bluuebunny/crossref_metadata_2025 huggingface dataset:
An extended [C ii] halo around a massive star-forming galaxy at z = 5.3
Authors: Lambert Trystan S , Posses A , Aravena M , Gónzalez-López J , Assef R J , Díaz-Santos T , Brisbin D , Decarli R , Herrera-Camus R , Mejía J , Ricci C
Published: October 2022

High-redshift observations are often biased towards massive and bright galaxies that are not necessarily representative of the full population. In order to accurately study galaxy evolution and mass assembly at these redshifts, observations of ‘normal’ main sequence galaxies are required. Here we present Atacama Large Millimeter/Submillimeter Array (ALMA) 0.3 arcsec resolution observations of the [C ii] emission line at 158 μm of HZ7, a main sequence galaxy at z = 5.25. Comparing to archival rest-frame UV observations taken by the Hubble Space Telescope (HST), we find strong evidence of the existence of extended [C ii] emission, which we estimate to be twice the size of the rest-frame UV emission, yielding one of the first high-redshift objects where a clear signature of a [C ii] ‘Halo’ has been detected to date. For a matched Sérsic profile with n  = 1, we measured a [C ii] effective radius of 0.50 ± 0.04 arcsec (3.07 ± 0.25 kpc) and an average rest-frame UV effective radius of 0.2 ± 0.04 arcsec (1.48 ± 0.16 kpc). The [C ii] morphology and kinematics of the system suggest a merging event resulting in a non-rotating disc system. This event could be responsible for the extended [CII] emission. Alternatively, some potential obscured emission could also explain the [C ii] to UV size ratio. These results contribute to the growing consensus with respect to the existence of extended [C ii] emission around galaxies.
The REBELS ALMA Survey: efficient Ly α transmission of UV-bright z ≃ 7 galaxies from large velocity offsets and broad line widths
Authors: Endsley Ryan , Stark Daniel P , Bouwens Rychard J , Schouws Sander , Smit Renske , Stefanon Mauro , Inami Hanae , Bowler Rebecca A A , Oesch Pascal , Gonzalez Valentino , Aravena Manuel , da Cunha Elisabete , Dayal Pratika , Ferrara Andrea , Graziani Luca , Nanayakkara Themiya , Pallottini Andrea , Schneider Raffaella , Sommovigo Laura , Topping Michael , van der Werf Paul , Hutter Anne
Published: October 2022

Recent work has shown that UV-luminous reionization-era galaxies often exhibit strong Lyman-alpha emission despite being situated at redshifts where the IGM is thought to be substantially neutral. It has been argued that this enhanced Ly α transmission reflects the presence of massive galaxies in overdense regions which power large ionized bubbles. An alternative explanation is that massive galaxies shift more of their Ly α profile to large velocities (relative to the systemic redshift) where the IGM damping wing absorption is reduced. Such a mass-dependent trend is seen at lower redshifts, but whether one exists at z ∼ 7 remains unclear owing to the small number of existing systemic redshift measurements in the reionization era. This is now changing with the emergence of [C ii]-based redshifts from ALMA. Here, we report MMT/Binospec Ly α spectroscopy of eight UV-bright (MUV ∼ −22) galaxies at z ≃ 7 selected from the ALMA REBELS survey. We detect Ly α in four of eight galaxies and use the [C ii] systemic redshifts to investigate the Ly α velocity profiles. The Ly α lines are significantly redshifted from systemic (average velocity offset = 223 km s–1) and broad (FWHM ≈ 300–650 km s−1), with two sources showing emission extending to ≈750 km s−1. We find that the broadest Ly α profiles are associated with the largest [C ii] line widths, suggesting a potential link between the Ly α FWHM and the dynamical mass. Since Ly α photons at high velocities transmit efficiently through the z = 7 IGM, our data suggest that velocity profiles play a significant role in boosting the Ly α visibility of the most UV-luminous reionization-era galaxies.
An Approximate Bayesian Computation Approach for Modeling Genome Rearrangements
Authors: Moshe Asher , Wygoda Elya , Ecker Noa , Loewenthal Gil , Avram Oren , Israeli Omer , Hazkani-Covo Einat , Pe’er Itsik , Pupko Tal
Published: October 2022

The inference of genome rearrangement events has been extensively studied, as they play a major role in molecular evolution. However, probabilistic evolutionary models that explicitly imitate the evolutionary dynamics of such events, as well as methods to infer model parameters, are yet to be fully utilized. Here, we developed a probabilistic approach to infer genome rearrangement rate parameters using an Approximate Bayesian Computation (ABC) framework. We developed two genome rearrangement models, a basic model, which accounts for genomic changes in gene order, and a more sophisticated one which also accounts for changes in chromosome number. We characterized the ABC inference accuracy using simulations and applied our methodology to both prokaryotic and eukaryotic empirical datasets. Knowledge of genome-rearrangement rates can help elucidate their role in evolution as well as help simulate genomes with evolutionary dynamics that reflect empirical genomes.
Archaeology and Material Culture of the Kingdom of Israel and the Israelites (C. 1000 – 722/21 BCE)
Authors: Greer Jonathan S.
Published: October 2022

