affect surgical treatment rate in pediatric patients with partial-thickness burns.
Age-stage, two-sex life table, and population projection of Ostrinia furnacalis (Lepidoptera: Crambidae) at different temperatures
Authors: Hu Xiaohua , Wang Zhenying , He Kanglai , Xie Haicui , Wang Yueqin
Published: April 2024

Ostrinia furnacalis (Guenée) (Lepidoptera: Crambidae), a highly destructive pest in Asia, poses a significant threat to maize production by causing substantial yield losses. However, there is a lack of information regarding the impact of temperature variations on its population dynamics and the age-stage and two-sex life table. This study aimed to investigate the impact of 4 temperatures (20 °C, 24 °C, 28 °C, 32 °C) on the development, reproduction, and survival of O. furnacalis under controlled laboratory conditions. Our results revealed that O. furnacalis successfully developed, survived, and laid eggs across the tested temperatures (20–32 °C). The shortest developmental duration for all immature stages was observed at 32 °C. Conversely, increasing temperatures led to decreased longevity. Among the temperatures tested, 28 °C proved to be optimal for O. furnacalis, exhibiting the highest intrinsic rate of increase, finite rate of increase, and net reproductive rate. Our findings indicate that O. furnacalis thrives within a wide temperature range of 20–32 °C, with 28 °C being the most favorable for reproduction. These insights are crucial for predicting population dynamics under diverse climatic conditions and developing effective control strategies against O. furnacalis. This study enhances our understanding of O. furnacalis’ life-history traits and provides valuable information for targeted pest management approaches.
Female patent attorneys and movements around the profession: achieving non-gendered decision-making
Authors: Lai Jessica C , Geldenhuys Ronelle , Khajeh Tabari Maryam , Summerfield Mark
Published: April 2024

Female patent attorneys face multiple layers of bias and discrimination. This article uses qualitative and quantitative data to analyse the experiences of female patent attorneys in Australia and New Zealand and their movements around the profession. Through interviews with 53 patent attorneys and an analysis of over 5 years of data on registered patent attorneys, we examine the experiences of women and how this can affect their decision to move to in-house roles, set up their own entities or move to smaller firms. While noting that women appear to face bias regardless of where they practice, the article concludes that the particular issues mothers face represent a key factor in why women are disproportionately over-represented in in-house roles. The issues also constitute a motivation for many women to set up their own entities and to move firms (though not necessarily from a larger to a smaller firm).
Farmers’ perceptions of integrated desert locust management: a case study in Isiolo and Meru Counties of Kenya
Authors: Lumumba Brian Omondi , Otieno David Jakinda , Nyikal Rose Adhiambo
Published: April 2024

The destructive nature of desert locust invasions in terms of reduced food security and loss of agricultural income necessitates effective control strategies. While chemical spraying is effective, it is harmful to the environment, human, and animal health. Therefore, an alternative is the implementation of an integrated desert locust management (IDLM) approach that entails surveillance and early warning systems, rational combination of chemicals, biological measures, and indigenous control methods. Adopting IDLM depends on an understanding of human behavior and perceptions as an avenue for disseminating information for effective control. However, there is limited knowledge of the drivers of farmers’ perceptions of IDLM. This study sought to fill the above knowledge gap by applying the principal component analysis method to develop a composite index that was subsequently used in a regression analysis of data collected from a sample of 391 farmers in Isiolo and Meru counties in Kenya. Descriptive results showed that informal sources and channels were the main sources of desert locust information, and most farmers held positive or neutral perceptions. The regression analysis results highlighted the role of formal and informal sources of information, private land ownership, and previous shocks in influencing farmers’ perceptions of integrated desert locust management. The study recommends targeted messaging of desert locust management approaches through coordinated surveillance and timely response by national and international agencies, empowering community leaders as the key entry point, and building local capacity for accurate observation and timely reporting of invasions as measures towards sustainable desert locust control efforts.
Organic management of the invasive swede midge (Diptera: Cecidomyiidae) on Brassica vegetables: multiple dead ends necessitate novel approaches
Authors: Hodgdon Elisabeth A , Stratton Chase A , Hoepting Christine A , Campbell Andrea E M , Gradish Angela E , Evans Braden G , Hallett Rebecca H , Chen Yolanda H
Published: April 2024

The distinctive biology and ecology of the invasive swede midge, Contarinia nasturtii Kieffer (Diptera: Cecidomyiidae), render organic management in North America particularly challenging, necessitating the search for novel out-of-the box approaches to control it. Native to Eurasia, this pest was first confirmed in North America in 2000 and has since spread to several states and provinces in the United States and Canada. As a galling midge, swede midge feeding causes distorted growth in Brassica (Brassicales: Brassicaceae) vegetables, resulting in major losses of marketable produce. While conventional growers typically use systemic insecticides for plant protection early in the season, equivalent approaches for organic production do not exist. The lack of effective organic management approaches for swede midge has resulted in devastating losses for heading Brassica vegetables, which are the most sensitive to midge feeding. Here, we review over 2 decades of research focused on developing organic approaches to manage swede midge. To encourage more rapid progress on swede midge management, we believe that it is important to review the widest array of work, including recent publications as well as our unpublished research. We conclude by highlighting the most promising strategies that should be utilized on farms and explored further for organic management of swede midge in vegetable crops.
VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes
Authors: Copeland Conner J , Roddy Jack W , Schmidt Amelia K , Secor Patrick R , Wheeler Travis J
Published: April 2024

Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists. Some prophages have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES (Viral Integrations in Bacterial genomES), a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab-separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES’s primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1072 Pseudomonas spp. genomes.
Teams in Transition: Increasing Role of Advanced Practice Providers in Antimicrobial Use and Infectious Diseases Consultation
Authors: Perez Reinaldo , Yarrington Michael E , Deri Connor R , Smith Michael J , Hayes Jillian , Wrenn Rebekah H , Moehring Rebekah W
Published: April 2024

Background

Advanced practice providers (APPs) have taken on increasing responsibilities as primary team members in acute care hospitals, but the impact of this practice shift on antimicrobial prescribing and infectious diseases (ID) consultation requests is unknown. Here we describe longitudinal trends in antimicrobial days of therapy (DOT) and ID consultation by attributed provider type in 3 hospitals.

Methods

We performed a retrospective time series analysis of antimicrobial use and ID consultation from July 2015 to June 2022 at a major university hospital and 2 community hospitals. We evaluated antimicrobial DOT and ID consultation over time and assessed attribution to 3 groups of providers: attending physicians, trainees, and APPs. We used multinomial logistic regression to measure changes in percentage of DOT and ID consultation across the clinician groups over time using physicians as the referent.

Results

Baseline distribution of antimicrobial DOT and ID consultation varied by practice setting, but all subgroups showed increases in the proportion attributable to APPs. Large increases were seen in the rate of ID consultation, increasing by >30% during the study period. At our university hospital, by study end >40% of new ID consults and restricted antimicrobial days were attributed to APPs.

Conclusions

Hospitals had differing baseline patterns of DOT attributed to provider groups, but all experienced increases in DOT attributed to APPs. Similar increases were seen in changes to ID consultation. APPs have increasing involvement in antimicrobial use decisions in the inpatient setting and should be engaged in future antimicrobial stewardship initiatives.
Real-World Effectiveness of Intravenous and Oral Antibiotic Stepdown Strategies for Gram-Negative Complicated Urinary Tract Infection With Bacteremia
Authors: Veillette John J , May Stephanie S , Alzaidi Sameer , Olson Jared , Butler Allison M , Waters C Dustin , Jackson Katarina , Hutton Mary A , Webb Brandon J
Published: April 2024

Background

Robust data are lacking regarding the optimal route, duration, and antibiotic choice for gram-negative bloodstream infection from a complicated urinary tract infection source (GN-BSI/cUTI).

Methods

In this multicenter observational cohort study, we simulated a 4-arm registry trial using a causal inference method to compare effectiveness of the following regimens for GN-BSI/cUTI: complete course of an intravenous β-lactam (IVBL) or oral stepdown therapy within 7 days using fluoroquinolones (FQs), trimethoprim-sulfamethoxazole (TMP-SMX), or high-bioavailability β-lactams (HBBLs). Adults treated between January 2016 and December 2022 for Escherichia coli or Klebsiella species GN-BSI/cUTI were included. Propensity weighting was used to balance characteristics between groups. The 60-day recurrence was compared using a multinomial Cox proportional hazards model with probability of treatment weighting.

Results

Of 2571 patients screened, 759 (30%) were included. Characteristics were similar between groups. Compared with IVBLs, we did not observe a difference in effectiveness for FQs (adjusted hazard ratio, 1.09 [95% confidence interval, .49–2.43]) or TMP-SMX (1.44 [.54–3.87]), and the effectiveness of TMP-SMX/FQ appeared to be optimal at durations of >10 days. HBBLs were associated with nearly 4-fold higher risk of recurrence (adjusted hazard ratio, 3.83 [95% confidence interval, 1.76–8.33]), which was not mitigated by longer treatment durations. Most HBBLs (67%) were not optimally dosed for bacteremia. Results were robust to multiple sensitivity analyses.

Conclusions

These real-world data suggest that oral stepdown therapy with FQs or TMP-SMX have similar effectiveness as IVBLs. HBBLs were associated with higher recurrence rates, but dosing was suboptimal. Further data are needed to define optimal dosing and duration to mitigate treatment failures.
BCAR4 facilitates trastuzumab resistance and EMT in breast cancer via sponging miR‐665 and interacting with YAP1
Authors: Ye Xingming , Liu Qinying , Qin Xin , Ma Yijing , Sheng Qingsong , Wu Xiufeng , Chen Shanshan , Huang Lijie , Sun Yang
Published: April 2024

Breast cancer antiestrogen resistance 4 (BCAR4) has been suggested that can modulate cell behavior, resulting in tumorigenesis and chemoresistance. However, the underlying mechanisms of BCAR4 in trastuzumab resistance (TR) is still elusive. Here, we explored the function and the underlying mechanism of BCAR4 involving in TR. We found that BCAR4 is significantly upregulated in trastuzumab‐resistant BC cells. Knockdown of BCAR4 could sensitize the BC cells to trastuzumab and suppress epithelial–mesenchymal transition (EMT). Mechanically, BCAR4 promotes yes‐associated protein 1 (YAP1) expression by competitively sponging miR‐665, to activated TGF‐β signaling. Reciprocally, YAP1 could occupy the BCAR4 promoter to enhance its transcription, suggesting that there exists a positive feedback regulation between YAP1 and BCAR4. Targeting the BCAR4/miR‐665/YAP1 axis may provide a novel insight of therapeutic approaches for TR in BC.