bluuebunny/crossref_metadata_2025 huggingface dataset:
Association between Genitourinary and Congenital Heart Defects: A 52-year Case-Control Study of the Latin American Collaborative Study of Congenital Malformations (ECLAMC)
Authors: Fernandez Nicolas , Varela Daniela , Villanueva Juliana , Lopez Camelo Jorge , Zarante Ignacio
Published: December 2022

Background Congenital urological anomalies are present in 4.3/10 thousand newborns, and their association with other anomalies may increase the overall mortality and disability. The present study establishes the risk of having congenital urological anomalies presenting associated cardiopathies.

Methods We conducted a retrospective case-control study using the Latin American Collaborative Study of Congenital Malformations (Estudio Colaborativo Latino Americano de Malformaciones Congénitas, ECLAMC, in Spanish). The analysis included all registered cases of congenital urological malformation from 1967 to 2019. Patients with or without associated heart defects were included for the statistical analysis. Odds ratios (ORs) were calculated using a 95% confidence interval (95% CI). We compared the variables with the Chi-squared test and analysis of variance (ANOVA). The statistical analysis was performed using the Statistical Package for the Social Sciences (IBM SPSS Statistics for Windows, IBM Corp., Armonk, NY, United States) software, version 27.0. Values of p < 0.05 were considered statistically significant.

Results A total of 7,767,161 newborns were evaluated, and 17,834 genital and upper urinary tract malformations were identified. Of these, 64.2% were genital anomalies, and 35.8% were abnormalities of the upper urinary tract. Genitourinary malformations and concomitant congenital heart defects (GU + C) were observed in 3.5% of the cases. Subjects with GU + C had a higher number of malformations (4.59 ± 2.3) than patients without heart defects (1.53 ± 1.58) (p < 0.000). The OR was of 3.61 (range: 1.86–7.00) for cloacal exstrophy, of 4.01 (range: 3.14–5.12) for imperforate anus, of 5.52 (range: 3.92–7.78) for horseshoe kidney, and of 13.7 (range: 6.65–28.22) for trisomy 21 (Down syndrome) with malformations of the upper urinary tract.

Conclusion The association of congenital heart defects with urological anomalies is higher for complex congenital anomalies such as imperforate anus, cloacal exstrophy, and horseshoe kidney. Patients with urological abnormalities and Down syndrome have the highest likelihood.
Prevalencia de portación nasal de Staphylococcus aureus sensible y resistente a la meticilina en candidatos a artroplastia total de cadera o rodilla
Authors: Dabed David , Valenzuela Joaquín , Salgado Martín , Carmona Maximiliano
Published: December 2022

Introducción Las infecciones perioperatorias en cirugía de reemplazo articular son fuente importante de morbimortalidad, así como de altos costos económicos y sociales, tanto para el paciente como para su entorno. La colonización preoperatoria por Staphylococcus aureus ha sido reconocida como un factor de riesgo importante para desarrollar una infección de sitio quirúrgico.

El objetivo de este estudio es conocer la prevalencia de portación nasal de S. aureus, tanto sensible a la meticilina (SASM) como resistente a la meticilina (SARM), en pacientes candidatos a cirugía de reemplazo articular de cadera o rodilla.

Materiales y métodos Se realizó un estudio observacional de una cohorte retrospectiva de pacientes con indicación de artroplastia total de cadera (ATC) y rodilla (ATR) electiva por artrosis severa en un hospital público de Chile. Los pacientes fueron sometidos a tamizaje preoperatorio de portación, cultivándose muestras obtenidas mediante hisopado de ambas fosas nasales. Los datos del laboratorio fueron recopilados y presentados como porcentaje de portación de S. aureus.

Resultados Se estudiaron 303 pacientes consecutivos de ATC y 343 de ATR. En total, 483 de los 646 pacientes (74,7%) tuvieron estudio preoperatorio de portación nasal. Se identificaron 123 pacientes (25,4%) portadores de S. aureus, de los cuales sólo 2 (0,41%) casos correspondieron a SARM.

Conclusión La prevalencia de portación nasal de S. aureus obtenida fue de 25%, similar a lo reportado en otras series. La prevalencia de SARM (0.41%), sin embargo, estuvo bajo lo descrito en la literatura internacional (0,6–6%). Sería de utilidad, dada la alta prevalencia de portación descrita en nuestro trabajo y de acuerdo a evidencia publicada recientemente, realizar protocolos de descolonización universales, sin necesidad de realizar tamizaje preoperatorio.
Koopman and Perron–Frobenius operators on reproducing kernel Banach spaces
Authors: Ikeda Masahiro , Ishikawa Isao , Schlosser Corbinian
Published: December 2022

Koopman and Perron–Frobenius operators for dynamical systems are becoming popular in a number of fields in science recently. Properties of the Koopman operator essentially depend on the choice of function spaces where it acts. Particularly, the case of reproducing kernel Hilbert spaces (RKHSs) is drawing increasing attention in data science. In this paper, we give a general framework for Koopman and Perron–Frobenius operators on reproducing kernel Banach spaces (RKBSs). More precisely, we extend basic known properties of these operators from RKHSs to RKBSs and state new results, including symmetry and sparsity concepts, on these operators on RKBS for discrete and continuous time systems.
A review of thermal management of proton exchange membrane fuel cell systems
Authors: He Liange , Yang Yuanyin , Zhang Yan , Li Pengpai , Xin Yajie
Published: December 2022