Biblical texts describe the foundation of the kingdom of Israel (also known as the “northern kingdom”) as a secession, in which the northern tribes revolted against the installation of Rehoboam son of Solomon and appointed Jeroboam son of Nebat as their king (1 Kgs 12). The resultant kingdom of Israel is described as enduring for some two hundred years reigned by twenty kings from nine dynastic houses (though some “dynasties” are only represented by ephemeral reigns of a single king), a portrayal broadly corroborated by ancient inscriptions, Neo-Assyrian annals, and archaeology for the later 9th and 8th centuries bce, though archaeological debate surrounds the origins of the kingdom. Its end was ushered in by the devastating 733–732 bce campaigns of Tiglath-Pileser III that resulted in the annexation of the Upper Galilee, with the final blow coming in 722 or 721 in the conquest of the capital of Samaria following a siege by Shalmanesser V and then Sargon II. The geographical boundaries of the region are described in the Hebrew Bible in terms of cities affiliated with varying degrees of centralization and those boundaries fluctuated some throughout the period. The extent of the kingdom at any given time is difficult to identify archaeologically, but the heartland of the northern central hills remained stable as the capital moved from Shechem to Tirzah and eventually to Samaria under the Omrides (cf. 1 Kgs 12:25; 15:33; 16:24). The kingdom reached its first peak of power and broad geographic extent under the Omrides encompassing the Galilee, the Sharon plain, the Jezreel Valley, and the Jordan Valley as well as regions of the Transjordan. There is also biblical and extrabiblical evidence for northern control of southern regions as far as the Gulf of Aqaba that would have included important caravan routes through the Sinai. Archaeological surveys and site excavations demonstrate the regional prominence of the kingdom, although debate remains regarding the appearance of monumental architecture and other material remains as part of a larger discussion surrounding the end of the Iron Age I and the beginning of the Iron Age II. Expansion under the Omrides in the 9th century bce brought the kingdom into conflict with other regional kingdoms and the Neo-Assyrian empire, as attested in a number of significant epigraphic discoveries including the Moabite Mesha stela, the Aramean Tel Dan stela, and many neo-Assyrian inscriptions. A second and perhaps more expansive peak of power occurred under the Nimshides in the 8th century bce, especially during the reign of Jeroboam II, due to the Neo-Assyrian domination of the rival kingdom of Aram Damascus before Assyria set its sights on Samaria. Archaeological discoveries have also shed light on the wealth and economy of the Israelite kingdom and have proved essential in reconstructing religious practices, social structures, and the activities of everyday life.
The Ovide moralisé
Authors: Trachsler Richard , Endress Laura
Published: October 2022

The anonymous French Ovide moralisé is the first full translation of Ovid’s Metamorphoses, covering nearly 72,000 lines of octosyllabic verse. Its author incorporated earlier renderings of the tragic love stories of Philomela and Pyrame et Thisbé, adapted the remaining myths recounted in Ovid’s poem, and inserted additional ones for a readership no longer familiar with classical mythology. The medieval French author, however, not only translated and compiled myths, but also attempted to explain them based on the Christian four senses of Scripture. Ovid, so goes the message transmitted in the medieval adaptation, was not so much writing about Antique mythology as he was attempting to convey a Christian meaning concealed beneath the individual myths. To unveil this hidden meaning, the medieval author added exegetical interpretations to his translation—i.e., the moralisations that give the text its name and turn it into what is presumably the longest verse text in medieval French literature. Its date of composition is unknown, but it must have existed in 1328, since a manuscript of the work is mentioned in an inventory of items owned by Clemence of Hungary established the same year. Today, the text is most commonly dated between 1315 and 1325. It is thus relatively late regarding what has famously been called the aetas ovidiana of the twelfth and thirteenth centuries, which also witnessed the first adaptations of the “Matter of Rome” into vernacular languages. The literary current that explains the emergence of the Ovide moralisé is the allegorical tradition, which took off toward the end of the thirteenth century with the Roman de la Rose and gradually touched a broad array of texts. Notwithstanding its length, the Ovide moralisé enjoyed a considerable career, as some twenty preserved manuscripts and two independent prose renderings show. Its considerable literary fortune during the Middle Ages stands in sharp contrast to the relative indifference of modern critics toward the work until relatively recently. Despite the existence of a reliable edition, it was not until the late twentieth century that the Ovide moralisé began to attract scholarly interest. Much remains to be said about its manuscript tradition and manifold sources. Moreover, the Latin and vernacular glosses in some witnesses offer a field of research modern critics have only just begun to explore. Around 2007 an international consortium of scholars—Ovide en Français (OEF)—formed in order to explore different aspects of the text and to prepare a new critical edition of the Ovide moralisé. The present bibliography relies heavily on the work accomplished by this team and aims to offer an overview of the relevant areas of ongoing research, as well as outline some of the crucial and as yet unanswered questions surrounding the work.
Mystics and Mysticism
Authors: Jaffary Nora
Published: October 2022

