bluuebunny/crossref_metadata_2025 huggingface dataset:
Discursive construction of collective identity in a global online
community of practice of English language teachers
Authors: Kulavuz-Onal Derya
Published: January 2022

In this chapter, I explore how members of Webheads in
Action, an online community of practice of English language
teachers, construct a collective identity of “webhead-ness” discursively,
how certain community values are realized at the linguistic level in their
email communication, and how the community’s collective identity and values
shape their professional development. Through a corpus-driven
discourse-analytic approach of the email communication and content analysis
of in-depth interviews with two long-term active members, I observed that
members frequently draw on specific discursive resources that seem to have
evolved as idiosyncratic linguistic practices in this community’s culture.
Such practices that reinforce a collective identity are critical for
cultivating and sustaining long-standing online communities of practice that
foster teacher participation and professional development.
Developing online language teacher identities
Authors: Reinhardt Jonathon
Published: January 2022

Informed by the other studies of the volume, this chapter argues
that online language teacher education (OLTE) should make five
considerations in reconceptualizing curricula and provides examples of
learning activities that address each. First it should acknowledge that
online digital language use differs considerably from in-person language
equivalents, and second, that technology knowledge includes not only how to
teach online but what digital language use is. Third, it should recognize
that learners and teachers have modern techno-identities developed not only
in their academic but their everyday lives as well. Fourth, it should
leverage the power of the Internet to develop translanguacultural awareness
and fifth, recognize that social presence is key to socio-collaborative
learning, both in-person and online.
The second language acquisition of grammatical gender and number in Italian
Authors: Ayoun Dalila , Maranzana Stefano
Published: January 2022

This cross-sectional empirical study tested the ability of Anglophone L2 learners of Italian
(n = 87) to assign grammatical gender and number to a subset of isolated nouns drawn from a
written corpus of current magazine and newspaper articles. Italian native speakers served as controls
(n = 109). We first present a descriptive account of grammatical gender that outlines several
idiosyncrasies and complexities than may lead to difficulties for L2 learners, particularly English native speakers,
from a Feature Reassembly approach and a Minimalist perspective. We then discuss L2 learnability implications in light
of the results of a written, computerized gender assignment task (GAT) showing significant effects for gender and
number, ambiguous vs. transparent nouns, but not for suffixed vs non-suffixed nouns.
Investigating grammatical gender agreement in Spanish
Authors: Spino LeAnne
Published: January 2022

The present eye-tracking study tests the assumption that online techniques can tap implicit
knowledge and reduce access to explicit knowledge by triangulating eye movements with a post-reading questionnaire. L1
English learners of L2 Spanish and Spanish native speakers (NSs) read sentences embedded with violations of
determiner-noun and noun-adjective agreement followed by comprehension questions. They then completed a post-reading
questionnaire that measured to what extent they were aware of the violations in the experimental stimuli. In the
eye-tracking experiment, both L2 learners and Spanish NSs were sensitive to violations of determiner-noun agreement,
but only Spanish NSs were sensitive to violations of noun-adjective agreement. On the post-reading questionnaire, most
participants were also aware of the grammatical gender agreement violations, with determiner-noun agreement violations
generally being more salient than noun-adjective violations. These results indicate that the violation detection
paradigm implemented in this experiment did not entirely obviate explicit knowledge. Results are discussed in terms of
methodological considerations researchers should keep in mind when designing and implementing studies that investigate
grammatical gender agreement and other linguistic phenomena.
Cross-linguistic influence in bilingual grammars
Authors: van Osch Brechje , Boers Ivo H.G. , Grijzenhout Janet , Parafita Couto M. Carmen , Sterken Bo , Tat Deniz
Published: January 2022

This study reports on grammatical gender assignment in elicited production data from heritage
speakers of Turkish, Papiamento, and Spanish in the Netherlands. We investigate the role of cross-linguistic influence
from the heritage language onto the societal language by comparing three heritage languages that differ in terms of
the properties of the nominal domain, including gender. Determiner-adjective-noun constructions were elicited by means
of a Director-Matcher task (Gullberg, Indefrey, & Muysken, 2009), which
was performed both in a unilingual Dutch mode, and in a code-switching mode from Dutch to the heritage language. The
results show that all groups tend to overgeneralize the common gender in the Dutch unilingual mode. Strikingly, the
performance of heritage speakers of Spanish was more target-like than the Papiamento and Turkish speakers, which may
be due to the fact that Spanish is the only language that has a grammatical gender system. In code-switching mode,
most speakers tend to assign common gender to inserted nouns, but some speakers also apply a gender assignment
strategy based on the translation equivalent of the noun in Dutch, or produce a postnominal adjective construction
with an uninflected adjective. An analysis of extra-linguistic variables demonstrated that gender assignment
strategies seem to be determined to some extent by the degree of dominance in the societal language.
The rivalry between definiteness and specificity
Authors: Osawa Fuyo
Published: January 2022