Proton exchange membrane fuel cells (PEMFCs) have the advantages of long operation cycles, high energy efficiency, and no pollution of reaction products. Temperature is an important factor to ensure the operation of fuel cell systems. Too high temperature will cause irreversible damage to the proton exchange membrane, and too low temperature will greatly reduce the power generation efficiency of fuel cells. Therefore, the effective thermal management temperature control can ensure the stable operation of the system under steady state and dynamic variable load. It can also improve the reaction efficiency of the fuel cell system and prolong the life of the fuel cell. This paper mainly summarized the cooling mode and control strategy of PEMFCs based on thermal management system. The application of different cooling methods is further discussed. The characteristics of traditional proportional-integral-derivative (PID) control, fuzzy PID control, predictive control, adaptive control, and other common thermal management control strategies were described in detail. The research status of scholars in various countries were analyzed, respectively, and the cooling effects of different strategies are compared. Through the review and research on the temperature control of PEMFCs, it is found that the stable operation of the stack is inseparable from the coordination of reasonable cooling mode and control strategy.
The tempo and mode of character evolution in the assembly of mimetic communities
Authors: Basu Dipendra Nath , Bhaumik Vaishali , Kunte Krushnamegh
Published: December 2022

Multitrait adaptive evolution is shaped by factors such as phylogenetic and functional constraints as well as the intensity and direction of selection. The tempo and mode of such multitrait evolution can differentially impact the assembly of biological communities. Batesian mimicry, in which undefended prey gain a fitness advantage by evolving a resemblance to aposematic models, involves adaptive evolution of multiple traits such as color patterns and flight morphology. To elucidate the evolutionary mechanisms of such multitrait adaptations, we evaluated the tempo and mode of adaptive convergence in flight morphology and color patterns in mimetic butterfly communities. We found that compared with Batesian mimics or nonmimetic sister species, models showed significantly faster rates of aposematic trait evolution, creating adaptive peaks for mimicry. At the community level, the degree of mimetic resemblance between mimics and models was positively correlated with the rate of character evolution, but independent of phylogenetic relatedness. Monomorphic mimics and female-limited mimics converged on the color patterns of models to a similar degree, showing that there were no constraints on mimetic trait evolution with respect to sex-specific selections. Convergence was driven by the greater lability of color patterns, which evolved at significantly faster rates than the phylogenetically conserved flight morphological traits, indicating that the two traits evolve under differential selection pressures and/or functional and genetic constraints. These community-wide patterns show that during the assembly of a community, the tempo of adaptive evolution is nonlinear, and specific to the underlying functional relationships and key traits that define the community.
Robotic data acquisition with deep learning enables cell image–based prediction of transcriptomic phenotypes
Authors: Jin Jianshi , Ogawa Taisaku , Hojo Nozomi , Kryukov Kirill , Shimizu Kenji , Ikawa Tomokatsu , Imanishi Tadashi , Okazaki Taku , Shiroguchi Katsuyuki
Published: December 2022

Single-cell whole-transcriptome analysis is the gold standard approach to identifying molecularly defined cell phenotypes. However, this approach cannot be used for dynamics measurements such as live-cell imaging. Here, we developed a multifunctional robot, the automated live imaging and cell picking system (ALPS) and used it to perform single-cell RNA sequencing for microscopically observed cells with multiple imaging modes. Using robotically obtained data that linked cell images and the whole transcriptome, we successfully predicted transcriptome-defined cell phenotypes in a noninvasive manner using cell image–based deep learning. This noninvasive approach opens a window to determine the live-cell whole transcriptome in real time. Moreover, this work, which is based on a data-driven approach, is a proof of concept for determining the transcriptome-defined phenotypes (i.e., not relying on specific genes) of any cell from cell images using a model trained on linked datasets.
Self-esteem trajectories over three decades predict opposition to social equality in midlife
Authors: Fluit Sam , Kunst Jonas R. , Bierwiaczonek Kinga , von Soest Tilmann
Published: December 2022

Although life trajectories are frequently theorized to explain people’s attitudes toward different social groups, few studies have been able to directly assess their importance with suitable data. Addressing this gap and focusing on the development of general and domain-specific self-esteem, we report results from a population-based sample of Norwegians (
N
= 2,215) followed over 28 years and five time points from adolescence to midlife. Growth curve models demonstrated that irrespective of self-esteem domain, low levels of self-esteem in adolescence as well as a depressed self-esteem development over the next three decades were related to more overall opposition to social equality as well as more opposition to gender equality and immigration in midlife. The results held when controlling for participants’ baseline political orientations and other key covariates in adolescence. Our findings indicate that low self-esteem and a lack of positive self-esteem development can be detrimental to harmonious intergroup relations in ever-diversifying societies. We discuss how future psychological interventions aimed at enhancing self-esteem may promote support for a more inclusive society.
Quantum transport in graphene nanoribbon networks: complexity reduction by a network decimation algorithm
Authors: Rodemund Tom Simon , Teichert Fabian , Hentschel Martina , Schuster Jörg
Published: December 2022

