bluuebunny/crossref_metadata_2025 huggingface dataset:
Experience of a 2-year spinal muscular atrophy NBS pilot study in Italy: towards specific guidelines and standard operating procedures for the molecular diagnosis
Authors: Abiusi Emanuela , Vaisfeld Alessandro , Fiori Stefania , Novelli Agnese , Spartano Serena , Faggiano Maria Vittoria , Giovanniello Teresa , Angeloni Antonio , Vento Giovanni , Santoloci Roberta , Gigli Francesca , D'Amico Adele , Costa Simonetta , Porzi Alessia , Panella Mara , Ticci Chiara , Daniotti Marta , Sacchini Michele , Boschi Ilaria , Dani Carlo , Agostiniani Rino , Bertini Enrico , Lanzone Antonio , Lamarca Giancarlo , Genuardi Maurizio , Pane Marika , Donati Maria Alice , Mercuri Eugenio , Tiziano Francesco Danilo
Published: November 2022

Background

Spinal muscular atrophy (SMA) is due to the homozygous absence ofSMN1in around 97% of patients, independent of the severity (classically ranked into types I–III). The high genetic homogeneity, coupled with the excellent results of presymptomatic treatments of patients with each of the three disease-modifying therapies available, makes SMA one of the golden candidates to genetic newborn screening (NBS) (SMA-NBS). The implementation of SMA in NBS national programmes occurring in some countries is an arising new issue that the scientific community has to address. We report here the results of the first Italian SMA-NBS project and provide some proposals for updating the current molecular diagnostic scenario.

Methods

The screening test was performed by an in-house-developed qPCR assay, amplifyingSMN1andSMN2. Molecular prognosis was assessed on fresh blood samples.

Results

We found 15 patients/90885 newborns (incidence 1:6059) having the followingSMN2genotypes: 1 (one patient), 2 (eight patients), 2+c.859G>C variant (one patient), 3 (three patients), 4 (one patient) or 6 copies (one patient). Six patients (40%) showed signs suggestive of SMA at birth. We also discuss some unusual cases we found.

Conclusion

The molecular diagnosis of SMA needs to adapt to the new era of the disease with specific guidelines and standard operating procedures. In detail, SMA diagnosis should be felt as a true medical urgency due to therapeutic implications;SMN2copy assessment needs to be standardised; commercially available tests need to be improved for higherSMN2copies determination; and theSMN2splicing-modifier variants should be routinely tested in SMA-NBS.
Percutaneous sclerotherapy for head and neck lymphatic malformations in neonates and infants ≤12 months of age
Authors: Caton M Travis , Duvvuri Madhavi , Baker Amanda , Smith Eric R , Narsinh Kazim H , Amans Matthew R , Hetts Steven W , Higashida Randall T , Cooke Daniel L , Dowd Christopher F
Published: November 2022

Background

Percutaneous sclerotherapy is an effective treatment for lymphatic malformations (LM) of the head and neck in adults. The purpose of this study was to examine the indications and efficacy of sclerotherapy for head/neck LM in the neonate and infant population.

Methods

We retrospectively reviewed patients treated with percutaneous sclerotherapy for LM of the head/neck at age ≤12 months at a single vascular anomalies clinic. The clinical, anatomic, and technical aspects of each treatment, complications, and post-treatment clinical and imaging outcomes were analyzed.

Results

22 patients underwent 36 treatments during the first year of life. Median age at first treatment was 6.2 months (range 2–320 days). Severe airway compromise was the most frequent indication for treatment (31.8%). Sclerosants included doxycycline (80.5%), sodium tetradecyl sulfate (55.5%), bleomycin (11.1%) and ethanol (2.8%). There were no immediate procedure-related complications; sclerosant-related laboratory complications included transient metabolic acidosis (8.3%) and hemolytic anemia (5.5%). Median follow-up was 3.7 years (IQR 0.6–4.8). 47.6% of patients showed >75% lesion size reduction and 19.0% showed minimal response (<25% improvement). At last follow-up, 71.4% of children were developmentally normal and asymptomatic, 23.8% had recurring symptoms, and 4.8% required permanent tracheostomy. Patients with ongoing symptoms or limited response to percutaneous sclerotherapy (33.3%) were treated with long-term sirolimus.

Conclusions

Percutaneous sclerotherapy is a safe and effective treatment for symptomatic LM of the head and neck in neonates and infants. Treatment strategy and management of recurrent symptoms requires consensus from an experienced, multidisciplinary team.
Intermuscular adipose tissue in patients with systemic lupus erythematosus
Authors: Gamboa Jorge Luis , Carranza-León Daniel , Crescenzi Rachelle , Pridmore Michael , Peng Dungeng , Marton Adriana , Oeser Annette , Chung Cecilia P , Titze Jens , Stein Charles Michael , Ormseth Michelle
Published: November 2022

Objective

Patients with SLE frequently have debilitating fatigue and reduced physical activity. Intermuscular adipose tissue (IMAT) accumulation is associated with reduced physical exercise capacity. We hypothesised that IMAT is increased in patients with SLE and associated with increased fatigue, reduced physical activity and increased inflammation.