This paper addresses the question of why Present-day English (hereafter PDE) grammaticalized definiteness, but not specificity, as a D head. Two semantic properties are involved in the use of nominals: [definite] and [specific]. Definiteness means that a nominal marked as [+definite] indicates that the speaker assumes that the hearer shares the speaker’s presupposition of the existence of an individual. The specific reading is characterized by the certainty of the speaker about the identity of the referent. Specificity is knowledge only held by the speaker. The PDE article system is based on definiteness, while specificity is not involved in article choice in English. This is puzzling because investigations of language acquisition have shown that article choice is cross-linguistically based on specificity rather than definiteness, irrespective of learners’ first language. Thus, specificity seems to be more suitable for a D head. I propose two reasons why the PDE article system is based on definiteness. Firstly, person properties were encoded into the D head since definiteness is to be assimilated to the category of person. Another reason, which I only hint at in this paper, might be intersubjectification: the shift of attention from the speaker to the hearer. Specificity involves the speaker only, while definiteness marking involves both the speaker and the hearer. These two are essential processes of grammaticalization, i.e. DP emergence.
Post-head compression in noun phrase referring expressions
Authors: Oppliger Rahel
Published: January 2022

In communication, language users frequently produce referring expressions with noun phrases at their centre (NP REs). Over the course of a communicative interaction, interlocutors’ use of NP REs tends to change: previous research has attested to speakers’ tendency to converge on linguistic forms – establishing routines (e.g. Pickering & Garrod 2004, 2005) – and to shorten their NP REs in the process (e.g. Clark & Wilkes-Gibbs 1986; Brennan & Clark 1996; Castillo et al. 2019). The present chapter investigates this shortening process and observes the structural changes in NP REs that accompany it. The study is based on data from an experimentally elicited corpus of spoken English consisting of conversational dyads producing repeated references to visual stimuli in a referential communication task. Interlocutors are indeed shown to shorten their NP REs over the course of the elicited dialogues: particularly, a decrease in longer clausal post-head elements is observed, while the use of only premodified NP REs and shorter phrasal postmodification shows a relative increase. These changes are indicative of shifts in the type of structural modification the NP REs contain: initially, speakers produce more clausal elements, which are associated with structural elaboration; later in the interaction, a decrease in clausal and relative increase in phrasal modification reveals structural compression (cf. Biber & Clark 2002).
From noun to verb
Authors: Maekelberghe Charlotte
Published: January 2022

This chapter reassesses the paradigmatic relations between present-day English nominal and verbal gerunds by examining their variation potential at an abstract-schematic level as well as at token-level. Results show that functional overlap is mainly instigated by verbal gerunds taking up more typically nominal uses, thus creating the conditions for variation with the nominal gerund. However, a collexeme analysis reveals that there is actually very little lexical overlap between both gerund types, as nominal gerunds are more restricted in terms of the verbs they can derive from. Thus, while paradigmatic links between nominal and verbal gerunds are present on an abstract-semantic level, their distinct lexical profiles confirm their reorientation to other constructional families.
Shell nouns as epistemic stance devices in English
Authors: Carretero Marta
Published: January 2022

This paper is concerned with the role of English Noun Phrases headed by shell nouns with epistemic modal and evidential meanings as devices for expressing epistemic stance. In line with previous work (Schmid 2000, Carretero 2016), this research adopts the notion of modal and evidential frames (Talmy 1996). The paper focuses on the distinction between epistemic uses, i.e. those uses that express commitment to communicated information, and non-epistemic uses. On the basis of data from the British National Corpus of four epistemic modal nouns (possibility, probability, likelihood, certainty) and four evidential nouns (evidence, indication, proof, sign), four factors that determine (non-)epistemicity have been identified, which are shown to have different relative weight for each of the nouns analysed. Based on these factors, an annotation scheme is proposed for the annotation of epistemic and non-epistemic uses of these nouns in further research.
Coordinated phrases as dvandvas
Authors: Nishimaki Kazuya
Published: January 2022

It is generally accepted that coordinated compounds known as dvandvas are attested in some languages but not in others. For instance, they are very common in Japanese (e.g. dan-zyo ‘lit. male-female = male and female’) but unattested in English (e.g. * male-female), which instead requires phrasal coordination. The present paper uses Competition Theory to explore where this cross-linguistic variation comes from, focusing on the unattestedness of dvandvas in English. This theory assumes that cross-linguistic variations occur when morphology and syntax compete to realize an underlying structure; languages are classified into two types in a macroparametric manner, depending on whether they prefer morphological or syntactic realization. Taking a competition-theoretic approach, this paper claims that the unattestedness reflects the nature of English as a particular type of language, which is determined by a macroparameter. Furthermore, Competition Theory predicts that dvandvas have phrasal counterparts in English. The correctness of this prediction will be verified by observing that a particular type of coordinated phrase exhibits the defining property of a dvandva regardless of their different surface forms. It will be proposed that the relevant type is derived in a specific way, which results in its dvandva status.
Inclusion and mobility in the multilingual region of Vojvodina
Authors: Dobos Edgár , Nagy Noémi , Vizi Balázs
Published: January 2022