We study electronic quantum transport (QT) in graphene nanoribbon (GNR) networks on mesoscopic length scales. We focus on zigzag GNRs and investigate the conductance properties of statistical networks. To this end we use a density-functional-based tight-binding model to determine the electronic structure and QT theory to calculate electronic transport properties. We then introduce a new efficient network decimation algorithm that reduces the complexity in generic three-dimensional GNR networks. We compare our results to semi-classical calculations based on the nodal analysis (NA) approach and discuss the dependence of the conductance on network density and network size. We show that a NA model cannot reproduce the QT results nor their dependence on model parameters well. Thus, solving the quantum network by our efficient approach is mandatory for accurate modelling the electron transport through GNR networks.
A new understanding of electron affinity of –OCH3 substituent groups based on single molecular conductance
Authors: Wang Ruixia , Zhou Jianghao , Wang Xu , Guo Jing , Qian Gongmin , Li Yuanchuan
Published: December 2022

To employ substituent groups to modulate the electronic properties of organic molecules as predicted, learning about their electron affinity is an important prerequisite. Herein, we used conventional electron-donating/withdrawing (ED/EW) substituent groups -OMe/-COOMe to modify TB, finding the resulting molecules OTB and CTB both demonstrated lower molecular conductance than TB. Current-voltage modeling and DFT calculation reveal –OCH3 demonstrated EW features instead of ED characteristics, which was supported by energy gap simulation and light emission as pulsed 365 nm light. This phenomenon was rarely observed, highlighting the importance of substituent groups’ electron affinity investigation in conductance based organic electronics.
Highly stable Ga-doped ZnO/polystyrene nanocomposite film with narrow-band cyan emission
Authors: Alamdari Sanaz , Tafreshi Majid Jafar , Ghamsari Morteza Sasani
Published: December 2022

In the present study, a simple method for the preparation of a luminescent flexible gallium doped zinc oxide (GZO)/polystyrene nanocomposite film was developed. The prepared GZO powder was characterized through different optical and structural techniques. The XRD study revealed the existence of a wurtzite structure with no extra oxide peaks. Elemental-mapping, EDX, FTIR and XPS analyses were used to confirm the presence of elements and the several groups present in the structure. Under excitations of UV, the prepared hybrid nanocomposite showed a strong cyan emission with narrow full width at half the maximum value (20 nm) that has not been reported before. X-ray and laser-induced luminescence results of the hybrid film revealed novel blue-green emission at room temperature. The prepared composite film showed a strong scintillation response to ionizing radiation. The strong emissions, very weak deep-level emissions, and low FWHM of composite indicate the desirable optical properties with low-density structural defects in the GZO composite structure. Therefore, the prepared hybrid film can be considered to be a suitable candidate for the fabrication of optoelectronic devices.
Discrimination of dislocations in 4H-SiC by inclination angles of molten-alkali etched pits
Authors: Yang Guang , Luo Hao , Li Jiajun , Shao Qinqin , Wang Yazhe , Zhu Ruzhong , Zhang Xi , Song Lihui , Zhang Yiqiang , Xu Lingbo , Cui Can , Pi Xiaodong , Yang Deren , Wang Rong
Published: December 2022

Discrimination of dislocations is critical to the statistics of dislocation densities in 4H silicon carbide (4H-SiC), which are routinely used to evaluate the quality of 4H-SiC single crystals and homoepitaxial layers. In this work, we show that the inclination angles of the etch pits of molten-alkali etched 4H-SiC can be adopted to discriminate threading screw dislocations (TSDs), threading edge dislocations (TEDs) and basal plane dislocations (BPDs) in 4H-SiC. In n-type 4H-SiC, the inclination angles of the etch pits of TSDs, TEDs and BPDs in molten-alkali etched 4H-SiC are in the ranges of 27°−35°, 8°−15° and 2°−4°, respectively. In semi-insulating 4H-SiC, the inclination angles of the etch pits of TSDs and TEDs are in the ranges of 31°−34° and 21°−24°, respectively. The inclination angles of dislocation-related etch pits are independent of the etching duration, which facilitates the discrimination and statistic of dislocations in 4H-SiC. More significantly, the inclination angle of a threading mixed dislocations (TMDs) is found to consist of characteristic angles of both TEDs and TSDs. This enables to distinguish TMDs from TSDs in 4H-SiC.
Quantifying electron cyclotron power deposition broadening in DIII-D and the potential consequences for the ITER EC system
Authors: Slief J.H. , van Kampen R.J.R. , Brookman M.W. , van Dijk J. , Westerhof E. , van Berkel M.
Published: December 2022

The injection of electron cyclotron (EC) waves fulfills a number of important tasks in nuclear fusion devices for which detailed knowledge of the spatial power deposition profile is critical. This deposition profile is commonly determined using forward models such as beam or ray tracing. Recent numerical and experimental studies have shown that small-angle scattering of the EC beam as it passes through the turbulent plasma edge can cause significant broadening of the effective deposition profile, leading to considerable underestimation of the deposition width by forward methods. However, traditional inverse methods to determine the deposition profile from measurements overestimate the deposition profile width due to transport broadening. In this work, we implement three novel methods to resolve the EC power deposition profile from measurements that counteract transport broadening by simultaneously resolving transport and power deposition. We validate their assumptions and compare the results from these methods to the traditional break-in-slope method as well as to the TORAY ray-tracing code in a set of DIII-D discharges spanning five different confinement modes. We show that the four different inverse methods, novel and established, paint a consistent picture of deposition broadening. Specifically, we show that the measured power deposition profile is between 1.6 and 3.6 times wider than the TORAY profiles. Moreover, we show the considerable consequences that this level of broadening can have for ITER.
Timing properties of blue-emitting scintillating fibers
Authors: Bravar A. , Demets Y.
Published: December 2022