Methods

In a cross-sectional study, 23 patients with SLE and 28 control participants were evaluated. IMAT was measured in the calf muscles using sequentialT1-weighted MRI. Patient-reported physical activity and fatigue were measured and a multiplex proteomic assay was used to measure markers and mediators of inflammation.

Results

IMAT accumulation (percentage of IMAT area to muscle area) was significantly higher in SLE versus control participants (7.92%, 4.51%–13.39% vs 2.65%, 1.15%–4.61%, median, IQR, p<0.001) and remained significant after adjustment for age, sex, race and body mass index (p<0.001). In patients with SLE, IMAT accumulation did not differ significantly among corticosteroid users and non-users (p=0.48). In the study cohort (patients and controls), IMAT was positively correlated with self-reported fatigue score (rho=0.52, p<0.001) and inversely correlated with self-reported walking distance (rho=−0.60, p<0.001). Several markers of inflammation were associated with IMAT accumulation in patients with SLE, and gene ontology analysis showed significant enrichment for pathways associated with macrophage migration and activation in relation to IMAT.

Conclusion

Patients with SLE have greater IMAT accumulation than controls in the calf muscles. Increased IMAT is associated with greater fatigue and lower physical activity. Future studies should evaluate the effectiveness of interventions that improve muscle quality to alleviate fatigue in patients with SLE.
Extensive stage small cell lung cancer (ES-SCLC) and palliative care disparities: a national cancer database study
Authors: Khullar Karishma , Plascak Jesse J , Habib Muhammad Hamza , Nagengast Samantha , Parikh Rahul R
Published: November 2022

Objectives

Literature on disparities in palliative care receipt among extensive stage small cell lung cancer (ES-SCLC) patients is scarce. The purpose of this study was to examine disparities in palliative care receipt among ES-SCLC patients.

Methods

Patients aged 40 years or older diagnosed with ES-SCLC between 2004 and 2015 in the National Cancer DataBase (NCDB) were eligible. Two palliative care variables were created: (1) no receipt of any palliative care and (2) no receipt of pain management-palliative care. The latter variable indicated pain management receipt among those who received any palliative care. Log binomial regression models were constructed to calculate risk ratios by covariates. Unadjusted and mutually adjusted models were created for both variables.

Results

Among 83 175 patients, the risk of no palliative care receipt was higher among Blacks compared with Whites in unadjusted and adjusted models (both model HRs 1.02; 95% CIs 1.00 to 1.03, p<0.05). Patients older than 59 years were at a higher risk of not receiving palliative care than younger patients (HR 1.02; 95% CI 1.01 to 1.03 for 59–66, HR 1.04; 95% CI 1.03 to 1.05 for 66–74, HR 1.06; 95% CI 1.05 to 1.08 for >74). Among 19 931 patients, the risk of no pain management-palliative care was higher among black patients on unadjusted analysis (HR 1.02; 95% CI 1.00 to 1.03, p<0.05). Patients between 66 and 74 years were at a higher risk of not receiving pain management-palliative care than patients younger than 59 years (HR 1.02; 95% CI 1.00 to 1.03, p<0.05).

Conclusions

Significant disparities exist in palliative care receipt among ES-SCLC patients.
Wildfire in western Oregon increases stream temperatures, benthic biofilms, and juvenile coastal cutthroat trout size and densities with mixed effects on adult trout and coastal giant salamanders
Authors: Swartz Allison , Warren Dana
Published: November 2022

Wildfire has become increasingly common and severe across forested landscapes. Shortly after wildfire, loss of riparian cover along streams and subsequent increases in light can elevate stream temperatures, a key control on metabolic rates of biota. Increased light can also increase autotrophic basal resource availability with potential bottom-up effects. We evaluated wildfire impacts on aquatic ecosystems in a replicated Before-After Control-Impact study 1 year after a severe wildfire in western Oregon, U.S. Stream temperature, chlorophyll a accrual, and age-0 coastal cutthroat trout size, density, and biomass increased in all three burned streams relative to changes in three unburned references. When streams were evaluated collectively, fire did not have an effect on larger vertebrate density or biomass. However, considering streams individually, two severely burned sites had substantial temperature increases and declines in larger vertebrate density and biomass, but the moderately burned site had modest temperature increases and adult cutthroat trout and Pacific giant salamanders increased. The loss of riparian canopies post-fire increased temperature and algae, but fish responses varied with age class and larger vertebrate responses were inconsistent.
Nature or nurture: a genetic basis for the behavioral selection of depth in siscowet and lean lake char (Salvelinus namaycush) ecomorphs
Authors: Goetz Frederick , Sitar Shawn , Seider Michael , Jasonowicz Andrew
Published: November 2022

Leans and siscowets are lake char ecomorphs in Lake Superior that exhibit distinct depth selection behavior in the wild with leans occupying shallow (<50 m) depths and undergoing small vertical movements. In contrast, siscowets exhibit several types of depth selection behavior but generally remain at great depths (>80 m) and undergo extreme vertical movements. The present study used movement and temperature data from popup satellite archival tags (PSATs) to test the hypothesis that the difference in depth selection behavior of leans and siscowets is a genetic trait. Laboratory leans and siscowets produced from wild gametes taken from Lake Superior and reared in a common garden study for nine years were tagged with PSATs and released in southern Lake Superior. Tagged siscowets remained deep after release and exhibited extensive vertical movements. Most tagged leans remained <50 m after deployment and exhibited smaller vertical movements. Overall, the depths and temperatures occupied by the laboratory ecomorphs were significantly different throughout the deployment and the results support the hypothesis that depth selection in lake char ecomorphs is heritable.
Design parameter optimization of a CPU heat sink using numerical simulation for steady-state thermal analysis and CFD-modeling
Authors: Iglin Pavel , Iglina Tatyana , Pashchenko Dmitry
Published: November 2022