International and internal mobility can result in both linguistic diversity and forced migration due to intended homogenisation efforts (e.g. “ethnic unmixing” in the successor states of former Yugoslavia). International minority rights instruments scarcely address the questions of mobility and multilingualism. Vojvodina is expected to be a multilingual region in Serbia, an EU-candidate state, according to the laws on language use. Recent migratory trends in Vojvodina – within Serbia and from Serbia to Hungary and other EU states – have changed the “identity landscape” of a region that possesses deeply anchored multinational–multilingual traditions. An important question, therefore, is how existing legal provisions on language rights could offer protection to minority language speakers. International actors also promote the respect for and protection of minority language rights, reflected in the broad political and normative commitments made by Serbia within the context of EU-accession process. However, this political objective is often not achieved, a frequently observed obstacle being that local authorities see any attempt at implementing those language rights more as a burden than an opportunity. This chapter addresses questions such as: How is the legal framework implemented in practice (de iure vs. de facto use of minority languages)? What influence may international norms have on language rights regime? What influence do kin-state policies have?
Migrants’ attitudes towards community interpreting
Authors: Pokorn Nike K. , Čibej Jaka
Published: January 2022

The aim of the chapter is to describe the attitude of different groups of migrants to community interpreting and the role of community interpreting in the inclusion process. The role of public-service translation and interpreting and attitudes towards community interpreting were studied in three groups of migrants in Slovenia: short-term (those who stay in the host country from one to 12 months), medium-term (those who intend to stay in the host country for a minimum of one year, but for a limited period of time), and long-term (those who intend to stay in the host country for the rest of their lives). The study covers 65 migrants from different language backgrounds (18 different L1s were identified) who intended to stay in the host country for various periods of time. First, the language profiles of migrants were defined on the basis of a questionnaire, then semi-structured interviews were conducted with 38 short-term, 9 medium-term and 18 long-term migrants. The results show that migrants, regardless of their country of origin, the status of their L1, their level of education and their intended length of stay in the host country, had a rather negative attitude towards interpreting. They were reluctant to use interpreters because they doubted the accuracy of this mediated transfer due to the fact that public-service institutions tend to employ unqualified interpreters for the languages of new migrants. In addition, migrants, regardless of the level of their education, gender and language background, mainly considered this mediation strategy to be a hindrance to their independence. However, they expressed the need to use interpreters and translators in the early stages of their stay in the host country, especially in high-risk situations such as multilingual encounters in health-care, court and police settings.
The language choices of exchange students
Authors: Fiedler Sabine , Brosch Cyril Robert
Published: January 2022

The Erasmus Programme is the flagship of the EU’s academic exchange programmes. Taking as a point of departure that language proficiency is a key factor of a successful stay abroad, this research focuses on exchange students’ language learning and language choices. It draws on data collected between autumn 2015 and spring 2018 by means of online questionnaires and interviews with more than 500 participants. A major finding is that a large majority of exchange students consider learning the language of the host country an important incentive for their stay. In practice, however, student enthusiasm is often stymied by a lack of adequate language courses and/or poor organisation, leading to students spending most of their time with other exchange students, as opposed to with locals. Countries with popular languages, especially English and French, performed very well in raising linguistic proficiency, while the results in other countries, especially those with less widely spoken languages, where the language of instruction is usually English, varied significantly. The chapter also includes a discussion of the Online Linguistic Support (OLS). It concludes by addressing the question of how the potential of the Erasmus Programme can be better exploited to support multilingualism and language diversity.
Effectiveness of policy measures and language dynamics
Authors: Templin Torsten , Wickström Bengt-Arne , Gazzola Michele
Published: January 2022

The effect of a given language policy can be very different in the short, medium and long run. We illustrate this, looking at the effects of language planning on inclusion given different mobility patterns. The choice is between different status and acquisition planning measures. This choice gives rise to different degrees of inclusion (in the form of bilingualism) given the costs of the policy and the linguistic environment. In a mobility/inclusion trade-off, a higher level of inclusion can be reached for a given amount of migration through a well-designed language policy. Different scenarios require different policy measures in the cost-effectiveness analysis. The effects of status and acquisition planning are modelled in a dynamic setting, where language learning depends on compulsory measures as well as voluntary decisions by the individuals involved based on their individual cost-benefit calculations (or those of their parents). The effects on inclusion are simulated in various scenarios when language skills are transferred from one generation to the next. The scenarios include migration of majority-language speakers into a region with a strong minority language (Spanish-speakers migrating into the Basque Country) and migration of speakers of a ‘foreign’ language into a country with enclaves of speakers of this language (Spanish-speakers in the USA).
The ontology of the linguistic territoriality principle
Authors: Morales-Gálvez Sergi , De Schutter Helder , Stojanović Nenad
Published: January 2022