Mystics and mysticism became a topic of interest to scholars of religion in colonial Latin America beginning in the late 1980s, particularly among those focusing on women’s spirituality. Because women were prohibited from participating in other aspects of Catholicism, including pronouncing on matters of doctrine, private, individual contemplation of God unmediated by male intercessors became an important form of female religious expression. This was evident from the High Middle Ages in Europe through the entire colonial period in Latin America. Those who engaged in this form of spirituality often sought “mystical union” with God that they experienced though ecstatic raptures and visions. These were often facilitated though severe forms of bodily mortification (fasting, sleep deprivation, and self-flagellation). Evidence of mystics’ connection to the divine was sometimes manifest in their supernatural abilities to perform miracles, to see the future, to levitate, and, paradoxically, in episodes of demonic possession as well. While some scholars initially viewed such acts as evidence of women’s acceptance of their inherently less intellectual and more corruptible nature in comparison to men, in recent decades, many scholars following Caroline Walker Bynum’s lead in the European context, see mystics as figures marginalized from traditional sources of Church power who nonetheless used their bodies, their imaginations, and their social standing within their communities to claim power and spiritual authority. In both Europe and the New World, mystics threatened the Church because of the alternative access to divine power they represented. Scholarship on mystics in Latin America has focused on such topics as the influences that important medieval and Reformation era figures like Catherine of Siena and Teresa of Ávila exerted on New World figures but has also examined how local contexts—the dynamics of race and gender, interactions with indigenous religions, and the emergence of creole patriotism—affected the production of mystics. Historians and religious scholars have also examined the confluences and divergences between those mystics whom the Catholic Church ultimately sanctioned (including Teresa, although even she came under severe ecclesiastical scrutiny) and those deemed heretical. The latter group importantly included the sect of alumbrados that emerged in Spain simultaneous to the Lutheran threat, and that was prosecuted by the courts of the Inquisition there. Witnesses and officers of the Inquisition then imported their knowledge of the same deviancy into Spanish America in the last decades of the sixteenth century and prosecuted this heresy in Mexico, Chile, and Peru.
Socialism and Labor
Authors: Holland Owen
Published: October 2022

The socialist movement emerged in Victorian Britain during the 1880s with the foundation of the Democratic Federation (later the Social Democratic Federation) in 1881, the Fabian Society in 1884, and the Socialist League in 1885. Sometimes referred to as a decade of “socialist revival,” owing to the existence of an earlier tradition of utopian socialism associated with the work of Robert Owen, the 1880s saw the establishment of political organizations that challenged the economic, social, political, and aesthetic foundations of Victorian capitalism. These organizations disagreed on questions of political strategy, but the movement, broadly defined, drew many prominent authors into its orbit, including William Morris, George Bernard Shaw, Oscar Wilde, H. G. Wells, Edward Carpenter, Henry Woodd Nevinson, Margaret Harkness, Constance Howell, Clementina Black, Olive Schreiner, Jane Hume Clapperton, Isabella Ford, Dollie Radford, Edith Nesbit, and others, as well as visual artists such as Walter Crane. An efflorescence of socialist periodicals gave rise to a rich print culture, in which fiction and poetry jostled alongside political journalism and polemic. In different ways, and across a variety of genres and styles, these writers explored questions pertinent to the movement, including the nature of post-capitalist society, the emancipation of labor, structures of Victorian patriarchy and imperialism, the economic and ethical foundations of socialism and the means of moving beyond capitalism. Some were willing to consider a revolutionary overthrow of the existing social order, while others pursued a more moderate, reform-oriented agenda. The movement’s strong emphasis on the class politics of Victorian Britain (see the Oxford Bibliographies in Victorian Literature article by Ruth Livesey, “Class”) means that there are clear continuities with the earlier working-class Chartist movement for parliamentary reform (see Kirstie Blair, “Chartism”), while the more reform-minded socialists share certain thematic concerns with the mid-century social-problem novelists (see Bethan Carney, “Social-Problem Novel”). As detailed in subsequent sections of this bibliography, socialist writers and thinkers also frequently explored ideas shared by fin-de-siècle feminists and, in some cases, developed distinctive and radical critiques of Victorian imperialism and the British Empire. Some socialist writers, notably Morris and Wells, experimented with utopian narratives as a means of speculatively imagining futures beyond capitalism, while others, such as Margaret Harkness and Henry Nevinson, inclined toward literary naturalism. The movement’s diverse print culture today offers an archive of journalistic polemic, literary experimentation and creative mediations of that much-maligned genre, propaganda.
Catholic Literature
Authors: Underwood Lucy , Gregory Eilish
Published: October 2022