This paper deals with the design of a CPU cooling system using a novel numerical modelling approach based on automatic calculation in a commercial software. A research object is an aluminium CPU heat sink with a thermal design power of 50 W with a new fin design. A numerical model of the cooling process has been developed, and the heat sink efficiency has been investigated. The main goal of optimization was to get the minimum temperature of the CPU processor at the minimum mass of the heat sink. The comparative analysis of the results that obtained via three methods (screening, adaptive multiple-objective, multi-objective genetic algorithm) was performed. This analysis showed that screening was the least time-consuming method, but it did not provide the required solution. Adaptive multiple-objective and multi-objective genetic algorithm solutions show similar results but significantly differ in time. It was established that the adaptive multiple-objective method is the best method for the heat sink optimization task. At the determined optimal design parameter, the CPU temperature is in the range 304–307 K, while the mass was 81–87 g. In comparison, the heat sink mass before optimization of the design parameters was 93 g at the CPU temperature of 309–311 K.
On the use of majority for investigating primeness of 3-permutability
Authors: Gyenizse Gergő , Maróti Miklós , Zádori László
Published: November 2022

We have recently published a result that [Formula: see text]-permutability is not join-prime in the lattice of interpretability types of varieties whenever [Formula: see text]. In the proof, we showed that if [Formula: see text], then the join of a properly chosen finitely generated non-[Formula: see text]-permutable variety and the variety [Formula: see text] defined by the majority identities is [Formula: see text]-permutable. In the present note, we prove that the join of any locally finite non-3-permutable variety with [Formula: see text] is non-3-permutable. We also prove that the join of any non-2-permutable variety with [Formula: see text] is non-2-permutable. Our non-3-permutable result gives that one has to use a nonlocally finite non-3-permutable variety [Formula: see text] if they want to prove that 3-permutability is not join-prime by arguing that [Formula: see text] is 3-permutable.
Functional reducts of the countable atomless Boolean algebra
Authors: Bodor Bertalan , Kalina Kende , Szabó Csaba
Published: November 2022

For an algebra [Formula: see text] the algebra [Formula: see text] is called a functional reduct if each [Formula: see text] is a term function of [Formula: see text]. We classify the functional reducts of the countable atomless Boolean algebra up to first-order interdefinability. That is, we consider two functional reducts the “same” if their group of automorphisms is the same. We show that there are 13 such reducts and describe their structures and group of automorphisms.
An Extended Necessity Measure Maximisation Incorporating the Trade-Off between Robustness and Satisfaction in Fuzzy LP Problems
Authors: Gao Zhenzhong , Inuiguchi Masahiro
Published: November 2022

When some coefficients of the constraints are uncertain with only their possible ranges being given, a conventional linear programming (LP) problem can be generalised to the one with set-inclusive constraints. We consider the case where the possible ranges are given by fuzzy sets in this paper. The set-inclusive constraints with fuzzy coefficients have been treated by a necessity measure. However, the usual necessity measure cannot express well the decision-maker’s requirement about the trade-off between the robustness level and the satisfaction level of the constraints. We extend the necessity measure to incorporate the trade-off between the robustness level and the satisfaction level of the constraints. We apply the extended necessity measure to LP problems with fuzzy coefficients. After the problem is formulated and reduced to the conventional programming problem, we propose a solution algorithm. Numerical examples are given to illustrate the proposed approach.
Data-Driven Information Management Method of Power Supply Chains Using Mobile Cloud Computing
Authors: Ma Jingze , Zhan Guoye , Yang Fan , Chen Xingpei
Published: November 2022

Based on the spring, spring MVC and MyBatis structures of the cloud platform SSM framework, an information management platform for power grid material supply chain is built. The data layer uses a variety of sensors to collect power grid material supply chain information, and the information is fed back to the data storage layer after being integrated by the logical reorganization function of the persistence layer. The data storage layer uses the multi-sensor supply chain information fusion method based on paste progress to fuse the information and store it in the database. The business logic layer calls the information in the database and uses the improved k-means clustering algorithm to detect the abnormal supply chain data information. After calculation and data control by the control layer, the data management results are displayed through the presentation layer. The experimental results show that the absolute error of data fusion is very low. It can effectively cluster data information and distinguish outlier anomaly information at the same time, and the effect of information management is good.
Towards Intelligent Control of Beaconing Power and Beaconing Rate in Vehicular Ad Hoc Networks
Authors: Ait Omar Driss , Garmani Hamid , El Amrani Mohamed , Azougaghe Es-said , Baslam Mohamed , Jourhmane Mostafa
Published: November 2022