The linguistic territoriality principle is popular both among theorists and practitioners of language policy. But its precise content is notoriously vague. A plethora of different meanings have been attached to it, leading to conceptual and normative confusion. This chapter proposes a novel conceptualization of this principle, in order to operationalize it both for theory and practice. It elaborates a proper definition of the LTP, illustrates its numerous versions and offers a state-of-the-art overview of justifications for and critiques of the LTP. The chapter works out, in short, a full ontology of the LTP, against the background of notions of mobility and inclusion. Our main research question is the following: what is at the conceptual and moral core of the territoriality principle? What are the crucial notions that need to be present in order to meaningfully speak of linguistic territoriality, and why do these notions matter morally? To address these questions, we offer and discuss two metrics that could constitute the core of the LTP: the linguistic coerciveness metric and the linguistic diversity metric. We argue that, although the coerciveness metric is relevant, the diversity metric is at the conceptual core of territoriality, such that we ought to understand linguistic territoriality as fundamentally characterized by linguistic monism, or monolingualism. Finally, we draw implications that such a view of LTP might have for the key concepts of mobility and inclusion.
Complexity in language matters
Authors: Civico Marco
Published: January 2022

Agent-based modelling belongs to the wider category of computational modelling and is used to replicate real-world social or physical systems and simulate their behaviour in a computer environment, with a view to studying the rules that govern them. Although agent-based modelling has quickly gained recognition in the natural sciences, social scientists only started to explore its potential in the last few decades. This trend has gained momentum over the last ten years, and applications of agent-based modelling to the social sciences have been steadily increasing. Researchers dealing with complex phenomena (in both the social and natural sciences) are increasingly switching from purely analytical (i.e. mathematical) approaches (which often attempt to find a ‘closed-form solution’ to a problem) to computation-based approaches (which rely on algorithms and simulations). Whereas applications of analytical methods to study language-related issues have a long-standing tradition, systematic adoption of a complexity-based view of language matters and application of computational methods have yet to establish themselves. However, recent research in language studies shows attempts to address the complexity of language-related issues in a more systematic way. Particular attention is devoted to the fact that such issues involve numerous agents and variables, and causal links between these variables are often non-linear. Although it may be challenging to model such systems through equations, agent-based modelling offers a natural solution, in that it provides an easy way of replicating various degrees of diversity in a computer environment. These models can then be run many times with various settings to study the system’s short-term and long-term behaviour and the way it responds to different initial conditions. Agent-based modelling lends itself very well both to studies that investigate the nature and functioning of languages and to sociolinguistic studies that focus on language-mediated interactions between individuals.
Multilingualism and consumer protection
Authors: Kaddous Christine , Marcus Laura
Published: January 2022

This chapter investigates the various language requirements in EU consumer law. The research conducted in this European project revealed that there is no general rule in the matter to guide the EU legislature. Requirements as to the use of languages vary from one field to another. The case law of the Court of Justice of the European Union also reflects this main finding.

As linguistic competences remain largely in the hands of the Member States, multilingualism is often at the origin of conflicts in the dichotomy between EU economic integration and Member States’ sovereignty. National linguistic requirements may conflict with EU law (primary and/or secondary legislation), unless accepted on the basis of reasonable justifications according to EU law.

This chapter first proposes to classify the language requirements in EU consumer law on the basis of the objectives pursued by different legislations. This classification may allow Member States to adopt and adapt their national regulations in accordance with predetermined EU language criteria.

The second proposal made in this chapter is to promote multilingualism in EU consumer legislation. This may be achieved by developing an EU policy to increase awareness of the importance of multilingualism as an objective to be promoted in its own right within the EU (and not only as a tool accompanying the achievement of economic objectives). Developing such a policy may foster mobility and inclusion of EU consumers, including EU economic operators and citizens in general.
Reliability improvement of gas discharge tube by suppressing the formation of short-circuit pathways
Authors: CHENG Lingyun , XIANG Nianwen , LI Kejie , CHEN Weijiang , BIAN Kai , YANG Jin , XU Zongqi , HAN Congying , GU Hongyang , YANG Chun
Published: January 2022

After cumulative discharge of gas discharge tube (GDT), it is easy to form a short circuit pathway between the two electrodes, which increases the failure risk and causes severe influences on the protected object. To reduce the failure risk of GDT and improve cumulative discharge times before failure, this work aims to suppress the formation of two short-circuit pathways by optimizing the tube wall structure, the electrode materials and the electrode structure. A total of five improved GDT samples are designed by focusing on the insulation resistance change that occurs after the improvement; then, by combining these designs with the microscopic morphology changes inside the cavity and the differences in deposition composition, the reasons for the differences in the GDT failure risk are also analyzed. The experimental results show that compared with GDT of traditional structure and material, the method of adding grooves at both ends of the tube wall can effectively block the deposition pathway of the tube wall, and the cumulative discharge time before device failure is increased by 149%. On this basis, when the iron-nickel electrode is replaced with a tungsten-copper electrode, the difference in the electrode’s surface splash characteristics further extends the discharge time before failure by 183%. In addition, when compared with the traditional electrode structure, the method of adding an annular structure at the electrode edge to block the splashing pathway for the particles on the electrode surface shows no positive effect, and the cumulative discharge time before the failure of the two structures is reduced by 22.8% and 49.7%, respectively. Among these improved structures, the samples with grooves at both ends of the tube wall and tungsten-copper as their electrode material have the lowest failure risk.
Solvability of a critical semilinear problem with the spectral Neumann fractional Laplacian
Authors: Ustinov N.
Published: January 2022