Catholic literature was a diverse field in early modern England. Manuscript and printed texts were an integral part of confessional identity for English Catholics. It enabled them to establish textual communities, to participate in private meditations, practice their faith, and for women to play an active role in Catholic book and literary culture, with images and mnemonic devices in printed texts offering a way for the illiterate to participate in private meditations. Catholic literature formed part of a Europe-wide movement linked to Catholic Reform and post-Tridentine spirituality, of which English Catholic readers and authors were a part. Print and manuscript circulation of Catholic texts was aided by illicit printing presses set up across England and Europe, which reveals the growing appetite for these texts, and which were also read and responded by Protestant readers, showing the appeal of Catholic religious and spiritual texts across the confessional divide. Once perceived as of interest only to historians of “recusant” post-Reformation Catholics, Catholic writers such as Robert Southwell are now frequently included in cross-confessional general works of literary criticism, and Catholic literary culture is better recognized as an integral part of the study of early modern English literature, literary culture, print and book culture. Setting the parameters for a bibliography on this subject requires a threefold definition. We have taken “early modern” fairly broadly, covering the sixteenth to eighteenth centuries, which includes some pre-Reformation as well as post-Reformation material. “Catholic” could be defined in a number of ways which would exclude or include different texts and scholarly works. We have focused on texts of Catholic authorship, generally meaning that the author identified as a member of the Catholic Church at the time of writing; we have also prioritized subject matter, so studies of texts by Catholic authors which are not distinctively Catholic in content may not appear. Finally, “literature”: once implying simply the “literary canon” in which Catholics who wrote after the Reformation rarely appeared, appreciation of the literary elements of all kinds of texts has widened the category. We have included such genres as devotional literature and martyrology, valuable in themselves for understanding early modern religious culture, and also as context for the more “canonical” literary productions of Southwell, Dryden, or Pope. We have included a section on translation, in recognition of the increasing scholarship on literary translators (especially women) and of the importance of continental European texts and spirituality in shaping English Catholicism after the Reformation. The bibliography is set out thematically, with works covering different genres of literature grouped together, but with dedicated sections on selected individual authors. Especially in the latter, the quantity of scholarly work on this field means that this bibliography must, for reasons of space, aim to be representative rather than comprehensive.
Firm Bribery
Authors: Kim Jinsil
Published: October 2022

Bribery is defined as the illegal exchange of money or favor for a benefit distributed by a public official. Firms may engage in bribery to secure their access to governmental services or preferential treatments, especially when legally obtaining such governmental services is costly and uncertain. Bribery and facilitation payments are thus regarded as an informal method to get vital jobs done. Bribery is a key type of corruption, and the most common form of corruption. The topic and phenomenon have been studied in numerous fields such as economics, laws, politics, public policy, decision making, and management.
Cytosolic disproportionating enzyme2 is essential for pollen germination and pollen tube elongation in rice
Authors: Chen Liangke , Dong Xiangbai , Yang Huifang , Chai Yaru , Xia Yan , Tian Lihong , Qu Le Qing
Published: October 2022

Degradation of starch accumulated in pollen provides energy and cellular materials for pollen germination and pollen tube elongation. Little is known about the function of cytosolic disproportionating enzyme2 (DPE2) in rice (Oryza sativa). Here, we obtained several DPE2 knockout mutant (dpe2) lines via genomic editing and found that the mutants grew and developed normally but with greatly reduced seed-setting rates. Reciprocal crosses between dpe2 and wild-type plants demonstrated that the mutant was male sterile. In vitro and in vivo examinations revealed that the pollen of the dpe2 mutant developed and matured normally but was defective in germination and elongation. DPE2 deficiency increased maltose content in pollen, whereas it reduced the levels of starch, glucose, fructose, and adenosine triphosphate (ATP). Exogenous supply of glucose or ATP to the germination medium partially rescued the pollen germination defects of dpe2. The expression of cytosolic phosphorylase2 (Pho2) increased significantly in dpe2 pollen. Knockout of Pho2 resulted in a semi-sterile phenotype. We failed to obtain homozygous dpe2 pho2 double mutant lines. Our results demonstrate that maltose catalyzed by DPE2 to glucose is the main energy source for pollen germination and pollen tube elongation, while Pho2 might partially compensate for deficiency of DPE2.
Predicting vigilance vulnerability during 1 and 2 weeks of sleep restriction with baseline performance metrics
Authors: Lo June C , Ang Jit Wei A , Koa Tiffany B , Ong Ju Lynn , Lim Julian
Published: October 2022

Study Objectives

We attempted to predict vigilance performance in adolescents during partial sleep deprivation using task summary metrics and drift diffusion modelling measures (DDM) derived from baseline vigilance performance.

Methods

In the Need for Sleep studies, 57 adolescents (age = 15–19 years) underwent two baseline nights of 9-h time-in-bed (TIB), followed by two cycles of weekday sleep-restricted nights (5-h or 6.5-h TIB) and weekend recovery nights (9-h TIB). Vigilance was assessed daily with the Psychomotor Vigilance Task (PVT), with the number of lapses (response times ≥ 500 ms) as the primary outcome measure. The two DDM predictors were drift rate, which quantifies the speed of information accumulation and determines how quickly an individual derives a decision response, and non-decision time range, which indicates within-subject variation in physical, non-cognitive responding, e.g. motor actions.

Results

In the first week of sleep curtailment, faster accumulation of lapses was significantly associated with more lapses at baseline (p = .02), but not the two baseline DDM metrics: drift and non-decision time range (p > .07). On the other hand, faster accumulation of lapses and greater increment in reaction time variability from the first to the second week of sleep restriction were associated with lower drift (p < .007) at baseline.

Conclusions

Among adolescents, baseline PVT lapses can predict inter-individual differences in vigilance vulnerability during 1 week of sleep restriction on weekdays, while drift more consistently predicts vulnerability during more weeks of sleep curtailment.

