bluuebunny/crossref_metadata_2025 huggingface dataset:
Tobacco, Cigarettes, and Women’s Status in Modern China
Authors: Benedict Carol
Published: February 2021

Cigarette smoking in the People’s Republic of China (PRC) is a highly gendered practice. The vast majority of China’s three hundred million plus smokers are men: in 2016, about 48 percent of men over age 15 were current smokers, but less than 2 percent of women smoked. The stark difference in this pattern of men and women’s smoking behavior is often attributed to lingering cultural taboos against female smoking assumed to have been in place for centuries. In fact, the virtual exclusivity of male smoking in China is of relatively recent vintage, dating only from the mid-1900s. From the 17th to the 19th centuries, smoking was socially acceptable for Chinese women. Granted, there were gendered and class differences in the location of tobacco consumption. Chinese men could smoke in public, but well-mannered women smoked privately out of view. After cigarettes were introduced into China at the end of the 19th century, some women, especially those living in coastal cities, took to smoking them rather than pipe tobacco. In the opening decades of the 20th century, the number of women who smoked cigarettes increased, but this trend was reversed in the 1930s and 1940s. After the establishment of the PRC in 1949, the number of women who smoked diminished even further such that by the 1980s, only a small percentage of women consumed tobacco products of any kind.

Many social, economic, and cultural factors contributed to the gendered pattern of smoking that emerged in China over the course of the 20th century. An essential aspect of this history was the transformation in social norms that made cigarette smoking less rather than more respectable for women as time went on. At the beginning of the century, many women were already accustomed to smoking pipe tobacco. Some women, including those who identified as forward-looking “New Women,” preferred cigarettes. However, by mid-century cigarettes came to be widely associated with a stigmatized type of New Woman known as the “Modern Girl.” Portrayed in popular culture and political rhetoric alike as extravagant and sexually promiscuous, the Modern Girl’s pursuit of luxury came to symbolize bourgeois decadence and insufficient national loyalty. These associations came forward into the PRC period and as a result, most women born after 1949 elected not to smoke at all. Major differences in male and female smoking prevalence rates persist because female smoking remains objectionable to many Chinese citizens in the 21st century.
Methodology of Macroeconometrics
Authors: Spanos Aris
Published: February 2021

The current discontent with the dominant macroeconomic theory paradigm, known as Dynamic Stochastic General Equilibrium (DSGE) models, calls for an appraisal of the methods and strategies employed in studying and modeling macroeconomic phenomena using aggregate time series data. The appraisal pertains to the effectiveness of these methods and strategies in accomplishing the primary objective of empirical modeling: to learn from data about phenomena of interest. The co-occurring developments in macroeconomics and econometrics since the 1930s provides the backdrop for the appraisal with the Keynes vs. Tinbergen controversy at center stage. The overall appraisal is that the DSGE paradigm gives rise to estimated structural models that are both statistically and substantively misspecified, yielding untrustworthy evidence that contribute very little, if anything, to real learning from data about macroeconomic phenomena. A primary contributor to the untrustworthiness of evidence is the traditional econometric perspective of viewing empirical modeling as curve-fitting (structural models), guided by impromptu error term assumptions, and evaluated on goodness-of-fit grounds. Regrettably, excellent fit is neither necessary nor sufficient for the reliability of inference and the trustworthiness of the ensuing evidence. Recommendations on how to improve the trustworthiness of empirical evidence revolve around a broader model-based (non-curve-fitting) modeling framework, that attributes cardinal roles to both theory and data without undermining the credibleness of either source of information. Two crucial distinctions hold the key to securing the trusworthiness of evidence. The first distinguishes between modeling (specification, misspeification testing, respecification, and inference), and the second between a substantive (structural) and a statistical model (the probabilistic assumptions imposed on the particular data). This enables one to establish statistical adequacy (the validity of these assumptions) before relating it to the structural model and posing questions of interest to the data. The greatest enemy of learning from data about macroeconomic phenomena is not the absence of an alternative and more coherent empirical modeling framework, but the illusion that foisting highly formal structural models on the data can give rise to such learning just because their construction and curve-fitting rely on seemingly sophisticated tools. Regrettably, applying sophisticated tools to a statistically and substantively misspecified DSGE model does nothing to restore the trustworthiness of the evidence stemming from it.
California Indians
Authors: Madley Benjamin L.
Published: February 2021

Human beings have inhabited the region known as California for at least 13,000 years, or as some believe since time immemorial. By developing technologies, honing skills, and implementing stewardship practices, California Indian communities maximized the bounty of their homelands during the precolonial period. Overall, their population grew to perhaps 310,000 people. Speaking scores of different languages, they organized themselves into at least sixty major tribes. Communities were usually politically autonomous but connected to larger tribal groups by shared languages and cultures while dense networks of economic exchange also bound tribes together.