Scintillating fibers are widely used in particle detectors, mainly for tracking. We have
studied the properties and have compared the performance of different blue-emitting 250 μm
diameter round double-clad scintillating fibers from Kuraray and Saint-Gobain. Here we focus on
the properties of the fibers over short lengths (< 50 cm), in particular on their timing
performances. We report on the light yield and attenuation, scintillation light decay time and
the achievable time resolution.
An attention-based LSTM model for long-term runoff forecasting and factor recognition
Authors: Han Dongyang , Liu Pan , Xie Kang , Li He , Xia Qian , Cheng Qian , Wang Yibo , Yang Zhikai , Zhang Yanjun , Xia Jun
Published: December 2022

With advances in artificial intelligence, machine learning-based models such as long short-term memory (LSTM) models have shown much promise in forecasting long-term runoff by mapping pathways between large-scale climate patterns and catchment runoff responses without considering physical processes. The recognition of key factors plays a vital role and thus affects the performance of the model. However, there is no conclusion on which recognition algorithm is the most suitable. To address this issue, an LSTM model combined with two attention mechanisms both in the input and hidden layers, namely AT-LSTM, is proposed for long-term runoff forecasting at Yichang and Pingshan stations in China. The added attention mechanisms automatically assign weights to 130 climate phenomenon indexes, avoiding the use of subjectively set recognition algorithms. Results show that the AT-LSTM model outperforms the Pearson’s correlation based LSTM model in terms of four evaluation metrics for monthly runoff forecasting. Further, the set indirect runoff prediction method verifies that the AT-LSTM model also performs effectively in precipitation and potential evapotranspiration forecasting, and the indirect runoff prediction is inferior to the AT-LSTM model to establish a direct link between climate factors and runoff. Finally, four key factors related to runoff are identified by the attention mechanism and their impacts on runoff are analyzed on intra- and inter-annual scales. The proposed AT-LSTM model can effectively improve the accuracy of long-term forecasting and identify the dynamic influence of input factors.
The generalized doubling method: (𝑘,𝑐) models
Authors: Cai Yuanqing , Friedberg Solomon , Gourevitch Dmitry , Kaplan Eyal
Published: December 2022

One of the key ingredients in the recent construction of the generalized doubling method is a new class of models, called

(
k
,
c
)

(k,c)

models, for local components of generalized Speh representations. We construct a family of

(
k
,
c
)

(k,c)

representations, in a purely local setting, and discuss their realizations using inductive formulas. Our main result is a uniqueness theorem which is essential for the proof that the generalized doubling integral is Eulerian.
Hadamard products and Schwartz functions
Authors: Hegde Devadatta
Published: December 2022

We show that functions of the form

∏

n
≥
1

(
1
+

x

2

/

a

n

2

)

−
1

\prod _{n\ge 1}\left (1+x^{2}/a_{n}^{2}\right )^{-1}

(

a

n

>
0
)

(a_{n}>0)

are in the Schwartz space of the real line whenever the infinite product converges uniformly on compact subsets of

C

\mathbb {C}

, answering a question of Bill Casselman. We also include a different proof due to Jean-Loup Waldspurger.
Lower bounds for Mahler-type measures of polynomials
Authors: Dubickas Artūras , Pritsker Igor
Published: December 2022

In this note we consider various generalizations of the classical Mahler measure<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper M left-parenthesis upper P right-parenthesis equals exp left-parenthesis StartFraction 1 Over 2 pi EndFraction integral Subscript 0 Superscript 2 pi Baseline log vertical-bar upper P left-parenthesis e Superscript i theta Baseline right-parenthesis d theta right-parenthesis">M(P)=exp⁡(12π∫02πlog⁡|P(eiθ)dθ)M(P)=\exp \left (\frac {1}{2\pi }\int _0^{2\pi } \log |P(e^{i\theta })\,d\theta \right )for complex polynomialsPP, and prove sharp lower bounds for them. For example, we show that for any monic polynomialP∈C[z]P \in {\mathbb {C}}[z]satisfying|P(0)|=1|P(0)|=1the quantity<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="upper M 0 left-parenthesis upper P right-parenthesis equals exp left-parenthesis StartFraction 1 Over 2 pi EndFraction integral Subscript 0 Superscript 2 pi Baseline max left-parenthesis 0 comma log StartAbsoluteValue upper P left-parenthesis e Superscript i theta Baseline right-parenthesis EndAbsoluteValue right-parenthesis d theta right-parenthesis">M0(P)=exp⁡(12π∫02πmax(0,log⁡|P(eiθ)|)dθ)M_0(P) = \exp \left (\frac {1}{2\pi }\int _0^{2\pi } \max (0,\log |P(e^{i\theta })|)\,d\theta \right )is greater than or equal toM(1+z1+z2)=1.381356…M(1+z_1+z_2)=1.381356\dots. This inequality is best possible, with equality being attained for allP(z)=zn+cP(z)=z^n+cwithn∈Nn \in \mathbb {N}and|c|=1|c|=1.
Galvin’s problem in higher dimensions
Authors: Raghavan Dilip , Todorcevic Stevo
Published: December 2022