Sufficient conditions are provided for the existence of a ground state solution for the problem generated by the fractional Sobolev inequality in

Ω
∈

C
2

:

\Omega \in C^2:

<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="left-parenthesis negative normal upper Delta right-parenthesis Subscript upper S p Superscript s Baseline u left-parenthesis x right-parenthesis plus u left-parenthesis x right-parenthesis equals u Superscript 2 Super Subscript s Super Superscript asterisk Superscript minus 1 Baseline left-parenthesis x right-parenthesis">

(
−
Δ

)

S
p

s

u
(
x
)
+
u
(
x
)
=

u

2
s
∗

−
1

(
x
)

(-\Delta )_{Sp}^s u(x) + u(x) = u^{2^*_s-1}(x)

. Here

(
−
Δ

)

S
p

s

(-\Delta )_{Sp}^s

stands for the

s
s

th power of the conventional Neumann Laplacian in

Ω
⋐

R

n

\Omega \Subset \mathbb {R}^n

,

n
≥
3

n \geq 3

,

s
∈
(
0
,
1
)

s \in (0, 1)

,

2
s
∗

=
2
n

/

(
n
−
2
s
)

2^*_s = 2n/(n-2s)

. For the local case where

s
=
1

s = 1

, corresponding results were obtained earlier for the Neumann Laplacian and Neumann

p
p

-Laplacian operators.
Schrödinger operator with decreasing potential in a cylinder
Authors: Filonov N.
Published: January 2022

The Schrödinger operator

−
Δ
+
V
(
x
,
y
)

-\Delta + V(x,y)

is considered in a cylinder

R

m

×
U

\mathbb {R}^m \times U

, where

U
U

is a bounded domain in

R

d

\mathbb {R}^d

. The spectrum of such an operator is studied under the assumption that the potential decreases in longitudinal variables,

|

V
(
x
,
y
)

|

≤
C
⟨
x

⟩

−
ρ

|V(x,y)| \le C \langle x\rangle ^{-\rho }

. If

ρ
>
1

\rho > 1

, then the wave operators exist and are complete; the Birman invariance principle and the limiting absorption principle hold true; the absolute continuous spectrum fills the semiaxis; the singular continuous spectrum is empty; the eigenvalues can accumulate to the thresholds only.
A note on the centralizer of a subalgebra of the Steinberg algebra
Authors: Hazrat R. , Li Huanhuan
Published: January 2022

For an ample Hausdorff groupoid

G

\mathcal {G}

, and the Steinberg algebra

A
R

(

G

)

A_R(\mathcal {G})

with coefficients in the commutative ring

R
R

with unit, the centralizer is described for the subalgebra

A
R

(
U
)

A_R(U)

with

U
U

an open closed invariant subset of the unit space of 

G

\mathcal {G}

. In particular, it is shown that the algebra of the interior of the isotropy is indeed the centralizer of the diagonal subalgebra of the Steinberg algebra. This will unify several results in the literature, and the corresponding results for Leavitt path algebras follow.
Psychological Predictors of Self-reported COVID-19 Outcomes: Results From a Prospective Cohort Study
Authors: Ayling Kieran , Jia Ru , Coupland Carol , Chalder Trudie , Massey Adam , Broadbent Elizabeth , Vedhara Kavita
Published: January 2022

Background

Previous research has shown that psychological factors, such as stress and social support, are associated with greater susceptibility to viral respiratory illnesses and more severe symptoms. During the COVID-19 pandemic there has been a well-documented deterioration in psychological well-being and increased social isolation. This raises questions as to whether those experiencing psychological adversity during the pandemic are more at risk of contracting and/or experiencing COVID-19 symptoms.

Purpose

To examine the relationship between psychological factors and the risk of COVID-19 self-reported infection and the symptomatic experience of SARS-CoV-2 (indicated by the number and severity of symptoms).

Methods

As part of a longitudinal prospective observational cohort study, 1,087 adults completed validated measures of psychological well-being during April 2020 and self-reported incidence of COVID-19 infection and symptom experience across the pandemic through to December 2020. Regression models were used to explore these relationships controlling for demographic and occupational factors.

Results

Greater psychological distress during the early phase of the pandemic was significantly associated with subsequent self-reported SARS-CoV-2 infection as well as the experience of a greater number and more severe symptoms.