Clinical Trial Information

Effects of Napping in Sleep-Restricted Adolescents, clinicaltrials.gov, NCT02838095. The Cognitive and Metabolic Effects of Sleep Restriction in Adolescents (NFS4), clinicaltrials.gov, NCT03333512.
Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae)
Authors: Ó Marcaigh Fionn , Kelly David J , O’Connell Darren P , Analuddin Kangkuso , Karya Adi , McCloughan Jennifer , Tolan Ellen , Lawless Naomi , Marples Nicola M
Published: October 2022

Birds of the Indo-Pacific have provided biologists with many foundational insights. This study presents evidence for strong phylogeographic structure in two sunbird species from the heart of this region, the olive-backed sunbird, Cinnyris jugularis, and the black sunbird, Leptocoma aspasia. We assessed population divergence using morphological, plumage, bioacoustic and molecular data (mitochondrial ND2/ND3). Our findings indicate that the olive-backed sunbird should be recognized as multiple species, because birds from Sulawesi and the Sahul Shelf are closely related to each other, but widely separated from those in other regions. In addition, we provide evidence for an endemic species on the Wakatobi Islands, an archipelago of deep-sea islands off south-east Sulawesi. That a small bird could exhibit a range all the way from Sulawesi to Australia, while diverging on a small archipelago within this range, illustrates the complex interplay between dispersal and speciation. Our black sunbird genetic data also suggest unrecognized population structure, despite relatively weak plumage divergence. Black sunbirds in Sulawesi are likely to be a separate species from those in New Guinea, with a mean genetic distance of 9.1%. Current taxonomy suggests these sunbird species transcend classic biogeographic barriers, but our results suggest that these barriers are not easily bypassed.
The PA profession in Israel
Authors: Ozer Roi
Published: October 2022

Implementation of physician assistants (PAs) in EDs throughout Israel began in May 2016. The profession is now showing some progress but at a relatively slow rate. This article provides an overview of Israel and its healthcare system, and describes the implementation, deployment, education, training, and scope of practice of PAs in Israel, plus recent developments and suggestions for advancing the profession.
Assessing and benchmarking equity, diversity, and inclusion in healthcare professions
Authors: Kayingo Gerald , Bradley-Guidry Carolyn , Burwell Nicole , Suzuki Sumihiro , Dorough Ramona , Bester Vanessa
Published: October 2022

Healthcare professions are among the fastest growing careers in the United States, but the issues of equity, diversity, and inclusion remain a challenge. The percentage of underrepresented minority groups is disproportionately small despite many efforts to increase workforce diversity over the past several decades. As the demographics in our nation are rapidly changing, increasing racial, ethnic, and cognitive diversity is crucial to achieving a workforce with the capacity to provide accessible and equitable healthcare. Given the growing evidence that a diverse workforce improves healthcare outcomes, fosters unique perspectives (cognitive diversity), and helps to reduce health disparities, there is an urgent need to address perennial barriers such as structural racism, biases, and stereotypes. Educational institutions should be held accountable to integrate equity, diversity, and inclusion in all aspects of healthcare professions education and practice. This article discusses potential areas for innovation and opportunities that can be leveraged in assessing and benchmarking equity, diversity, and inclusion in healthcare professions. The ability to thoroughly assess the PA profession's culture in relationship to diversity, equity, and inclusion provides an opportunity to determine how well the profession is performing, and to strategically plan for what else need to be done.
What is rilonacept's role in treating recurrent pericarditis?
Authors: Schwier Nicholas C.
Published: October 2022

The interleukin (IL)-1 antagonist rilonacept is approved by the FDA to treat recurrent pericarditis. In adults and adolescents with multiple recurrences of pericarditis, compared with placebo, rilonacept is associated with a lower risk of recurrent pericarditis, more persistent clinical response, normalized C-reactive protein within 7 days, and a higher number of days with no or minimal pericarditis symptoms. Patients receiving rilonacept could be weaned off of standard therapies for recurrent pericarditis and eventually be transitioned to rilonacept monotherapy. The most common adverse reactions to rilonacept include injection-site reactions, upper respiratory tract infections, and increased lipids. A loading dose of rilonacept is administered subcutaneously (SQ), along with weekly SQ maintenance dosing, which can be self-administered. Rilonacept is indicated for the treatment of recurrent pericarditis and reduction in risk of recurrence in patients age 12 years and older who have an elevated C-reactive protein level and significant disease burden.
Natural Language Processing CAM Algorithm Improves Delirium Detection Compared With Conventional Methods
Authors: Pagali Sandeep R. , Kumar Rakesh , Fu Sunyang , Sohn Sunghwan , Yousufuddin Mohammed
Published: October 2022