It is proved that for each natural number

n
n

, if

|

R

|

=

ℵ

n

\left |\mathbb {R}\right |= {\aleph }_{n}

, then there is a coloring of

[

R

]

n
+
2

{\left [\mathbb {R}\right ]}^{n+2}

into

ℵ

0

{\aleph }_{0}

colors that takes all colors on

[
X
]

n
+
2

{\left [X\right ]}^{n+2}

whenever

X
X

is any set of reals which is homeomorphic to

Q

\mathbb {Q}

. This generalizes a theorem of Baumgartner and sheds further light on a problem of Galvin from the 1970s. Our result also complements and contrasts with our earlier result saying that any coloring of

[

R

]

2

{\left [\mathbb {R}\right ]}^{2}

into finitely many colors can be reduced to at most

2
2

colors on the pairs of some set of reals which is homeomorphic to

Q

\mathbb {Q}

when large cardinals exist.
On congruences involving Apéry numbers
Authors: Xia Wei , Sun Zhi-Wei
Published: December 2022

In this paper, we mainly establish a congruence for a sum involving Apéry numbers, which was conjectured by Z.-W. Sun. Namely, for any prime

p
>
3

p>3

and positive odd integer

m
m

, we prove that there is a

p
p

-adic integer

c
m

c_m

only depending on

m
m

such that
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="sigma-summation Underscript k equals 0 Overscript p minus 1 Endscripts left-parenthesis 2 k plus 1 right-parenthesis Superscript m Baseline left-parenthesis negative 1 right-parenthesis Superscript k Baseline upper A Subscript k Baseline identical-to c Subscript m Baseline p left-parenthesis StartFraction p Over 3 EndFraction right-parenthesis left-parenthesis mod p cubed right-parenthesis comma">

∑

k
=
0

p
−
1

(
2
k
+
1

)

m

(
−
1

)
k

A
k

≡

c
m

p

(

p
3

)

(
mod

p
3

)
,

\begin{equation*} \sum _{k=0}^{p-1}(2k+1)^{m}(-1)^kA_k\equiv c_mp\left (\frac {p}{3}\right )\pmod {p^3}, \end{equation*}

where

A
k

=

∑

j
=
0

k

(

k
j

)

2

(

k
+
j

j

)

2

A_k=\sum _{j=0}^{k}\binom {k}{j}^2\binom {k+j}{j}^2

is the Apéry number and

(

.
p

)

(\frac {.}{p})

is the Legendre symbol.
Territoriality varies across elevation in a Hawaiian songbird
Authors: Names Gabrielle R , Hahn Thomas P , Wingfield John C , Hunt Kathleen E
Published: December 2022

Reproductive territoriality can be influenced by external and internal variables. Trade-offs between reproductive behaviors and other costly biological processes, such as immunity, exist across taxa, but the effects of novel diseases on these trade-offs remain poorly understood. Since the introduction of avian malaria to Hawaii in the early 1900s, low elevation Hawaii Amakihi (Chlorodrepanis virens) populations, which have undergone strong selection by the disease, have evolved increased malaria resilience. However, the effects of malaria selection on trade-offs between immunity and reproduction in Amakihi remain largely unknown. To begin exploring this relationship, we conducted simulated territorial intrusions on Amakihi at low elevation (where malaria selection has been stronger) and high elevation (where selection has been weaker) on Hawaii Island during the breeding season. We hypothesized that selection by avian malaria has favored greater investment in avian malaria resilience at the cost of reproductive behaviors. We predicted that low elevation Amakihi would be less territorial compared with high elevation Amakihi, while recognizing that variables other than disease pressures that may differ across elevation (e.g., competition, predation) could explain behavioral variation. Territoriality was reduced in low compared with high elevation Amakihi as measured by proximity and chases in response to the intrusion. Low elevation Amakihi generally flew less than high elevation individuals, although this relationship varied across the breeding season. Our correlational results demonstrate that territoriality is greater in high compared with low elevation Amakihi. Further investigations would help determine which factors differing across elevation underlie this variation in territoriality.
Eyes on the future: buffering increased costs of incubation by abandoning offspring
Authors: Hanssen Sveinn Are , Erikstad Kjell Einar , Sandvik Hanno , Tveraa Torkild , Bustnes Jan Ove
Published: December 2022

Life history theory states that the resources invested in current reproduction must be traded off against resources needed for survival and future reproduction. Long-lived organisms have a higher residual reproductive value and are therefore expected to be sensitive to reproductive investments that may reduce survival and future reproduction. Individuals within a population may vary in phenotypic quality, experience, access to resources etc. This may affect their optimal reproductive investment level. In this study we manipulated reproductive costs by shortening and extending the incubation period in common eiders Somateria mollissima without altering clutch size. Females whose incubation time was prolonged experimentally, suffered higher mass loss and increased clutch loss/nest desertion. These females were also more prone to abandon their brood after hatching. Both clutch loss and brood abandonment decreased with clutch size in all treatment categories, indicating higher phenotypic quality and/or better access to resources for females producing more eggs. However, although females with prolonged incubation were lighter at hatching, their return rate and breeding performance in the following year were unaffected. These results show that individual quality as expressed through clutch size and body mass is affecting current reproductive investment level as well as future survival and breeding performance. The results also show that individual birds are sensitive to changes in their own condition, and when reproductive effort is approaching a level where survival or future survival may be compromised, they respond by terminating their current reproductive attempt.
SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants
Authors: Fan Xiao , Pan Hongbing , Tian Alan , Chung Wendy K , Shen Yufeng
Published: December 2022