Conclusions

COVID-19 infection and symptoms may be more common among those experiencing elevated psychological distress. Further research to elucidate the mechanisms underlying these associations is needed.
Alpha-Tri: a deep neural network for scoring the similarity between predicted and measured spectra improves peptide identification of DIA data
Authors: Song Jian , Yu Changbin
Published: January 2022

Motivation

Peptide identification of data-independent acquisition (DIA) mass spectrometry applying the peptide-centric approach heavily relies on the spectral library matching, such as the fragment intensity similarity. If the intensity similarity is calculated through all possible fragment ions of a targeted peptide instead of just a few fragment ions provided by the spectral library, the matching will be more comprehensive and reliable, and thus the identification will be more confident. In addition, the emergence of high precision spectrum predictors, like Prosit, also makes it possible to capitalize on the predicted spectrum, which contains all possible fragment ion intensities, to calculate the intensity similarity for DIA data.

Results

In this work, we propose Alpha-Tri, a neural-network-based model to calculate intensity similarity as a post-processing score using the predicted spectrum, measured spectrum and correlation spectrum (triple-spectrum). The predicted spectrum is generated by Prosit, the measured spectrum is retrieved from the apex of the chromatograms of all possible fragment ions and the correlation spectrum is used to indicate the present probabilities of these fragment ions as the link between the precursor and its fragment ions is lost in DIA. By adopting a data-driven method, Alpha-Tri is able to learn the intensity similarity from the triple-spectrum. This learned value is appended to initial scores from DIA-NN, allowing the ensuing statistical validation tool to report more peptides at the same false discovery rate (FDR). In our evaluation of the HeLa dataset with gradient lengths ranging from 0.5 to 2 h, Alpha-Tri delivered 3.0–7.2% gains in peptide detections at 1% FDR. On LFQbench dataset, a mixed-species dataset with known ratios, Alpha-Tri identified more peptides and proteins fell within the valid ratio ranges by up to 8.6% and 7.6%, respectively, compared with DIA-NN solely.

Availability and implementation

The original datasets for benchmarks are downloaded from the ProteomeXchange with the identifiers PXD005573, PXD000954 and PXD002952. Source code is available at https://github.com/YuAirLab/Alpha-Tri.
Deletion of Orc4 during oogenesis severely reduces polar body extrusion and blocks zygotic DNA replication
Authors: Nguyen Hieu , Wu Hongwen , Ung Anna , Yamazaki Yukiko , Fogelgren Ben , Ward W Steven
Published: January 2022

Origin recognition complex subunit 4 (ORC4) is a DNA-binding protein required for DNA replication. During oocyte maturation, after the last oocyte DNA replication step and before zygotic DNA replication, the oocyte undergoes two meiotic cell divisions in which half the DNA is ejected in much smaller polar bodies. We previously demonstrated that ORC4 forms a cytoplasmic cage around the DNA that is ejected in both polar body extrusion (PBE) events. Here, we used ZP3 activated Cre to delete exon 7 of Orc4 during oogenesis to test how it affected both predicted functions of ORC4: its recently discovered role in PBE and its well-known role in DNA synthesis. Orc4 deletion severely reduced PBE. Almost half of Orc4-depleted germinal vesicle (GV) oocytes cultured in vitro were arrested before anaphase I (48%), and only 25% produced normal first polar bodies. This supports the role of ORC4 in PBE and suggests that transcription of the full-length Orc4 during oogenesis is required for efficient PBE. Orc4 deletion also abolished zygotic DNA synthesis. Fewer Orc4-depleted oocytes developed to the metaphase II (MII) stage, and after activation these oocytes were arrested at the two-cell stage without undergoing DNA synthesis. This confirms that transcription of full-length Orc4 after the primary follicle stage is required for zygotic DNA replication. The data also suggest that MII oocytes do not have a replication licensing checkpoint as cytokinesis progressed without DNA synthesis. Together, the data confirm that oocyte ORC4 is important for both PBE and zygotic DNA synthesis.
How “Subclinical” is Subclinical Tuberculosis? An Analysis of National Prevalence Survey Data from Zambia
Authors: Stuck Logan , van Haaster Aimee Claire , Kapata-Chanda Pascalina , Klinkenberg Eveline , Kapata Nathan , Cobelens Frank
Published: January 2022

Background

Pulmonary tuberculosis infection can manifest in different states, including subclinical tuberculosis. It is commonly defined as confirmed tuberculosis without the classic symptoms (commonly, persistent cough for ≥2 weeks). This narrow definition likely poses limitations for surveillance and control measures. The aims of the current study were to characterize the clinical presentation of tuberculosis; estimate the prevalence of subclinical tuberculosis among individuals with bacteriologically confirmed tuberculosis, using various definitions; and investigate risk factors for subclinical as opposed to clinical tuberculosis in a population-based survey.

Methods

We conducted a secondary analysis of data from a nationally representative tuberculosis prevalence survey from Zambia in 2013–2014, in which participants were screened for tuberculosis based on chest radiographic findings and symptoms. Tuberculosis was defined as culture-positive or GeneXpert MTB/RIF test–positive sputum. Risk factors for subclinical tuberculosis were assessed by means of multivariable logistic regression.