Delirium is known to be underdiagnosed and underdocumented. Delirium detection in retrospective studies occurs mostly by clinician diagnosis or nursing documentation. This study aims to assess the effectiveness of natural language processing-confusion assessment method (NLP-CAM) algorithm when compared to conventional modalities of delirium detection. A multicenter retrospective study analyzed 4351 COVID-19 hospitalized patient records to identify delirium occurrence utilizing three different delirium detection modalities namely clinician diagnosis, nursing documentation, and the NLP-CAM algorithm. Delirium detection by any of the 3 methods is considered positive for delirium occurrence as a comparison. NLP-CAM captured 80% of overall delirium, followed by clinician diagnosis at 55%, and nursing flowsheet documentation at 43%. Increase in age, Charlson comorbidity score, and length of hospitalization had increased delirium detection odds regardless of the detection method. Artificial intelligence-based NLP-CAM algorithm, compared to conventional methods, improved delirium detection from electronic health records and holds promise in delirium diagnostics.
The effect of sarcopenia and serum myokines on prognosis and survival in cirrhotic patients: a multicenter cross-sectional study
Authors: Boga Salih , Yildirim Abdullah Emre , Ucbilek Enver , Koksal Ali Riza , Sisman Sevil Tokdemir , Durak Ibrahim , Sen Ilker , Dogu Beril , Serin Erdinc , Ucbilek Ayse Bolat , Yildirim Makbule Ozge , Erturk Sukru Mehmet , Alkim Huseyin , Alkim Canan
Published: October 2022

Objective

Sarcopenia is one of the most significant contributors to morbidity in patients with chronic liver disease. Serum myokines are potential biomarkers for detecting early sarcopenia. We aimed to investigate the relationship between serum myokines and cirrhosis-related mortality in the early stages of the disease.

Methods

In total, 262 patients and 50 healthy controls were enrolled in this study, which was designed as a multicenter cross-sectional study. At the beginning of the study, sarcopenia was defined by computed tomography scans using the third lumbar vertebra skeletal muscle index. Serum myostatin, irisin, and follistatin levels, nutritional status of the patients, and muscle strength as measured by the handgrip test were recorded. Cirrhosis-related mortality and overall survival were evaluated in the fourth year of the study as the second checkpoint of cross-sectional analysis.

Results

A total of 145 (55.3%) patients were diagnosed with sarcopenia. Multivariate analysis revealed that low BMI, high levels of myostatin, and decreased irisin levels were independent predictors of sarcopenia. While serum irisin level was the most predictive parameter in terms of 4th-year cirrhosis-related mortality in the CHILD A group, serum myostatin levels were found more indicative in the CHILD BC group regardless of sarcopenia status (P < 0.001).

Conclusion

Serum myostatin levels predict sarcopenia in all stages of cirrhosis. Serum irisin levels can also be used as a potential biomarker to predict both treatable sarcopenia and cirrhosis-related mortality in CHILD A patients.
Mycolicibacterium aurantiacum sp. nov. and Mycolicibacterium xanthum sp. nov., two novel actinobacteria isolated from mangrove sediments
Authors: Pan Xinli , Li Zhe , Huang Shushi , Huang Yuanlin , Wang Qiaozhen , Tao Zhanhua , Hu Wenjin
Published: October 2022

Two novel actinobacteria with the ability to degrade kerosene, designated as B3033Tand Y57T, were isolated from mangrove sediments in Tieshan Harbour, South China Sea. Both strains are Gram-staining-positive, non-spore forming, slow-growing, oxidase-positive, non-motile and aerobic. Their major cellular fatty acids were C16 : 0and C18 : 1ω9c. Analysis of 16S rRNA gene sequences revealed the close relationship of strain B3033TtoMycobacterium kyogaenseDSM 107316T(99.4 % nucleotide identity) and strain Y57TtoMycolicibacterium chubuenseATCC 27278T(98.7 %) andMycolicibacterium rufumJS14T(98.7 %). Whole genome average nucleotide blast identity (ANI) and the digital DNA–DNA hybridization (dDDH) values between the two isolates and the type strains of species of the genusMycolicibacteriumwere lower than 94 and 45 %, respectively, which were below the threshold values of 95 % (for ANI) and 70 % (for dDDH) recommended for bacterial species differentiation. The genome sequence of B3033Tcomprised a circular 11.0 Mb chromosome with a DNA G+C content of 68.1 mol%. Y57Thad a genome size of 5.6 Mb and a DNA G+C content of 68.7 mol%. Genes involved in degradation of aromatic compounds and copper resistance were identified in the genomes of both strains that could improve their adaptive capacity to the mangrove environment. These results combined with those of chemotaxonomic analyses, MALDI-TOF MS profiles and phenotypic analyses support the affiliation of these strains to two novel species within the genusMycolicibacterium, for which we propose the namesMycolicibacterium aurantiacumsp. nov. B3033T(=KCTC 49712T=MCCC 1K04526T) andMycolicibacterium xanthumsp. nov. Y57T(=KCTC 49711T=MCCC 1K04875T) as type strains.
A NiCoT family metal transporter of Mycobacterium tuberculosis (Rv2856/NicT) behaves as a drug efflux pump that facilitates cross-resistance to antibiotics
Authors: Adhikary Anwesha , Biswal Sarmistha , Chatterjee Debasmita , Ghosh Anindya S.
Published: October 2022

Metals often act as a facilitator in the proliferation and persistence of antibiotic resistance. Efflux pumps play key roles in the co-selection of metal and antibiotic resistance. Here, we report the ability of a putative nickel/cobalt transporter (NiCoT family), Rv2856 or NicT of