In this paper, to avoid congestion in the wireless channel of vehicular ad hoc networks (VANETs), a joint beaconing rate and beaconing power based on game theory are proposed in this paper. The game is formulated as a non-cooperative game, a Bayesian game, and a cooperative game. Three distributed and iterative algorithms (Best Response Algorithm, Fictitious Play Algorithm, and Cooperative Bargaining Algorithm) are proposed for computing the beaconing power and beaconing rate of each vehicle. Extensive simulations show the convergence of a proposed algorithm to the equilibrium beaconing power and beaconing rate and give some insights on how the game parameters may vary the game outcome.
Secondary transpose of matrix and generalized inverses
Authors: Varkady Savitha , Purushothama Divya Shenoy , Kelathaya Umashankara , Bapat Ravindra B
Published: November 2022

In this paper, several existing results related to secondary transpose are critically reviewed and a result analogous to spectral decomposition theorem is obtained for a real secondary symmetric matrix. Noting that Moore–Penrose inverse with reference to secondary transpose involution, namely [Formula: see text]-g inverse, need not always exist, we explore a few necessary sufficient conditions for the existence of such Moore–Penrose inverse. Further, we provide expressions and determinantal formula to compute the same.
Projective rigidity and Alexander polynomials of certain nodal hypersurfaces
Authors: Escudero Juan García
Published: November 2022

We present nodal algebraic hypersurfaces in the complex projective space which are projectively rigid. Defects and Alexander polynomials associated with the hypersurfaces are obtained. There are families of nodal hypersurfaces with nontrivial Alexander polynomials and nodal threefolds with projective rigidity which are potentially infinite.
Gamma ray bursters and black holes in gravity’s rainbow
Authors: Akram Moh Vaseem , Bhat Imtiyaz Ahmad , Aziz Anver
Published: November 2022

In this paper, we analyze the modification to the thermodynamics of a Schwarzschild black hole and a Kerr black hole due to gravity’s rainbow. The metric for these black holes will be made energy dependent. This will be done by using rainbow functions motivated from the hard spectra from gamma-ray bursters at cosmological distances. This modification of the metric by these rainbow functions will in turn modify the temperature and entropy of these black holes. We will also discuss how this affects the formation of virtual black holes.
Cosmic evolution of holographic dark energy in f(Q,T) gravity
Authors: Mandal S. , Singh A. , Chaubey R.
Published: November 2022

In this paper, we investigate the dynamic evolution of universe in the models of holographic dark energy with [Formula: see text] gravity framework where, [Formula: see text] is the non-metricity scalar and [Formula: see text] is the energy–momentum tensor trace. We have considered [Formula: see text] framework and investigated the evolution of cosmological quantities like energy density, equation of state (EoS) parameter and classical stability parameter with redshift. We parameterize the deceleration parameter and confront the Hubble parameter with the observational data. We investigate for the late-time accelerated expansion of universe and discuss the stability of the model by using adiabatic sound speed squared parameter. A comparison among these derived models suggest that the Renyi holographic dark energy model with GO cutoff satisfies the observational constraint of Planck+SNe+BAO on EoS parameter at present time as compared to other models. Diagnostic tools such as Statefinders and Om diagnostic have been used to classify the dark energy evolution regions.
Petrogenesis of the Limerick Igneous Suite: insights into the causes of post-eruptive alteration and the magmatic sources underlying the Iapetus Suture in SW Ireland
Authors: Slezak Paul , Hitzman Murray W. , van Acken David , Dunlevy Eoin , Chew David , Drakou Foteini , Holdstock Mark
Published: November 2022

The Limerick Igneous Suite (LIS) in County Limerick, SW Ireland, contains two distinct basaltic igneous units: the Knockroe and Knockseefin, which are expressed as hypabyssal intrusions, porphyritic dykes, diatremes, lava flows, agglomerates and tuffs. These units make up two distinct evolutionary trends: the Knockroe igneous units which range from alkaline basalts to trachyandesites, and the Knockseefin igneous units which range from alkaline basalts to basanites. U‒Pb dating of apatite establishes a primary crystallization age of
c.
350 Ma for the Knockroe units. Strontium and Nd isotopes from the least-altered Knockroe bulk rock samples range over 0.70301–0.70454 and 0.512457–0.512493, respectively. The Sr isotopes for the least-altered Knockseefin samples are similar, ranging over 0.70325–0.70386, but the Nd values are slightly more radiogenic, spanning 0.512431–0.512437. Altered samples are buffered against changes in Nd, but some show excursions towards radiogenic Sr, suggesting contamination from Carboniferous seawater and/or introduction of Rb. Rb–Sr calculations conducted on altered Knockroe samples returned ages within uncertainty of the U‒Pb dates. The bulk rock isotope values, normalized trace element plots as well as Zr/Sm, Ce/Pb and Nb/U values demonstrate the LIS is comparable to ocean island basalts and Ce/Y and Zr/Nb values suggest the units likely originated from low degrees of partial melting likely caused by extension related to the amalgamation of Laurussia and Gondwana.