Results

Of 257 participants with confirmed tuberculosis, 104 (40.5%) were without cough persisting ≥2 weeks. Only 23 (22.1%) of these did not present with any other common symptoms. Those without cough persisting ≥2 weeks frequently reported other symptoms, particularly chest pain (46.2%) and weight loss (38.5%); 36 (34.6%) reported experiencing other symptoms persisting ≥4 weeks. Female subjects were more likely to report no cough persisting ≥2 weeks, as were relatively wealthier individuals.

Conclusions

The commonly used definition of subclinical tuberculosis includes a large proportion of individuals who have other tuberculosis-suggestive symptoms. Requiring cough ≥2 weeks for tuberculosis diagnosis likely misses many active tuberculosis infections and allows a large reservoir of likely transmissible tuberculosis to remain undetected.
The effectiveness of M-Health associated with cardiac rehabilitation on functional capacity and cardiovascular risk factors: a systematic review and meta-analysis
Authors: Campagnolo Goncalves Toledo A C , Soares De Almeida N , Pierucci A , Straioto Salomao A , Ribeiro Lemes I , Flavio Milanez V , Romero Nakagaki W , Kretli Winkelstroter Eller L , Milanez Morgado De Abreu M A , Bitencourt Oliveira C
Published: January 2022

Introduction

Smartphone applications for health (M-Health) seem to overcome barriers to access Cardiovascular Rehabilitation Programs (CRP), because of their high degree of acceptance and also their potential to influence the frequency of physical exercise in weight loss.

Objective

To analyze the effectiveness of the combination of M-Health and CRP compared to CRP alone on functional capacity, adherence to CRP, management of cardiovascular risk factors in cardiac patients.

Design

Systematic Review and Meta-Analysis.

Methods

The following databases were used Medline via Ovid, EMBASE, Central, PEDro and SPORTDiscus via EBSCOhost from their inception until July/2020. We included randomized controlled trials investigating the effects of M-Health in combination with CRP compared to CRP alone in adults with heart disease, and the interventions with M-Health consisted of text messages, e-mails, and applications. The primary outcome of this review was functional capacity, measured by VO2peak, or self-reported physical activity (METs.min/week). PEDro scale was used to assess the methodological quality of the studies and the GRADE approach to assess the overall quality of evidence. Pooled estimates were calculated using a random effect model to obtain mean difference (MD) or standardized mean differences (SMD) and their respectives 95% confidence intervals (CI).

Results

Nineteen RCTs were eligible, the median risk of bias was 7 out of 10 points. The primary endpoint was analyzed by subgroups, time of intervention and kind of type CRP, eigthteen of these studies assessed functional capacity. CRP in combination with a m-health intervention was more effective than CRP alone in improving VO2peak, ml/min/kg, (MD: 0.84, CI: 0.30 to 1.38; I2=0%, high quality evidence, 12 trials, n=1889) at short-term follow-up, but at medium-term follow-up (MD: 0.84, CI: −0.26 to 1.41; I2=0%, high quality evidence, 8 trials, n=927,). Similarly, CRP associated with m-health was superior to CRP alone in increasing self-reported at short-term, METs.min/week, (MD:1.31, CI: −0.24 to 2.37; I2 = not aplicable, very low quality evidence, 1 trial, n=18), and at medium-term follow-up (MD: 0.18, CI: −0.01 to 0.36; I2=56%, moderate quality evidence, 4 trials, n=1107).

Conclusion

High quality of evidence shows that M-Health improves cardiorespiratory fitness at short-term follow-up. In addition, supervised program showed to be more effective than non-supervised.

Funding Acknowledgement

Type of funding sources: None.
Methane production potential of pulp mill sludges: microbial community and substrate constraints
Authors: Chan-Yam Kelly , Meyer Torsten , Scott J Ashley , Basiliko Nathan
Published: January 2022

Sludges from pulp and paper mills represent a major ecological and environmental cost, and anaerobic digestion represents a method of waste reduction and energy recovery for these mills. This study compared methane production potential and microbial communities across 11 primary and biosludges from 5 pulp and paper mills using various mill processes. We measured methane production from sludges in anaerobic batch reactor experiments over 64d. Sludges were incubated with and without added substrate to test for organic substrate limitation versus inhibition of methanogens. Initial microbial communities and changes to community composition were determined using Illumina MiSeq for metabarcoding of bacterial and archaeal 16S rRNA genes. Mean methane production potential varied greatly between sludges (0.002–79 mL CH4 g–1 TS). Among primary sludges, kraft mill sludge produced more methane than other mill types. For these other mills, biosludge produced more methane than primary sludge, which had evidence of methanogen inhibition. Microbial communities and diversity were influenced by the initial community composition, and high methane production was only seen in sludges with high diversity. A number of sludges innately produced substantial methane and may be targets for further modelling and larger-scale testing of anaerobic digestion.
Enhanced anaerobic degradation of thiobencarb using horizontal-flow anaerobic immobilized biomass bioreactor
Authors: Oanh Nguyen Thi , Duc Ha Danh
Published: January 2022