Newcomers brought devastating change, but California Indians resisted and survived. During the Russo-Hispanic period (1769–1846), the Indigenous population fell to perhaps 150,000 people due to diseases, environmental transformation, and colonial policies. The organized mass violence and other policies of early United States rule (1846–1900) further reduced the population. By 1900, census takers counted only 15,377 California Indian people. Still, California Indians resisted. During the 1900–1953 period, the federal government continued its national Allotment Policy but initiated healthcare, land policy, education, and citizenship reforms for California Indians even as they continued to resist and their population grew. During the termination era (1953–1968), California Indians faced federal attempts to obliterate them as American Indians. Finally, California Indian people achieved many hard-won victories during the self-determination era (1968–present).
African American Soldiers in World War I
Authors: Nagel Amanda M.
Published: February 2021

In the midst of the long black freedom struggle, African American military participation in the First World War remains central to civil rights activism and challenges to systems of oppression in the United States. As part of a long and storied tradition of military service for a nation that marginalized and attempted to subjugate a significant portion of US citizens, African American soldiers faced challenges, racism, and segregation during the First World War simultaneously on the home front and the battlefields of France. The generations born since the end of the Civil War continually became more and more militant when resisting Jim Crow and insisting on full, not partial, citizenship in the United States, evidenced by the events in Houston in 1917. Support of the war effort within black communities in the United States was not universal, however, and some opposed participation in a war effort to “make the world safe for democracy” when that same democracy was denied to people of color. Activism by organizations like the National Association for the Advancement of Colored People (NAACP) challenged the War Department’s official and unofficial policy, creating avenues for a larger number of black officers in the US Army through the officers’ training camp created in Des Moines, Iowa. For African American soldiers sent to France with the American Expeditionary Forces (AEF), the potential for combat experience led to both failures and successes, leading to race pride as in the case of the 93rd Division’s successes, and skewed evidence for the War Department to reject increasing the number of black officers and enlisted in the case of the 92nd Division. All-black Regular Army regiments, meanwhile, either remained in the United States or were sent to the Philippines rather than the battlefields of Europe. However, soldiers’ return home was mixed, as they were both celebrated and rejected for their service, reflected in both parades welcoming them home and racial violence in the form of lynchings between December 1918 and January 1920. As a result, the interwar years and the start of World War II roughly two decades later renewed the desire to utilize military service as a way to influence US legal, social, cultural, and economic structures that limited African American citizenship.
Adventism in America
Authors: Valentine Gilbert
Published: February 2021

The term “Adventist” embraces a cluster of fifteen or so Protestant religious communities in America for whom the central conviction in their belief system is the idea of the imminence of the Parousia, meaning the premillennial, personal, literal return of Christ to earth and the end of the evil world. The suffix, -ist, compounded with Advent, first used in the late 1830s to describe the sharp sense of imminence that motivated the movement, soon came to be used as the common term to identify those who held the conviction. By 1844 they were called Adventists. Almost all American Adventist churches are native to the United States and arose from the Millerite movement of 1831–1844 that marked the end of the Second Great Awakening (1790–1850). The churches it birthed were shaped by the cultural and religious impulses of the period.

Most of the Adventist churches remain small, with an aggregate membership within the United States approaching 3 million. Worldwide Adventist memberships, however, exceed 40 million and represent a significant export of American religious beliefs and values. The two largest churches in the group, Jehovah’s Witnesses and the Seventh-day Adventist church, have both established a substantial presence in America, each reporting domestic memberships of approximately 1.25 million in 2018, placing both within the largest twenty-five denominations in the nation. Both religions have also developed significant international branches, organically and hierarchically linked to their American headquarters. Almost 9 million international members are reported by Jehovah’s Witnesses and 21 million for Seventh-day Adventists. Conservative growth projections for Seventh-day Adventists envisage that the number of worldwide adherents may approach 100 million by the mid-to-late 21st century. Both churches have impacted church–state relations in the United States through the legal system, seeking protection of civil rights and religious liberty. Seventh-day Adventism also has influenced American culture through its emphasis on health and education.
Jewish American Cinema
Authors: Grinberg Marat
Published: February 2021

There is an intricate, long, and rich history of Jewish presence in Hollywood, from executives to producers to directors to screenwriters to performers. It starts with the Jewish moguls who were at the helm of most major studios in the 1920s and 30s and tried to separate as much as possible from their Jewish heritage and past. This preponderance of Jews prompted an anti-Semitic response in the American entertainment scene which could hardly be ignored. The result was an overt timidity in the representation of Jews and Jewish topics on screen, with some Jewish actors perceived as “too Jewish” for the general taste.