Supplementary material:
ESM 1, whole rock geochemistry data; ESM 2, apatite chemistry and geochronology data; and ESM 3, supplementary figures are available at
https://doi.org/10.6084/m9.figshare.c.6297395
Global perspectives of diversity, equity, and inclusion
Authors: Barroso L. A. , Choudhury T. , Gupta M. , Olukotun O. , Popa R. A. , Song D. , Patterson David A.
Published: November 2022

ACM luminaries describe how their experiences with DEI issues vary between the different continents where they have lived.
The evolution of mathematical software
Authors: Dongarra Jack J.
Published: November 2022

Tracing how software and algorithms follow the hardware.
Deception Detection Within and Across Domains: Identifying and Understanding the Performance Gap
Authors: Panda Subhadarshi , Levitan Sarah
Published: November 2022

NLP approaches to automatic deception detection have gained popularity over the past few years, especially with the proliferation of fake reviews and fake news online. However, most previous studies of deception detection have focused on single domains. We currently lack information about how these single-domain models of deception may or may not generalize to new domains. In this work, we conduct empirical studies of cross-domain deception detection in five domains to understand how current models perform when evaluated on new deception domains. Our experimental results reveal a large gap between within and across domain classification performance. Motivated by these findings, we propose methods to understand the differences in performances across domains. We formulate five distance metrics that quantify the distance between pairs of deception domains. We experimentally demonstrate that the distance between a pair of domains negatively correlates with the cross-domain accuracies of the domains. We thoroughly analyze the differences in the domains and the impact of fine-tuning BERT based models by visualization of the sentence embeddings. Finally, we utilize the distance metrics to recommend the optimal source domain for any given target domain. This work highlights the need to develop robust learning algorithms for cross-domain deception detection that generalize and adapt to new domains and contributes toward that goal.
The context problem in artificial intelligence
Authors: Denning Peter J. , Arquilla John
Published: November 2022

The artificial intelligence design challenge of teaming humans and machines is difficult because machines cannot read the context of use.
Five Facets of 6G: Research Challenges and Opportunities
Authors: Shen Li-Hsiang , Feng Kai-Ten , Hanzo Lajos
Published: November 2022

While the fifth-generation systems are being rolled out across the globe, researchers have turned their attention to the exploration of radical next-generation solutions. At this early evolutionary stage, we survey five main research facets of this field, namelyFacet 1: next-generation architectures, spectrum, and services; Facet 2: next-generation networking; Facet 3: Internet of Things; Facet 4: wireless positioning and sensing; and Facet 5: applications of deep learning in 6G networks.In this article, we provide a critical appraisal of the literature of promising techniques ranging from the associated architectures, networking, and applications, as well as designs. We portray a plethora of heterogeneous architectures relying on cooperative hybrid networks supported by diverse access and transmission mechanisms. The vulnerabilities of these techniques are also addressed and carefully considered for highlighting the most of promising future research directions. Additionally, we list a rich suite of learning-driven optimization techniques. We conclude by observing the evolutionary paradigm shift that has taken place from pure single-component bandwidth efficiency, power efficiency, or delay optimization toward multi-component designs, as exemplified by the twin-component ultra-reliable low-latency mode of the fifth-generation system. We advocate a further evolutionary step toward multi-component Pareto optimization, which requires the exploration of the entire Pareto front of all optimal solutions, where none of the components of the objective function may be improved without degrading at least one of the other components.
Similarity-based Web Element Localization for Robust Test Automation
Authors: Nass Michel , Alégroth Emil , Feldt Robert , Leotta Maurizio , Ricca Filippo
Published: November 2022

Non-robust (fragile) test execution is a commonly reported challenge in GUI-based test automation, despite much research and several proposed solutions. A test script needs to be resilient to (minor) changes in the tested application but, at the same time, fail when detecting potential issues that require investigation. Test script fragility is a multi-faceted problem. However, one crucial challenge is how to reliably identify and locate the correct target web elements when the website evolves between releases or otherwise fail and report an issue. This article proposes and evaluates a novel approach called similarity-based web element localization (Similo), which leverages information from multiple web element locator parameters to identify a target element using a weighted similarity score. This experimental study compares Similo to a baseline approach for web element localization. To get an extensive empirical basis, we target 48 of the most popular websites on the Internet in our evaluation. Robustness is considered by counting the number of web elements found in a recent website version compared to how many of these existed in an older version. Results of the experiment show that Similo outperforms the baseline; it failed to locate the correct target web element in 91 out of 801 considered cases (i.e., 11%) compared to 214 failed cases (i.e., 27%) for the baseline approach. The time efficiency of Similo was also considered, where the average time to locate a web element was determined to be 4 milliseconds. However, since the cost of web interactions (e.g., a click) is typically on the order of hundreds of milliseconds, the additional computational demands of Similo can be considered negligible. This study presents evidence that quantifying the similarity between multiple attributes of web elements when trying to locate them, as in our proposed Similo approach, is beneficial. With acceptable efficiency, Similo gives significantly higher effectiveness (i.e., robustness) than the baseline web element localization approach.
ColBERT-PRF: Semantic Pseudo-Relevance Feedback for Dense Passage and Document Retrieval
Authors: Wang Xiao , MacDonald Craig , Tonellotto Nicola , Ounis Iadh
Published: November 2022