Mycobacterium tuberculosis

(Mtb), to transport metal and antibiotics and identified some key amino acid residues that are important for its function. Ectopic expression of NicT in

Escherichia coli

CS109 resulted in the increase of intracellular nickel uptake. Additionally, enhanced tolerance towards several antibiotics (norfloxacin, sparfloxacin, ofloxacin, gentamicin, nalidixic acid and isoniazid) was observed with NicT overexpression in

E. coli

and

Mycobacterium smegmatis

. A comparatively lower intracellular accumulation of norfloxacin upon NicT overexpression than that of the cells without NicT indicated the involvement of NicT in an active efflux process. Although expression of NicT did not alter the sensitivity towards kanamycin, doxycycline, tetracycline, apramycin, neomycin and ethambutol, the presence of a sub-inhibitory dose of Ni2+ resulted in the manifestation of low-level tolerance towards these drugs. Further, substitution of four residues (H77I, D82I, H83L and D227I) in the conserved regions of NicT by isoleucine and leucine resulted in reduced to nearly complete loss of the transport function for both metals and antimicrobials. Therefore, the study suggests that nickel transporter Rv2856/NicT may actively export different drugs and the presence of nickel might drive the cross-resistance to some of the antibiotics.
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors
Authors: Singh Rohit , Wu Alexander P. , Mudide Anish , Berger Bonnie
Published: October 2022

Single-cell expression dynamics from differentiation trajectories or RNA velocity have the potential to reveal causal links between transcription factors (TFs) and their target genes in gene regulatory networks (GRNs). However, existing methods either neglect these expression dynamics or require cells to be ordered along a linear pseudotemporal axis, which is incompatible with branching trajectories. We introduce Velorama, an approach to causal GRN inference that represents single-cell differentiation dynamics as a directed acyclic graph (DAG) of cells constructed from pseudotime or RNA velocity measurements. In contrast to previous approaches, Velorama is able to work directly with RNA velocity-based cell-to-cell transition probabilities and enables estimates of TF interaction speeds with their target genes. On a set of synthetic datasets, Velorama substantially outperforms existing approaches, improving area under the precision-recall curve (AUPRC) by 3.7–4.8x over the next best method. Applying Velorama to four RNA velocity datasets, we uncover evidence that the speed of a TF’s interactions is tied to its regulatory function. For human corticogenesis, we find slow TFs to be linked to gliomas and co-regulate preferentially with fast TFs, while fast TFs are associated with neuropsychiatric diseases. We expect Velorama to be a critical part of the RNA velocity toolkit for investigating the causal drivers of differentiation and disease.

Software availability

https://cb.csail.mit.edu/cb/velorama
Insitutype: likelihood-based cell typing for single cell spatial transcriptomics
Authors: Danaher Patrick , Zhao Edward , Yang Zhi , Ross David , Gregory Mark , Reitz Zach , Kim Tae K. , Baxter Sarah , Jackson Shaun , He Shanshan , Henderson Dave , Beechem Joseph M.
Published: October 2022

Accurate cell typing is fundamental to analysis of spatial single-cell transcriptomics, but legacy scRNA-seq algorithms can underperform in this new type of data. We have developed a cell typing algorithm, Insitutype, designed for statistical and computational efficiency in spatial transcriptomics data.

Insitutype is based on a likelihood model that weighs the evidence from every expression value, extracting all the information available in each cell’s expression profile. This likelihood model underlies a Bayes classifier for supervised cell typing, and an Expectation-Maximization algorithm for unsupervised and semi-supervised clustering. Insitutype also leverages alternative data types collected in spatial studies, such as cell images and spatial context, by using them to inform prior probabilities of cell type calls. We demonstrate rapid clustering of millions of cells and accurate fine-grained cell typing of kidney and non-small cell lung cancer samples.
Identification of RNA-based cell-type markers for the stem cell manufacture system with a statistical scoring function
Authors: Shi Yu , Yang Weilong , Lin Haishuang , Han Li , Cai Alyssa J. , Saraf Ravi , Lei Yuguo , Zhang Chi
Published: October 2022

Cell-type biomarkers are useful in stem cell manufacture to monitor cell purification, cell quantity, and quality. However, the study on cell-type markers, specifically for stem cell manufacture, is limited. The emerging questions are which RNA transcripts can serve as biomarkers during stem cell culture, and what method can efficiently and accurately discover these biomarkers. We developed a scoring function system to identify RNA biomarkers with RNA-seq data. We applied the method to two data sets, one for extracellular RNAs (ex-RNAs) and the other for intracellular microRNAs (miRNAs). The data set have RNA-seq data of ex-RNAs from cell culture media for six different types of cells, including human embryonic stem cells. To get the RNA-seq data from intracellular miRNAs, we cultured three types of cells: human embryonic stem cells (H9), neural stem cells (NSC), hESC-derived endothelial cells (EC) and conducted small RNA-seq to their intracellular miRNAs. Using these data, we identified a set of ex-RNAs/smRNAs as candidates of biomarkers for different types of cells for cell manufacture. We also used deep-learning based prediction methods and simulated data to validate these discovered biomarkers.
QClus: A droplet-filtering algorithm for enhanced snRNA-seq data quality in challenging samples
Authors: Schmauch Eloi , Ojanen Johannes , Galani Kyriakitsa , Jalkanen Juho , Harju Kristiina , Hollmén Maija , Kokki Hannu , Gunn Jarmo , Halonen Jari , Hartikainen Juha , Kiviniemi Tuomas , Tavi Pasi , Kaikkonen Minna U. , Kellis Manolis , Linna-Kuosmanen Suvi
Published: October 2022