The changes in the perception of identity in the 1960s, marked by culture wars and the Civil Rights movement, on the one hand, and the flourishing of American Jewish literature and the pride many American Jews took in Israel’s triumph in the Six-Day War of 1967, on the other, enabled a much more open and unabashed embrace of Jewishness in Hollywood. Consequently, the late 1960s usher in the New Jewish Wave, when the issues of Jewish identity and experience start to dominate the screen and are defined by such auteurs as Woody Allen, Mel Brooks, Sidney Lumet, and Paul Mazursky, and such actors as Dustin Hoffman, Barbra Streisand, Richard Dreyfuss, Eliot Gould, George Seagal, and Woody Allen throughout the 1970s and 80s. The Jewish representation grows in the 1990s and 2010s with such directors as the Coen brothers, Darren Aronofsky, David Cronenberg, David Mamet, Jonathan Glazer, Stephen Spielberg, and the Safdie brothers.
Judaism in America
Authors: Wertheimer Jack
Published: February 2021

It is impossible to understand American Judaism without reference to its adaptation to American social mores and religious models. Among the important aspects of the American ethos that would shape Judaism in this country were voluntarism, the choice Americans enjoy whether to join or stay aloof; congregationalism, the near autonomy of each house of worship to regulate its own services; egalitarianism, which levels differences between different socioeconomic classes and eventually the genders; democratic ideals of governance; individualism and personalism, both elevating the needs and interests of each person over those of the group; moralism, the belief that the most important, if not sole, purpose of religion is to enable believers to become better human beings; and decorum, evolving conceptions of how one is to behave in a house of worship.

Successive waves of Jewish immigrants initially aimed to transplant customary ways of enacting Judaism in the Old World to the New. But in time, the children and grandchildren of immigrants adapted to American religious models, thereby reconceiving synagogue functions, home practices, and everyday lived Judaism. Not only did synagogues introduce English language prayers and sermons; they also incorporated democratic norms and egalitarian ideals to varying degrees. Though laxity in the practice of religious rituals and customs by “average” Jews is hardly unique to American Jews, ideological justifications for “pick and choose” religion draw upon American conceptions of individualism and personalism. By the end of the 20th century, Do-It-Yourself Religion—the apotheosis of individualism and personalism—had triumphed in most sectors of American Judaism (with the exception of Orthodoxy)—just as it had in other faith communities. The porousness of American society, the free flow of ideas and assumptions, render it virtually impossible for religious groups, such as Jewish ones, to insulate themselves in physical or intellectual enclaves. Indeed, many—though certainly not all—controversies about reforming American Judaism have pitted traditionalists against progressives over just how much Jewish religious practices can or should accommodate to American society’s ever-evolving ethos.
An Empire in the Tropics, 1808–1821: A Historiographical Review
Authors: Baptista Bicalho Maria Fernanda , Franco Schiavinatto Iara Lis
Published: February 2021

The Portuguese Empire in the tropics, established in Rio de Janeiro, the political center of Portuguese America between 1808 and 1821, was characterized by a government in flux, dealing with a revolutionary Atlantic, an immediate result of the French Revolution and the Napoleonic invasions. This was a period of instability and transition. Studies from the perspective of political culture analysis have demonstrated the strength of enlightened ideas, the reformist strategy of the Portuguese monarchy in the reorganization of its overseas empire, and the regimentation of Luso-Brazilian elites since the 1780s and 1790s. After 1808, the association of interests between those born in Brazil and those from Portugal benefited from King João’s policy to distribute lands, offices, privileges, and mercês (favours). The process of the interiorization of the metropole in Southern Central Portuguese America corresponded with the interests of the Luso-Brazilian elites around the city of Rio de Janeiro, who expanded their political projects toward other regions of Brazil. In Pernambuco, by contrast, the 1817 insurrection and the republican choice of its leaders explained the fracturing of the empire and monarchical authority. Revisiting debates about the empire in the tropics—including in the press that emerged following the establishment of the court of Rio de Janeiro—implies rethinking the dynamics of the reconfiguration and apprehension of the territories and their geopolitics, thinking about heterogeneous temporalities, and investigating the transit of people on a large scale across the world, the increase in black slave traffic, and forms of compulsory labor.

These dynamics were the subject of innovative studies during the bicentenary of the transfer of the court, providing details of the unprecedented experience of a European king in the Americas. In 2008, many academic, cultural, and artistic events were held, and numerous books, collections, and catalogues were published, fruit of a dialogue between Brazilian and Portuguese historians. Among these were the publication of biographies, correspondence, and studies of scientists and artists who were in the court in Rio de Janeiro and who traveled through Brazil from north to south at the beginning of the 19th century. Furthermore, the project of civility in the tropics helped gestate liberal constitutional politics and a limit on the Joanino government in relation to the forms of reappropriation of the revolutionary ideal. Thus, the court in exile was an important element of the redefinition of the autonomization process in Brazil in the 1820s.
The First Censuses and the History of Statistics in Mexico
Authors: Mayer Leticia
Published: February 2021