Pseudo-relevance feedback mechanisms, from Rocchio to the relevance models, have shown the usefulness of expanding and reweighting the users’ initial queries using information occurring in an initial set of retrieved documents, known as the pseudo-relevant set. Recently, dense retrieval – through the use of neural contextual language models such as BERT for analysing the documents’ and queries’ contents and computing their relevance scores – has shown a promising performance on several information retrieval tasks still relying on the traditional inverted index for identifying documents relevant to a query. Two different dense retrieval families have emerged: the use of single embedded representations for each passage and query, e.g., using BERT’s [CLS] token, or via multiple representations, e.g., using an embedding for each token of the query and document (exemplified by ColBERT). In this work, we conduct the first study into the potential for multiple representation dense retrieval to be enhanced using pseudo-relevance feedback and present our proposed approach ColBERT-PRF. In particular, based on the pseudo-relevant set of documents identified using a first-pass dense retrieval, ColBERT-PRF extracts the representative feedback embeddings from the document embeddings of the pseudo-relevant set. Among the representative feedback embeddings, the embeddings that most highly discriminate among documents are employed as the expansion embeddings, which are then added to the original query representation. We show that these additional expansion embeddings both enhance the effectiveness of a reranking of the initial query results as well as an additional dense retrieval operation. Indeed, experiments on the MSMARCO passage ranking dataset show that MAP can be improved by up to 26% on the TREC 2019 query set and 10% on the TREC 2020 query set by the application of our proposed
ColBERT-PRF
method on a ColBERT dense retrieval approach.We further validate the effectiveness of our proposed pseudo-relevance feedback technique for a dense retrieval model on MSMARCO document ranking and TREC Robust04 document ranking tasks. For instance,
ColBERT-PRF
exhibits up to 21% and 14% improvement in MAP over the ColBERT E2E model on the MSMARCO document ranking TREC 2019 and TREC 2020 query sets, respectively. Additionally, we study the effectiveness of variants of the
ColBERT-PRF
model with different weighting methods. Finally, we show that
ColBERT-PRF
can be made more efficient, attaining up to 4.54× speedup over the default
ColBERT-PRF
model, and with little impact on effectiveness, through the application of approximate scoring and different clustering methods.
Reminiscences on Influential Papers
Authors: Özcan Fatma , Tian Yuanyuan
Published: November 2022

This issue's contributors are two women who have been extremely influential mentors in my life. I feel privileged that I had the chance to work with them during my time at IBM Almaden. So I asked what influenced them. Enjoy reading!
The Formidable Mid-Career Crisis
Authors: Ailamaki Anastasia
Published: November 2022

My high school grades were top except for one subject: composition. Free text was (and still is) my absolute nightmare. After high school I only had to do technical writing, which is much easier: it boils down to math. Fact, supporting evidence, implication, which leads to another fact, repeat. So, when Tamer asked me to write a piece about mid-career challenges, I was excited at first, and then I was terrified. I wrote five outlines and veto'ed them all. "I am not good at this," I wanted to say, "ask somebody else!" But, then I remembered - this happens every time I get into unknown territory.
Characterizing I/O in Machine Learning with MLPerf Storage
Authors: Balmau Oana
Published: November 2022

Data is the driving force behind machine learning (ML) algorithms. The way we ingest, store, and serve data can impact the performance of end-to-end training and inference significantly [11]. However, efficient storage and pre-processing of training data has received far less focus in ML compared to efforts in building specialized software frameworks and hardware accelerators. The amount of data that we produce is growing exponentially, making it expensive and difficult to keep entire training datasets in main memory. Increasingly, ML algorithms will need to access data from persistent storage in an efficient way.
Lipid Droplets: Packing Hydrophobic Molecules Within the Aqueous Cytoplasm
Authors: Guzha Athanas , Whitehead Payton , Ischebeck Till , Chapman Kent D.
Published: November 2022

Lipid droplets, also known as oil bodies or lipid bodies, are plant organelles that compartmentalize neutral lipids as a hydrophobic matrix covered by proteins embedded in a phospholipid monolayer. Some of these proteins have been known for decades, such as oleosins, caleosins, and steroleosins, whereas a host of others have been discovered more recently with various levels of abundance on lipid droplets, depending on the tissue and developmental stage. In addition to a growing inventory of lipid droplet proteins, the subcellular machinery that contributes to the biogenesis and degradation of lipid droplets is being identified and attention is turning to more mechanistic questions regarding lipid droplet dynamics. While lipid droplets are mostly regarded as storage deposits for carbon and energy in lipid-rich plant tissues such as seeds, these organelles are present in essentially all plant cells, where they display additional functions in signaling, membrane remodeling, and the compartmentalization of a variety of hydrophobic components. Remarkable metabolic engineering efforts have demonstrated the plasticity of vegetative tissues such as leaves to synthesize and package large amounts of storage lipids, which enable future applications in bioenergy and the engineering of high-value lipophilic compounds. Here, we review the growing body of knowledge about lipid droplets in plant cells, describe the evolutionary similarity and divergence in their associated subcellular machinery, and point to gaps that deserve future attention.
Gas-Phase Computational Spectroscopy: The Challenge of the Molecular Bricks of Life
Authors: Barone Vincenzo , Puzzarini Cristina
Published: November 2022