Single nuclei RNA sequencing (snRNA-seq) remains a challenge for many human tissues, as incomplete removal of background signal masks cell-type-specific signals and interferes with downstream analyses. Here, we present QClus, a droplet-filtering algorithm targeted toward challenging samples, using cardiac tissue as an example. QClus uses specific metrics such as cell-type-specific marker gene expression to cluster nuclei and filter empty and highly contaminated droplets, providing reliable cleaning of samples with varying number of nuclei and contamination levels. In a benchmarking analysis against seven alternative methods across six datasets consisting of 252 samples and over 1.9 million nuclei, QClus achieved the highest quality in the greatest number of samples over all evaluated quality metrics and recorded no processing failures, while robustly retaining numbers of nuclei within the expected range. QClus combines high quality, automation, and robustness with flexibility and user-adjustability, catering to diverse experimental needs and datasets.
scCobra: Contrastive cell embedding learning with domain-adaptation for single-cell data integration and harmonization
Authors: Zhao Bowen , Wei Dong-Qing , Xiong Yi , Ding Jun
Published: October 2022

The rapid development of single-cell technologies has underscored the need for more effective methods in the integration and harmonization of single-cell sequencing data. The prevalent challenge of batch effects, resulting from technical and biological variations across studies, demands accurate and reliable solutions for data integration. Traditional tools often have limitations, both due to reliance on gene expression distribution assumptions and the common issue of over-correction, particularly in methods based on anchor alignments. Here we introduce scCobra, a deep neural network tool designed specifically to address these challenges. By leveraging a deep generative model that combines a contrastive neural network with domain adaptation, scCobra effectively mitigates batch effects and minimizes over-correction without depending on gene expression distribution assumptions. Additionally, scCobra enables online label transfer across datasets with batch effects, facilitating the continuous integration of new data without retraining, and offers features for batch effect simulation and advanced multi-omic batch integration. These capabilities make scCobra a versatile data integration and harmonization tool for achieving accurate and insightful biological interpretations from complex datasets.
ROI-Finder: machine learning to guide region-of-interest scanning for X-ray fluorescence microscopy
Authors: Chowdhury M. A. Z. , Ok K. , Luo Y. , Liu Z. , Chen S. , O'Halloran T. V. , Kettimuthu R. , Tekawade A.
Published: October 2022

The microscopy research at the Bionanoprobe (currently at beamline 9-ID and later 2-ID after APS-U) of Argonne National Laboratory focuses on applying synchrotron X-ray fluorescence (XRF) techniques to obtain trace elemental mappings of cryogenic biological samples to gain insights about their role in critical biological activities. The elemental mappings and the morphological aspects of the biological samples, in this instance, the bacterium Escherichia coli (E. Coli), also serve as label-free biological fingerprints to identify E. coli cells that have been treated differently. The key limitations of achieving good identification performance are the extraction of cells from raw XRF measurements via binary conversion, definition of features, noise floor and proportion of cells treated differently in the measurement. Automating cell extraction from raw XRF measurements across different types of chemical treatment and the implementation of machine-learning models to distinguish cells from the background and their differing treatments are described. Principal components are calculated from domain knowledge specific features and clustered to distinguish healthy and poisoned cells from the background without manual annotation. The cells are ranked via fuzzy clustering to recommend regions of interest for automated experimentation. The effects of dwell time and the amount of data required on the usability of the software are also discussed.
Indirect X-ray detectors with single-photon sensitivity
Authors: Pauwels Kristof , Douissard Paul-Antoine
Published: October 2022

The new generation of synchrotron light sources are pushing X-ray detectors to their limits. Very demanding conditions with unprecedented flux and higher operating energies now require high-performance X-ray detectors combining sensitivity, efficiency and scalability. Over the years, hybrid pixel detectors have supplemented indirect detectors based on scintillation, with undeniable advantages. Such detectors based on silicon are, however, rather expensive to produce and are no more satisfying in terms of X-ray stopping power when targeting energies above 20 keV. An indirect detector with single X-ray photon sensitivity therefore offers promising opportunities for applications operating over a wide range of energies and fluxes. In this work, the performances of such an approach are investigated with state-of-the-art elements: a commercial sCMOS camera with fiber-optics plate coupling and a Gd2O2S:Tb powder-based scintillator. A simple method is presented for evaluation of the single X-ray photon detection limit and single X-ray sensitivity is demonstrated with the studied detector above 20 keV. Geant4 simulations also provide insight to better define the limiting factors. Finally, guidelines are provided for future R&D in the design and assembly of an innovative detector combining advantages of direct and indirect detection schemes.