During the viceregal period, the population of New Spain was counted various times. However, censuses, which can be called modern, did not begin until the end of the 18th century. The most important of these is the so-called Revillagigedo census, which led to a very interesting debate: should the population be counted one by one or is it better to calculate it with indirect data? This is a problem that continues to exist in the 21st century. In 1812, under the Constitution of Cádiz, all provinces, including overseas ones, were asked to carry out censuses and produce statistics, which led to a proliferation of figures during the first years of the War of Independence and afterward. From 1826 onward, “deviation from the norm” was registered. It was now important not only to count inhabitants but also to calculate how many criminals there were and how many sick people were registered in the statistics, which led to an effort at quantification. Both public officials and those regarded as “wise,” the scientists of the day, were interested in statistics. The low crime rate in Mexico City compared to Paris led to the assumption of the existence of an exceptional “Mexican type of man” with a very low percentage of criminals. The regularity offered by the “Law of Great Numbers” fascinated the inhabitants of the 19th century. However, in the second half of the century, statistical bulletins contained very grim data. Some doctors concerned with collecting statistics—who were actually public health reformers—produced terrible numbers; the mortality in Mexico City was horrifying. In order to verify and compare data, there was a great demand to create a specialized central office. This was founded in 1882 and was given the task of carrying out censuses at the end of the 19th century, something done successfully.
Comparatives and Superlatives in the Romance Languages
Authors: Van Peteghem Marleen
Published: February 2021

Comparison expresses a relation involving two or more entities which are ordered on a scale with respect to a gradable property, called the parameter of comparison. In European languages, it is typically expressed through two constructions, comparatives and superlatives. Comparative constructions generally involve two entities, and indicate whether the compared entity shows a higher, lesser, or equal degree of the parameter with respect to the other entity, which is the standard of comparison. Superlatives set out one entity against a class of entities and indicate that the compared entity shows the highest or lowest degree of the parameter. Hence, comparatives may express either inequality (superiority or inferiority) or equality, whereas superlatives necessarily express superiority or inferiority.

In traditional grammar, the terms comparative and superlative are primarily used to refer to the morphology of adjectives and adverbs in languages with synthetic marking (cf. Eng. slow, slower, slowest). However, while Latin has such synthetic marking, modern Romance languages no longer possess productive comparative or superlative suffixes. All Romance languages use analytic markers consisting of dedicated adverbs (e.g., Fr. plus ‘more’, moins ‘less’, aussi ‘as, also’) and determiners (e.g., Sp./It. tanto, Ro. atât ‘so much’). Superlatives are marked with the same markers and are mainly distinguished from comparatives by their association with definiteness. Another difference between comparatives and superlatives lies in the complements they license. Comparatives license a comparative complement, which may be clausal or phrasal, and which identifies the standard of comparison. As for superlatives, they license partitive PPs denoting the comparison set, which may be further specified by other PPs, a relative clause, or an infinitive clause.

The Romance languages show many similarities with respect to the morphosyntactic encoding of comparatives and superlatives, but they also display important cross-linguistic differences. These differences may be related to the status of the comparative marker, the encoding of the standard marker, ellipsis phenomena in the comparative clause, and the dependence of the superlative on the definite article.
Mastering the difficulties presented by the peculiarities of island life. A commentary on: ‘Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequence data’
Authors: Carine Mark
Published: February 2021

This article comments on:

Rafael G. Albaladejo, Sara Martín-Hernanz, J. Alfredo Reyes-Betancort, Arnoldo Santos-Guerra, María Olangua-Corral and Abelardo Aparicio Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data, Annals of Botany, Volume 127, Issue 5, 16 April 2021, Pages 597–611, https://doi.org/10.1093/aob/mcaa090
VoroCNN: deep convolutional neural network built on 3D Voronoi tessellation of protein structures
Authors: Igashov Ilia , Olechnovič Kliment , Kadukova Maria , Venclovas Česlovas , Grudinin Sergei
Published: February 2021

Motivation

Effective use of evolutionary information has recently led to tremendous progress in computational prediction of three-dimensional (3D) structures of proteins and their complexes. Despite the progress, the accuracy of predicted structures tends to vary considerably from case to case. Since the utility of computational models depends on their accuracy, reliable estimates of deviation between predicted and native structures are of utmost importance.

Results

For the first time, we present a deep convolutional neural network (CNN) constructed on a Voronoi tessellation of 3D molecular structures. Despite the irregular data domain, our data representation allows us to efficiently introduce both convolution and pooling operations and train the network in an end-to-end fashion without precomputed descriptors. The resultant model, VoroCNN, predicts local qualities of 3D protein folds. The prediction results are competitive to state of the art and superior to the previous 3D CNN architectures built for the same task. We also discuss practical applications of VoroCNN, for example, in recognition of protein binding interfaces.