Accurate variant pathogenicity predictions are important in genetic studies of human diseases. Inframe insertion and deletion variants (indels) alter protein sequence and length, but not as deleterious as frameshift indels. Inframe indel Interpretation is challenging due to limitations in the available number of known pathogenic variants for training. Existing prediction methods largely use manually encoded features including conservation, protein structure and function, and allele frequency to infer variant pathogenicity. Recent advances in deep learning modeling of protein sequences and structures provide an opportunity to improve the representation of salient features based on large numbers of protein sequences. We developed a new pathogenicity predictor for SHort Inframe iNsertion and dEletion (SHINE). SHINE uses pretrained protein language models to construct a latent representation of an indel and its protein context from protein sequences and multiple protein sequence alignments, and feeds the latent representation into supervised machine learning models for pathogenicity prediction. We curated training data from ClinVar and gnomAD, and created two test datasets from different sources. SHINE achieved better prediction performance than existing methods for both deletion and insertion variants in these two test datasets. Our work suggests that unsupervised protein language models can provide valuable information about proteins, and new methods based on these models can improve variant interpretation in genetic analyses.
Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer
Authors: Liao Zhirui , Xie Lei , Mamitsuka Hiroshi , Zhu Shanfeng
Published: December 2022

Motivation

Finding molecules with desired pharmaceutical properties is crucial in drug discovery. Generative models can be an efficient tool to find desired molecules through the distribution learned by the model to approximate given training data. Existing generative models (i) do not consider backbone structures (scaffolds), resulting in inefficiency or (ii) need prior patterns for scaffolds, causing bias. Scaffolds are reasonable to use, and it is imperative to design a generative model without any prior scaffold patterns.

Results

We propose a generative model-based molecule generator, Sc2Mol, without any prior scaffold patterns. Sc2Mol uses SMILES strings for molecules. It consists of two steps: scaffold generation and scaffold decoration, which are carried out by a variational autoencoder and a transformer, respectively. The two steps are powerful for implementing random molecule generation and scaffold optimization. Our empirical evaluation using drug-like molecule datasets confirmed the success of our model in distribution learning and molecule optimization. Also, our model could automatically learn the rules to transform coarse scaffolds into sophisticated drug candidates. These rules were consistent with those for current lead optimization.

Availability and implementation

The code is available at https://github.com/zhiruiliao/Sc2Mol.

Supplementary information

Supplementary data are available at Bioinformatics online.
Graph lesion-deficit mapping of fluid intelligence
Authors: Cipolotti Lisa , Ruffle James K , Mole Joe , Xu Tianbo , Hyare Harpreet , Shallice Tim , Chan Edgar , Nachev Parashkev
Published: December 2022

Fluid intelligence is arguably the defining feature of human cognition. Yet the nature of its relationship with the brain remains a contentious topic. Influential proposals drawing primarily on functional imaging data have implicated ‘multiple demand’ frontoparietal and more widely distributed cortical networks, but extant lesion-deficit studies with greater causal power are almost all small, methodologically constrained, and inconclusive. The task demands large samples of patients, comprehensive investigation of performance, fine-grained anatomical mapping, and robust lesion-deficit inference, yet to be brought to bear on it.

We assessed 165 healthy controls and 227 frontal or non-frontal patients with unilateral brain lesions on the best-established test of fluid intelligence, Raven’s Advanced Progressive Matrices, employing an array of lesion-deficit inferential models responsive to the potentially distributed nature of fluid intelligence. Non-parametric Bayesian stochastic block models were used to reveal the community structure of lesion deficit networks, disentangling functional from confounding pathological distributed effects.

Impaired performance was confined to patients with frontal lesions [F(2,387) = 18.491; P < 0.001; frontal worse than non-frontal and healthy participants P < 0.01, P <0.001], more marked on the right than left [F(4,385) = 12.237; P < 0.001; right worse than left and healthy participants P < 0.01, P < 0.001]. Patients with non-frontal lesions were indistinguishable from controls and showed no modulation by laterality. Neither the presence nor the extent of multiple demand network involvement affected performance. Both conventional network-based statistics and non-parametric Bayesian stochastic block modelling heavily implicated the right frontal lobe. Crucially, this localization was confirmed on explicitly disentangling functional from pathology-driven effects within a layered stochastic block model, prominently highlighting a right frontal network involving middle and inferior frontal gyrus, pre- and post-central gyri, with a weak contribution from right superior parietal lobule. Similar results were obtained with standard lesion-deficit analyses.