Gas-phase molecular spectroscopy is a natural playground for accurate quantum-chemical computations. However, the molecular bricks of life (e.g., DNA bases or amino acids) are challenging systems because of the unfavorable scaling of quantum-chemical models with the molecular size (active electrons) and/or the presence of large-amplitude internal motions. From the theoretical point of view, both aspects prevent the brute-force use of very accurate but very expensive state-of-the-art quantum-chemical methodologies. From the experimental point of view, both features lead to congested gas-phase spectra, whose assignment and interpretation are not at all straightforward. Based on these premises, this review focuses on the current status and perspectives of the fully a priori prediction of the spectral signatures of medium-sized molecules (containing up to two dozen atoms) in the gas phase with special reference to rotational and vibrational spectroscopies of some representative molecular bricks of life.
Approximate Methods for Bayesian Computation
Authors: Craiu Radu V. , Levi Evgeny
Published: November 2022

Rich data generating mechanisms are ubiquitous in this age of information and require complex statistical models to draw meaningful inference. While Bayesian analysis has seen enormous development in the last 30 years, benefitting from the impetus given by the successful application of Markov chain Monte Carlo (MCMC) sampling, the combination of big data and complex models conspire to produce significant challenges for the traditional MCMC algorithms. We review modern algorithmic developments addressing the latter and compare their performance using numerical experiments.
Effects of Standardized Brazilian Green Propolis Extract (EPP-AF®) on Inflammation in Haemodialysis Patients: A Clinical Trial
Authors: Duarte Silveira Marcelo Augusto , Malta-Santos Hayna , Rebouças-Silva Jéssica , Teles Flávio , Batista dos Santos Galvão Erica , Pinto de Souza Sergio , Dantas Dutra Fábio Ricardo , Dantas Gomes Marcel Miranda , Teixeira Maurício Brito , Miranda Rebelo da Conceição Luis Filipe , Nascimento Carolina Sa , Vasques Nonaka Carolina Kymie , Cezar Rodrigo Silva , Pena Batista Paulo Benigno , Berretta Andresa Aparecida , Borges Valeria M. , da Hora Passos Rogerio
Published: November 2022

Background. Patients on haemodialysis (HD) present a significant inflammatory status, which has a pronounced negative impact on their outcomes. Propolis is a natural resin with anti-inflammatory and immunomodulatory properties. We assessed the safety and impact of a standardized Brazilian green propolis extract (EPP-AF®) on the inflammatory status in patients under conventional HD. Methods. Patients were assigned to receive 200 mg/day of EPP-AF® for 4 weeks followed by 4 weeks without the drug, and changes in plasma levels of interleukins (ILs), interferon gamma (IFN-γ), tumour necrosis factor-alpha (TNF-α), and high-sensitivityc-reactive protein (HsCRP) were measured. A heatmap was used to illustrate trends in data variation. Results. In total, 37 patients were included in the final analysis. Patients presented an exacerbated inflammatory state at baseline. During EPP-AF® use, there was a significant reduction in IFN-γ (

p
=
0.005

), IL-13 (

p
=
0.04

2), IL-17 (

p
=
0.039

), IL-1ra (

p
=
0.008

), IL-8 (

p
=
0.009

), and TNF-α (

p
 
<
 
0.001

) levels compared to baseline, and significant changes were found in Hs-CRP levels. The heatmap demonstrated a pattern of pronounced proinflammatory status at baseline, especially in patients with primary glomerulopathies, and a clear reduction in this pattern during the use of EPP-AF®. There was a tendency to maintain this reduction after suspension of EPP-AF®. No significant side effects were observed. Conclusion. Patients under haemodialysis presented a pronounced inflammatory status, and EPP-AF® was demonstrated to be safe and associated with a significant and maintained reduction in proinflammatory cytokines in this population. This trial is registered with Clinicaltrials.gov NCT04072341.
Effects of Feeding Frequency for Nile Tilapia Fingerlings (Oreochromis niloticus)
Authors: Fava Aldo Felipe , de Souza Bezerra Gildete , Neu Dacley Hertes , Bittencourt Fabio , Signor Altevir , Carvalho Kerolay Valadão , Gomes Ricacio Luan Marques , Boscolo Wilson Rogério
Published: November 2022

This study is aimed at assessing the feeding frequency for tilapia fingerlings. 240 fishes were randomly distributed in 24 containers. The feeding consisted of six frequencies: 4 (F4), 5 (F5), 6 (F6), 7 (F7), 8 (F8), and 9 (F9) times a day. The weight gain was significantly higher in F5 and F6 when compared to F4 (

p
=
0.0409

and 0.0306, respectively). Feed intake and apparent feed conversion did not differ between treatments (

p
=
0.129

and

p
=
0.451

). About water quality, the nitrogen levels in the water from the treatments differed between F4 and F5 (

p
=
0.0478

) and F4 and F6 (

p
=
0.0283

) and for P between F4 and F6 (

p
=
0.0215

) and F4 and F9 (

p
=
0.0432

). The

x

2

test showed a dependence relationship between feed frequencies and the muscle fibers frequency (

p
<
22
×

10

−
17

), prevailing fibers between 10-20 micrometers in F4, F5, F6, and F7 and 30-40 in F8 and F9. The area of the hepatocytes differed only between F5 and F9, while the nucleus area did not. Partial net revenue differed in 10% between F5 and F4 (

p
=
0.0812

) and between F6 and F4 (

p
=
0.0568

). In conclusion, fingerlings fed 5 to 6 times a day have better zootechnical and partial recipes.
3D Finite Element Study of the Physiological Anchorage Control Concept on Anchorage Molars in Lingual Orthodontics
Authors: Zhao Jiayuan , Su Majing , Zhao Qian , Liu Jiajie , Wang Junbin , Wang Junjie , An Xiaoli
Published: November 2022