Availability and implementation

The model, data and evaluation tests are available at https://team.inria.fr/nano-d/software/vorocnn/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Prolonged disorders of consciousness: a critical evaluation of the new UK guidelines
Authors: Scolding Neil , Owen Adrian M , Keown John
Published: February 2021

In March 2020, the Royal College of Physicians in the UK published national guidelines on the management of patients with prolonged disorders of consciousness, updating their 2013 guidance ‘particularly in relation to recent developments in assessment and management and … changes in the law governing … the withdrawal of clinically assisted nutrition and hydration’. The report’s primary focus is on patients who could live for many years with treatment and care. This update, by a neurologist, an imaging neuroscientist, and a lawyer-ethicist, questions the document’s rejection of any significant role for neuroimaging techniques including functional MRI and/or bedside EEG to detect covert consciousness in such patients. We find the reasons for this rejection unconvincing, given (i) the significant advances made in the use of this technology in recent years; and (ii) the wider scope for its use envisaged by the earlier (2018) guidelines issued by the American Academy of Neurology. We suggest that, since around one in five patients diagnosed with prolonged disorders of consciousness are in fact conscious enough to follow commands in a neuroimaging context (i.e. those who are ‘covertly conscious’ or those with ‘cognitive motor dissociation’), and given the clinical, ethical and legal importance of determining whether patients with prolonged disorders of consciousness are legally competent or at least able to express their views and feelings, the guidance from the Royal College of Physicians requires urgent review.
Design of Experiment (DoE)-Approach Based RP-HPLC Analytical Method Development and Validation for Estimation of Efavirenz in Bulk and Formulations
Authors: Saha Paramita , Pandey Murali Monohar
Published: February 2021

Present study reports design of experiment (DoE) based development and validation of a simple, rapid and sensitive reversed-phase high-performance liquid chromatography (RP-HPLC) method for estimation of efavirenz (EFZ), a non-nucleotide reverse transcriptase inhibitor (NNRTs), used in the treatment of acquired immunodeficiency syndrome (AIDS). Plackett–Burman design was explored to screen the critical method variables (CMVs) for the RP-HPLC method. A response surface Box–Behnken design was employed to optimize the screened CMVs which affect the analytical responses (ARs) of RP-HPLC method. Using the optimized CMVs the HPLC method was developed and validated according to International Conference on Harmonization (ICH) guidelines. EFZ in marketed formulation was estimated using the validated method. Acetonitrile proportion, pH of the phosphate buffer and mobile phase flow rate were the CMVs and retention time and number of theoretical plates were the ARs for the study. The optimized chromatographic parameters were acetonitrile proportion in mobile phase: 51.17%v/v, pH of phosphate buffer: 4.04 and flow rate: 1.25 mL/min. Use of these optimized parameters resulted in retention time of 11.031 min and 9,498.787 number of theoretical plates as ARs of the HPLC method. The method was further validated in harmony with current ICH guidelines Q2 (R1). The method was capable of the successful estimation of EFZ in marketed formulation. The study depicts successful development and validation of a simple RP-HPLC method of EFZ using DoE approach.
High-Dose Oral and Intravenous Rifampicin for the Treatment of Tuberculous Meningitis in Predominantly Human Immunodeficiency Virus (HIV)-Positive Ugandan Adults: A Phase II Open-Label Randomized Controlled Trial
Authors: Cresswell Fiona V , Meya David B , Kagimu Enock , Grint Daniel , te Brake Lindsey , Kasibante John , Martyn Emily , Rutakingirwa Morris , Quinn Carson M , Okirwoth Micheal , Tugume Lillian , Ssembambulidde Kenneth , Musubire Abdu K , Bangdiwala Ananta S , Buzibye Allan , Muzoora Conrad , Svensson Elin M , Aarnoutse Rob , Boulware David R , Elliott Alison M
Published: February 2021

Background

High-dose rifampicin may improve outcomes of tuberculous meningitis (TBM). Little safety or pharmacokinetic (PK) data exist on high-dose rifampicin in human immunodeficiency virus (HIV) coinfection, and no cerebrospinal fluid (CSF) PK data exist from Africa. We hypothesized that high-dose rifampicin would increase serum and CSF concentrations without excess toxicity.

Methods

In this phase II open-label trial, Ugandan adults with suspected TBM were randomized to standard-of-care control (PO-10, rifampicin 10 mg/kg/day), intravenous rifampicin (IV-20, 20 mg/kg/day), or high-dose oral rifampicin (PO-35, 35 mg/kg/day). We performed PK sampling on days 2 and 14. The primary outcomes were total exposure (AUC0–24), maximum concentration (Cmax), CSF concentration, and grade 3–5 adverse events.