Our study represents the first large-scale investigation of the distributed neural substrates of fluid intelligence in the focally injured brain. Combining novel graph-based lesion-deficit mapping with detailed investigation of cognitive performance in a large sample of patients provides crucial information about the neural basis of intelligence. Our findings indicate that a set of predominantly right frontal regions, rather than a more widely distributed network, is critical to the high-level functions involved in fluid intelligence. Further they suggest that Raven’s Advanced Progressive Matrices is a useful clinical index of fluid intelligence and a sensitive marker of right frontal lobe dysfunction.
Metformin Use Is Associated With Lower Mortality in Veterans With Diabetes Hospitalized With Pneumonia
Authors: Mohammed Turab , Bowe Michael , Plant Alexandria , Perez Mario , Alvarez Carlos A , Mortensen Eric M
Published: December 2022

Background

Recent studies suggest that metformin use may be associated with improved infectious disease–related outcomes, whereas other papers suggest potentially worse outcomes in serious bacterial infections. Our purpose was to examine the association of prior outpatient prescription of metformin on 30- and 90-day mortality for older veterans with pre-existing diabetes hospitalized with pneumonia.

Methods

We conducted a retrospective cohort study using national Department of Veterans Affairs data of patients ≥65 years with a prior history of diabetes who were hospitalized with pneumonia over a 10-year period (fiscal years 2002–2012.) For our primary analysis, we created a propensity score and matched metformin users to nonusers 1:1.

Results

We identified 34 759 patients who met the inclusion criteria, 20.3% of whom were prescribed metformin. Unadjusted 30-day mortality was 9.6% for those who received metformin versus 13.9% in nonusers (P < .003), and 90-day mortality was 15.8% for those who received metformin versus 23.0% for nonusers (P < .0001). For the propensity score model, we matched 6899 metformin users to 6899 nonusers. After propensity matching, both 30-day (relative risk [RR]: .86; 95% confidence interval [CI]: .78–.95) and 90-day (RR: .85; 95% CI: .79–.92) mortality was significantly lower for metformin users.

Conclusions

Prior receipt of metformin was associated with significantly lower mortality after adjusting for potential confounders. Additional research is needed to examine the safety and potential benefits of metformin use in patients with respiratory infections.
Testing for Mycoplasma genitalium and Using Doxycycline as First-Line Therapy at Initial Presentations for Non-Gonococcal Urethritis (NGU) Correlate With Reductions in Persistent NGU
Authors: Johnson Kelly A , Sankaran Madeline , Kohn Robert P , Bacon Oliver , Cohen Stephanie E
Published: December 2022

We found that the odds of return clinic visits for persistent non-gonococcal urethritis (NGU) were significantly lower (odds ratio: .4; 95% confidence interval: .3–.6; P < .0001) after implementing (1) testing for Mycoplasma genitalium during initial evaluations for NGU and (2) switching from azithromycin to doxycycline as first-line NGU treatment.
Wall shear stress–related plaque growth of lipid-rich plaques in human coronary arteries: an near-infrared spectroscopy and optical coherence tomography study
Authors: Hartman Eline M J , De Nisco Giuseppe , Kok Annette M , Tomaniak Mariusz , Nous Fay M A , Korteland Suze-Anne , Gijsen Frank J H , den Dekker Wijnand K , Diletti Roberto , van Mieghem Nicolas M D A , Wilschut Jeroen M , Zijlstra Felix , van der Steen Anton F W , Budde Ricardo P J , Daemen Joost , Wentzel Jolanda J
Published: December 2022

Aims

Low wall shear stress (WSS) is acknowledged to play a role in plaque development through its influence on local endothelial function. Also, lipid-rich plaques (LRPs) are associated with endothelial dysfunction. However, little is known about the interplay between WSS and the presence of lipids with respect to plaque progression. Therefore, we aimed to study the differences in WSS-related plaque progression between LRPs, non-LRPs, or plaque-free regions in human coronary arteries.

Methods and results

In the present single-centre, prospective study, 40 patients who presented with an acute coronary syndrome successfully underwent near-infrared spectroscopy intravascular ultrasound (NIRS-IVUS) and optical coherence tomography (OCT) of at least one non-culprit vessel at baseline and completed a 1-year follow-up. WSS was computed applying computational fluid dynamics to a three-dimensional reconstruction of the coronary artery based on the fusion of the IVUS-segmented lumen with a CT-derived centreline, using invasive flow measurements as boundary conditions. For data analysis, each artery was divided into 1.5 mm/45° sectors. Plaque growth based on IVUS-derived percentage atheroma volume change was compared between LRPs, non-LRPs, and plaque-free wall segments, as assessed by both OCT and NIRS. Both NIRS- and OCT-detected lipid-rich sectors showed a significantly higher plaque progression than non-LRPs or plaque-free regions. Exposure to low WSS was associated with a higher plaque progression than exposure to mid or high WSS, even in the regions classified as a plaque-free wall. Furthermore, low WSS and the presence of lipids had a synergistic effect on plaque growth, resulting in the highest plaque progression in lipid-rich regions exposed to low shear stress.