Objective. To study the effect of the physiological anchorage control concept on anchorage molars in lingual and labial orthodontic techniques. Methods. Three-dimensional finite element models, including the right maxillary first molar, periodontal ligament, alveolar bone, and buccal tube, were established. The models were divided into the McLaughlin–Bennett–Trevisi (MBT™) straight-wire model with 0-degree maxillary first molar axial inclination and the physiologic anchorage Speewire system (PASS) model with −7-degree maxillary first molar axial inclination. Simulated sliding retraction forces (1 N, 1.5 N, and 2 N) were loaded on the buccal side and lingual side, and retraction forces (0.5 N, 0.75 N, and 1 N) were loaded on the buccal and lingual sides simultaneously. The displacements, principal stresses, and von Mises stresses of the periodontal ligament under different conditions were derived. Results. The anchorage molars showed different degrees of rotation, tipping, intrusion, and extrusion. As the force increased, these displacement trends also increased. The mesial displacement of the buccal + lingual force loading was less than that of the other two groups. Under the same force load method, the mesial displacement of the PASS group was less than that of the MBT group. Tilt movement increases the tensile stress of the distal cervical margin and root mesial apical third and the compressive stress of the mesial cervical margin and root distal apical third. The maximum stress of the periodontal ligament was less than that of the other two groups when the lingual force was loaded. Conclusion. The physiological anchorage control concept in lingual orthodontics provides better sagittal anchorage control than in labial orthodontics, but there is no significant difference numerically. Attention should be given to the control of torsion, torque, and arch width. Tilt movement increases the PDL stress of the cervical margin and root apical third. The sliding retraction force should be loaded lingually to maintain the force value of 1∼1.5 N.
Identification of a Prognostic Pyroptostic-Related Model for Head and Neck Squamous Cell Carcinoma Based on LASSO-Cox Regression Analysis
Authors: Wu Donglei , Fan Wanting , Zhang Zheng , Tang Jianming , Zhang Chenping , Chen Weixuan , Qin Nianhong , Zheng Yuyan
Published: November 2022

Pyroptosis is associated with the biological behavior of the tumor and with tumor immunity. We investigated the effect of pyroptosis on the tumor microenvironment and tumor immunity in head and neck squamous cell carcinoma (HNSCC). RNA sequencing data and clinical information of HNSCC were downloaded from TCGA. Differentially expressed pyroptosis-related genes in HNSCC were identified between HNSCC and normal tissue. Pyroptosis-related classification of HNSCC was conducted based on consensus clustering analysis. LASSO-Cox regression analysis was used to construct a prognostic risk model-based pyroptosis-related gene. Evaluation of the immune microenvironment was conducted in prognostic risk signature based on pyroptosis-related genes. Total 22 differentially expressed pyroptosis-related genes were identified in HNSCC. Six prognostic-related genes were included to construct a LASSO regression model with a prognostic risk score = (0.133 ∗ GSDME (DFNA5) + 0.084 ∗ NOD1 + 0.039 ∗ IL6 + 0.003 ∗ IL1B + 0.084 ∗ CASP3 + 0.028 ∗ NLRP2). Higher fraction of resting memory CD4+ T cells and macrophages M1 was infiltrated in the high-risk group compared with the low-risk group in HNSCC. Furthermore, the PI3K-Akt signaling pathway and the IL-17 signaling pathways were identified to be involved in the development of high-risk HNSCC. Our study constructed a prognostic risk signature based on pyroptosis-related genes, which emphasizes the critical importance of pyroptosis in HNSCC and provided a novel perspective of HNSCC therapy.
The Impact of the Tips from Former Smokers® Campaign on Reducing Cigarette Smoking Relapse
Authors: Davis Kevin , Murphy-Hoefer Rebecca , Dutra Lauren , King Brian , Bradfield Brian , Rodes Robert , Beistle Diane , Mushtaq Nasir
Published: November 2022

Evidence-based mass-reach health communication campaigns can increase tobacco cessation, use of cessation resources such as quitlines, and change tobacco-related social norms. These interventions have been associated with a lower likelihood of cigarette smoking relapse in studies conducted internationally; however, no studies have assessed this outcome for a national campaign in the United States. This study examined the relationship between Tips from Former Smokers® (Tips®) campaign exposure and the odds of cigarette smoking relapse among adults who formerly smoked. Using data from the 2014 to 2019 Tips longitudinal campaign surveys, we estimated first episode of relapse (versus remaining a former smoker) as a function of Tips gross rating points (GRPs, a measure of media exposure). Higher levels of Tips GRPs were associated with lower odds of relapse (aOR = 0.63, 95% CI: 0.50-0.78). These results suggest that the Tips campaign may reduce smoking relapse, in addition to the established effect of increasing smoking cessation. Former smokers can be considered a secondary target audience for smoking cessation mass media campaigns, and mass media campaigns could be considered a component of smoking relapse prevention efforts.