Results

We enrolled 61 adults, 92% were living with HIV, median CD4 count was 50 cells/µL (interquartile range [IQR] 46–56). On day 2, geometric mean plasma AUC0–24hr was 42.9·h mg/L with standard-of-care 10 mg/kg dosing, 249·h mg/L for IV-20 and 327·h mg/L for PO-35 (P < .001). In CSF, standard of care achieved undetectable rifampicin concentration in 56% of participants and geometric mean AUC0–24hr 0.27 mg/L, compared with 1.74 mg/L (95% confidence interval [CI] 1.2–2.5) for IV-20 and 2.17 mg/L (1.6–2.9) for PO-35 regimens (P < .001). Achieving CSF concentrations above rifampicin minimal inhibitory concentration (MIC) occurred in 11% (2/18) of standard-of-care, 93% (14/15) of IV-20, and 95% (18/19) of PO-35 participants. Higher serum and CSF levels were sustained at day 14. Adverse events did not differ by dose (P = .34).

Conclusions

Current international guidelines result in sub-therapeutic CSF rifampicin concentration for 89% of Ugandan TBM patients. High-dose intravenous and oral rifampicin were safe and respectively resulted in exposures ~6- and ~8-fold higher than standard of care, and CSF levels above the MIC.
Accuracy of clinical staging for T2N0 oesophageal cancer: systematic review and meta-analysis
Authors: Wolfson Paul , Ho Kai Man Alexander , Bassett Paul , Haidry Rehan , Olivo Alessandro , Lovat Laurence , Sami Sarmed S
Published: February 2021

Oesophageal cancer is the sixth commonest cause of overall cancer mortality. Clinical staging utilizes multiple imaging modalities to guide treatment and prognostication. T2N0 oesophageal cancer is a treatment threshold for neoadjuvant therapy. Data on accuracy of current clinical staging tests for this disease subgroup are conflicting. We performed a meta-analysis of all primary studies comparing clinical staging accuracy using multiple imaging modalities (index test) to histopathological staging following oesophagectomy (reference standard) in T2N0 oesophageal cancer. Patients that underwent neoadjuvant therapy were excluded. Electronic databases (MEDLINE, Embase, Cochrane Library) were searched up to September 2019. The primary outcome was diagnostic accuracy of combined T&N clinical staging. Publication date, first recruitment date, number of centers, sample size and geographical location main histological subtype were evaluated as potential sources of heterogeneity. The search strategy identified 1,199 studies. Twenty studies containing 5,213 patients met the inclusion criteria. Combined T&N staging accuracy was 19% (95% CI, 15–24); T staging accuracy was 29% (95% CI, 24–35); percentage of patients with T downstaging was 41% (95% CI, 33–50); percentage of patients with T upstaging was 28% (95% CI, 24–32) and percentage of patients with N upstaging was 34% (95% CI, 30–39). Significant sources of heterogeneity included the number of centers, sample size and study region. T2N0 oesophageal cancer staging remains inaccurate. A significant proportion of patients were downstaged (could have received endotherapy) or upstaged (should have received neoadjuvant chemotherapy). These findings were largely unchanged over the past two decades highlighting an urgent need for more accurate staging tests for this subgroup of patients.
State-of-the-art intra-procedural imaging for the mitral and tricuspid PASCAL Repair System
Authors: Hahn Rebecca T , Kodali Susheel K
Published: February 2021

Advanced intra-procedural imaging techniques have been integral to technical and procedural success transcatheter devices. A novel leaflet approximation therapy, the PASCAL Transcatheter Valve Repair System (Edwards Lifesciences, Irvine, CA, USA) has demonstrated high procedural success, acceptable safety, and significant clinical improvement in patients with severe mitral and tricuspid regurgitation and has CE mark approval in Europe with pivotal trials underway in the USA. This review outlines the pre-procedural imaging views and advanced transoesophageal imaging protocols both mitral and tricuspid valve device implantation.
Myocardial work in Stage 1 and 2 hypertensive patients
Authors: Jaglan Akshar , Roemer Sarah , Perez Moreno Ana Cristina , Khandheria Bijoy K
Published: February 2021

Aims

Myocardial work (MW) is a novel parameter that can be used in a clinical setting to assess left ventricular (LV) pressures and deformation. We sought to distinguish patterns of global MW index in hypertensive vs. non-hypertensive patients and to look at differences between categories of hypertension.

Methods and results

Sixty-five hypertensive patients (mean age 65 ± 13 years; 30 male) and 15 controls (mean age 38 ± 12 years; 7 male) underwent transthoracic echocardiography at rest. Hypertensive patients were subdivided into Stage 1 (n = 32) and Stage 2 (n = 33) hypertension based on 2017 American College of Cardiology guidelines. Exclusion criteria were suboptimal image quality for myocardial deformation analysis, reduced ejection fraction, valvular heart disease, intracardiac shunt, and arrhythmia. Global work index (GWI), global constructive work (GCW), global wasted work (GWW), and global work efficiency were estimated from LV pressure–strain loops utilizing proprietary software from speckle-tracking echocardiography. LV systolic and diastolic pressures were estimated using non-invasive brachial artery cuff pressure. Global longitudinal strain and LV ejection fraction were preserved between the groups with no statistically significant difference, whereas there was a statically significant difference between the control and two hypertension groups in GWI (P = 0.01), GCW (P < 0.001), and GWW (P < 0.001).