Thiobencarb is an herbicide globally used in the agricultural sector, and its extensive application leads to severe environmental pollution. In this study, the thiobencarb supplementation caused a significant shift in the bacterial community in the sediment slurry. An analysis of the degradation metabolites of microorganisms from the sediment indicated deschlorothiobencarb, S-4-chlorobenzyl ethylthiocarbamate, 4-chlorobenzyl mercaptan, 4-chlorobenzyl alcohol, 4-chlorobenzoic acid, and chlorobenzene were the main intermediates. The degradation rates were significantly enhanced using a horizontal-flow anaerobic reactor with immobilized cells in polyurethane foam. The degradation rates at 2.6, 12.9, and 25.6 mg/L concentrations by suspended microorganisms from the sediment in the mineral medium supplemented with glucose were 0.085 ± 0.000, 0.383 ± 0.010, and 0.500 ± 0.045 mg d–1, respectively. The corresponding data for degradation in the reactor were 2.54 ± 0.03, 11.69 ± 0.72, and 18.58 ± 1.83 mg d–1 at the sixth operation period. Moreover, COD removal efficiencies were more than 90% achieved in the reactor. The proposed method facilitates degradation using a horizontal-flow anaerobic immobilized biomass bioreactor. Moreover, this study reveals the degradation of metabolites of thiobencarb under anaerobic conditions.
Identification of immunodominant epitopes on nucleocapsid and spike proteins of the SARS-CoV-2 in Iranian COVID-19 patients
Authors: Maghsood Faezeh , Shokri Mohammad-Reza , Jeddi-Tehrani Mahmood , Torabi Rahvar Monireh , Ghaderi Abbas , Salimi Vahid , Kardar Gholam Ali , Zarnani Amir-Hassan , Amiri Mohammad Mehdi , Shokri Fazel
Published: January 2022

Given the emergence of SARS-CoV-2 virus as a life-threatening pandemic, identification of immunodominant epitopes of the viral structural proteins, particularly the nucleocapsid (NP) protein and receptor-binding domain (RBD) of spike protein, is important to determine targets for immunotherapy and diagnosis. In this study, epitope screening was performed using a panel of overlapping peptides spanning the entire sequences of the RBD and NP proteins of SARS-CoV-2 in the sera from 66 COVID-19 patients and 23 healthy subjects by enzyme-linked immunosorbent assay (ELISA). Our results showed that while reactivity of patients' sera with reduced recombinant RBD protein was significantly lower than the native form of RBD (P < 0.001), no significant differences were observed for reactivity of patients' sera with reduced and non-reduced NP protein. Pepscan analysis revealed weak to moderate reactivity towards different RBD peptide pools, which was more focused on peptides encompassing amino acids (aa) 181–223 of RBD. NP peptides, however, displayed strong reactivity with a single peptide covering aa 151–170. These findings were confirmed by peptide depletion experiments using both ELISA and western blotting. Altogether, our data suggest involvement of mostly conformational disulfide bond-dependent immunodominant epitopes in RBD-specific antibody response, while the IgG response to NP is dominated by linear epitopes. Identification of dominant immunogenic epitopes in NP and RBD of SARS-CoV-2 could provide important information for the development of passive and active immunotherapy as well as diagnostic tools for the control of COVID-19 infection.
A B73×Palomero Toluqueño mapping population reveals local adaptation in Mexican highland maize
Authors: Perez-Limón Sergio , Li Meng , Cintora-Martinez G Carolina , Aguilar-Rangel M Rocio , Salazar-Vidal M Nancy , González-Segovia Eric , Blöcher-Juárez Karla , Guerrero-Zavala Alejandro , Barrales-Gamez Benjamin , Carcaño-Macias Jessica , Costich Denise E , Nieto-Sotelo Jorge , Martinez de la Vega Octavio , Simpson June , Hufford Matthew B , Ross-Ibarra Jeffrey , Flint-Garcia Sherry , Diaz-Garcia Luis , Rellán-Álvarez Rubén , Sawers Ruairidh J H
Published: January 2022

Generations of farmer selection in the central Mexican highlands have produced unique maize varieties adapted to the challenges of the local environment. In addition to possessing great agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterize a recombinant inbred line population derived from the B73 reference line and the Mexican highland maize variety Palomero Toluqueño. B73 and Palomero Toluqueño showed classic rank-changing differences in performance between lowland and highland field sites, indicative of local adaptation. Quantitative trait mapping identified genomic regions linked to effects on yield components that were conditionally expressed depending on the environment. For the principal genomic regions associated with ear weight and total kernel number, the Palomero Toluqueño allele conferred an advantage specifically in the highland site, consistent with local adaptation. We identified Palomero Toluqueño alleles associated with expression of characteristic highland traits, including reduced tassel branching, increased sheath pigmentation and the presence of sheath macrohairs. The oligogenic architecture of these three morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role of de novo mutation and the acquisition of adaptive variation by gene flow from endemic wild relatives.