Conclusion

Non-invasive MW analysis allows better understanding of LV response under conditions of increased afterload. MW is an advanced assessment of LV systolic function in hypertension patients, giving a closer look at the relationship between LV pressure and contractility in settings of increased load dependency than LV ejection fraction and global longitudinal strain.
Use of sepsis-related diagnostic criteria in primary care: a survey among general practitioners
Authors: Mulders Merijn C F , Loots Feike J , van Nieuwenhoven Joey , ter Maaten Jan C , Bouma Hjalmar R
Published: February 2021

Background

Use of sepsis-criteria in hospital settings is effective in realizing early recognition, adequate treatment and reduction of sepsis-associated morbidity and mortality. Whether general practitioners (GPs) use these diagnostic criteria is unknown.

Objective

To gauge the knowledge and use of various diagnostic criteria. To determine which parameters GPs associate with an increased likelihood of sepsis.

Methods

Two thousand five hundred and sixty GPs were invited and 229 agreed to participate in a survey, reached out to through e-mail and WhatsApp groups. The survey consisted of two parts: the first part aimed to obtain information about the GP, training and knowledge about sepsis recognition, and the second part tested specific knowledge using six realistic cases.

Results

Two hundred and six questionnaires, representing a response rate of 8.1%, were eligible for analysis. Gut feeling (98.1%) was the most used diagnostic method, while systemic inflammatory response syndrome (37.9%), quick Sequential Organ Failure Assessment (qSOFA) (7.8%) and UK Sepsis Trust criteria (UKSTc) (1.5%) were used by the minority of the GPs. Few of the responding GPs had heard of either the qSOFA (27.7%) or the UKSTc (11.7%). Recognition of sepsis varied greatly between GPs. GPs most strongly associated the individual signs of the qSOFA (mental status, systolic blood pressure, capillary refill time and respiratory rate) with diagnosing sepsis in the test cases.

Conclusions

GPs mostly use gut feeling to diagnose sepsis and are frequently not familiar with the ‘sepsis-criteria’ used in hospital settings, although clinical reasoning was mostly in line with the qSOFA score. In order to improve sepsis recognition in primary care, GPs should be educated in the use of available screening tools.
Sea foams are ephemeral hotspots for distinctive bacterial communities contrasting sea-surface microlayer and underlying surface water
Authors: Rahlff Janina , Stolle Christian , Giebel Helge-Ansgar , Mustaffa Nur Ili Hamizah , Wurl Oliver , P. R. Herlemann Daniel
Published: February 2021

The occurrence of foams at oceans’ surfaces is patchy and generally short-lived, but a detailed understanding of bacterial communities inhabiting sea foams is lacking. Here, we investigated how marine foams differ from the sea-surface microlayer (SML), a <1-mm-thick layer at the air–sea interface, and underlying water from 1 m depth. Samples of sea foams, SML and underlying water collected from the North Sea and Timor Sea indicated that foams were often characterized by a high abundance of small eukaryotic phototrophic and prokaryotic cells as well as a high concentration of surface-active substances (SAS). Amplicon sequencing of 16S rRNA (gene) revealed distinctive foam bacterial communities compared with SML and underlying water, with high abundance of Gammaproteobacteria. Typical SML dwellers such as Pseudoalteromonas and Vibrio were highly abundant, active foam inhabitants and thus might enhance foam formation and stability by producing SAS. Despite a clear difference in the overall bacterial community composition between foam and SML, the presence of SML bacteria in foams supports the previous assumption that foam is strongly influenced by the SML. We conclude that active and abundant bacteria from interfacial habitats potentially contribute to foam formation and stability, carbon cycling and air–sea exchange processes in the ocean.
Effects of Sample Plot Size and Prediction Models on Diameter Distribution Recovery
Authors: Bankston Josh B , Sabatia Charles O , Poudel Krishna P
Published: February 2021

Distribution of tree diameters in a stand is characterized using models that predict diameter moments and/or percentiles in conjunction with a mathematical system to recover the parameters of an assumed statistical distribution. Studies have compared Weibull diameter distribution recovery systems but arrived at different conclusions regarding the best approach for recovering a stand’s diameter distribution from predicted stand-level statistics. We assessed the effects of sample plot size and diameter moments/percentiles prediction models on the accuracy of three approaches used in recovering Weibull distribution parameters—method of moments, percentile method, and moments-percentile hybrid method. Data from five plot sizes, four of which were virtually created from existing larger plots, from unthinned loblolly pine (Pinus taeda) plantations, were used to fit moments/percentile prediction models and to evaluate the accuracy of the diameter distribution recovered using three approaches. Both plot size and prediction model form affected the accuracy of the recovery approaches as indicated by the changes in their ranking from one plot size to another for the same model form. The method of moments approach ranked best when the evaluation error index did not account for tree stumpage value, but the moments-percentile hybrid approach ranked best when stumpage value was considered.
Mutation of a major CG methylase alters genome-wide lncRNA expression in rice
Authors: Li Juzuo , Li Ning , Zhu Ling , Zhang Zhibin , Li Xiaochong , Wang Jinbin , Xun Hongwei , Zhao Jing , Wang Xiaofei , Wang Tianya , Wang Hongyan , Liu Bao , Li Yu , Gong Lei
Published: February 2021

Plant long non-coding RNAs (lncRNAs) function in diverse biological processes, and lncRNA expression is under epigenetic regulation, including by cytosine DNA methylation. However, it remains unclear whether 5-methylcytosine (5mC) plays a similar role in different sequence contexts (CG, CHG, and CHH). In this study, we characterized and compared the profiles of genome-wide lncRNA profiles (including long intergenic non-coding RNAs [lincRNAs] and long noncoding natural antisense transcripts [lncNATs]) of a null mutant of the rice DNA methyltransferase 1, OsMET1-2 (designated OsMET1-2−/−) and its isogenic wild type (OsMET1-2+/+). The En/Spm transposable element (TE) family, which was heavily methylated in OsMET1-2+/+, was transcriptionally de-repressed in OsMET1-2−/− due to genome-wide erasure of CG methylation, and this led to abundant production of specific lncRNAs. In addition, RdDM-mediated CHH hypermethylation was increased in the 5′-upstream genomic regions of lncRNAs in OsMET1-2−/−. The positive correlation between the expression of lincRNAs and that of their proximal protein-coding genes was also analyzed. Our study shows that CG methylation negatively regulates the TE-related expression of lncRNA and demonstrates that CHH methylation is also involved in the regulation of lncRNA expression.
Implementation of dCas9-mediated CRISPRi in the fission yeast Schizosaccharomyces pombe
Authors: Ishikawa Ken , Soejima Saeko , Masuda Fumie , Saitoh Shigeaki
Published: February 2021

Controllable and reversible transcriptional repression is an essential method to study gene functions. A systematic knock-down method using catalytically inactive Cas9 (dCas9) was originally established in bacteria. dCas9 forms a ribonucleoprotein with a small guide RNA and uses it to recognize a specific DNA sequence via Watson-Crick base-pairing. When specifically bound to a targeted DNA, dCas9 impairs RNA polymerase activity and represses transcription of that target gene. This technology, CRISPRi, has been implemented in several organisms, but not in Schizosaccharomyces pombe using dCas9. Here, we provide a plasmid that expresses dCas9 and sgRNA in fission yeast. With this plasmid, CRISPRi repressed endogenous gene transcription by as much as 87%. This transcriptional repression method is controllable, reversible, and efficient enough to alter cellular phenotypes. Here, we offer a CRISPRi method to choose proper targeting sequences for transcriptional repression in fission yeast. Implementation of CRISPRi will help to reveal gene functions and to develop tools based on dCas9 technology in S. pombe.
A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout
Authors: Gao Guangtu , Magadan Susana , Waldbieser Geoffrey C , Youngblood Ramey C , Wheeler Paul A , Scheffler Brian E , Thorgaard Gary H , Palti Yniv
Published: February 2021

Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is shown through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.
Using WhatsApp messenger for health systems research: a scoping review of available literature
Authors: Manji Karima , Hanefeld Johanna , Vearey Jo , Walls Helen , de Gruchy Thea
Published: February 2021

Globally, the use of mobile phones for improving access to healthcare and conducting health research has gained traction in recent years as rates of ownership increase, particularly in low- and middle-income countries (LMICs). Mobile instant messaging applications, including WhatsApp Messenger, provide new and affordable opportunities for health research across time and place, potentially addressing the challenges of maintaining contact and participation involved in research with migrant and mobile populations, for example. However, little is known about the opportunities and challenges associated with the use of WhatsApp as a tool for health research. To inform our study, we conducted a scoping review of published health research that uses WhatsApp as a data collection tool. A key reason for focusing on WhatsApp is the ability to retain contact with participants when they cross international borders. Five key public health databases were searched for articles containing the words ‘WhatsApp’ and ‘health research’ in their titles and abstracts. We identified 69 articles, 16 of which met our inclusion criteria for review. We extracted data pertaining to the characteristics of the research. Across the 16 studies—11 of which were based in LMICs—WhatsApp was primarily used in one of two ways. In the eight quantitative studies identified, seven used WhatsApp to send hyperlinks to online surveys. With one exception, the eight studies that employed a qualitative (n = 6) or mixed-method (n = 2) design analysed the WhatsApp content generated through a WhatsApp-based programmatic intervention. We found a lack of attention paid to research ethics across the studies, which is concerning given the controversies WhatsApp has faced with regard to data protection in relation to end-to-end encryption. We provide recommendations to address these issues for researchers considering using WhatsApp as a data collection tool over time and place.