Conclusion

This study demonstrates that NIRS- and OCT-detected lipid-rich regions exposed to low WSS are subject to enhanced plaque growth over a 1-year follow-up. The presence of lipids and low WSS proves to have a synergistic effect on plaque growth.
Abaloparatide and teriparatide enhance mandibular growth in adolescent rats with site-specific and mechano-related effects
Authors: Wang Ruyi , Qiao Hui , Qian Yuran , Zhen Gehua , Zhao Zhihe , Li Yu
Published: December 2022

Objective

Teriparatide (TPTD) and abaloparatide (ABL) are two osteoanabolic drugs targeting parathyroid hormone (PTH)1R signalling. This study aimed to investigate the effects of TPTD and ABL on the adolescent mandibular growth.

Method

In total, 70 4-week-old male Sprague-Dawley rats were randomly divided into 14 groups, treated with intermittent TPDT or ABL at various doses, accompanied by mandibular advancement (MA) or not. 3D printing was used to fabricate an innovative splint for MA. After a 4-week treatment, morphological measurement, histological and immunohistochemical analysis were performed. Mandibular condylar chondrocytes (MCCs) were treated with TPTD or ABL, followed by CCK-8 assay, alcian blue staining, real time–PCR and immunofluorescent staining.

Result

In vivo, TPTD or ABL alone increased the condylar length and cartilage thickness, with up-regulated SOX9 and COL II, whilst down-regulated COL X; however, when combined with MA, the promotive effects were attenuated. TPTD or ABL alone increased the mandibular body height and mandibular angle width, whilst increased the mandibular body length and alveolar bone width when combined with MA. In vitro, TPTD or ABL enhanced the MCC proliferation, glycosaminoglycan synthesis, COL II and SOX9 expression, whilst down-regulated COL X, Ihh and PTH1R expression.

Conclusion

Both ABL and TPTD enhance mandibular growth in adolescent rats with site-specific and mechano-related effects, including propelling chondrogenesis at the condylar cartilage and promoting bone apposition at other mechano-responsive sites. They behave as promising drugs for mandibular growth modification, and in general ABL seems more potent than TPTD in this context.
Escaping one’s disadvantage? Neighbourhoods, socioeconomic origin and children’s adult life outcomes
Authors: Brandén Maria , Haandrikman Karen , Birkelund Gunn Elisabeth
Published: December 2022

This study investigates if neighbourhoods can alter the strong relationship between parental background and children’s adult outcomes. In particular, we examine if neighbourhood effects are heterogeneous in such a way that they are particularly important for children from disadvantaged backgrounds, and if school quality has a mediating effect in this equation. Using register data and individualized neighbourhoods, we follow five full birth cohorts of individuals born from 1983 to 1987. We examine the interaction between social background and neighbourhoods in shaping (i) the risk of children relying on social welfare when they are aged 30, and (ii) the probability of belonging to the highest income decile at age 30–34. Growing up in a resource-rich neighbourhood is associated with better life outcomes. Contrary to what several neighbourhood theories predict, we find that neighbourhood effects operate similarly regardless of social background. Differences in peer composition of schools does not explain these local neighbourhood effects, whereas own school results attenuate neighbourhood effects substantially. Our findings are in contrast to results from the United States studies but are in line with historical Swedish studies; and contribute to further disentangling the various mechanisms through which the neighbourhood operates.
Application of the fission yeast Schizosaccharomyces pombe in human nutrition
Authors: Chen Ee Sin
Published: December 2022

Fission yeast Schizosaccharomyces pombe (S. pombe) is renowned as a powerful genetic model for deciphering cellular and molecular biological phenomena, including cell division, chromosomal events, stress responses, and human carcinogenesis. Traditionally, Africans use S. pombe to ferment the beer called ‘Pombe’, which continues to be consumed in many parts of Africa. Although not as widely utilized as the baker's yeast Saccharomyces cerevisiae, S. pombe has secured several niches in the food industry for human nutrition because of its unique metabolism. This review will explore three specific facets of human nutrition where S. pombe has made a significant impact: namely, in wine fermentation, animal husbandry and neutraceutical supplementation coenzyme Q10 production. Discussions focus on the current gaps in these areas, and the potential research advances useful for addressing future challenges. Overall, gaining a better understanding of S. pombe metabolism will strengthen production in these areas and potentially spearhead novel future applications.
Anti-restriction protein ArdA promotes clinical Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae spread and its molecular mechanism
Authors: Chen Huimin , Tao Shuan , Li Na , Zhu Qing , Liu Liping , Fang Yeiwei , Xu Yao , Liang Wei
Published: December 2022

Background

Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) has spread worldwide and has become a major threat to public health. The restriction modification system provides an innate defence of bacteria against plasmids or transposons, while many different types of plasmid encoding the anti-restriction protein ArdA can specifically affect the restriction activity in bacteria.

Objectives

To detect the codistribution of ArdA and blaKPC-2 plasmids in KPC-KP and explore the molecular mechanism of ArdA promoting KPC-KP spread.

Methods

We collected 65 clinical CRKP isolates from Ningbo, China, and 68 cases of plasmid complete sequences in GenBank to determine the prevalence of ArdA gene on the K. pneumoniae blaKPC-2 plasmid. The anti-restriction function of ArdA in promoting horizontal gene transfer (HGT) was verified by transformation, conjugation and transduction methods, and the pull-down experiment was used to investigate the molecular mechanism of ArdA protein in vitro.

Results

We found that ArdA was widely distributed in KPC-KP in 100% of cases, which was detected in 0% of drug susceptible K. pneumoniae, and the plasmids containing the ArdA gene in 90% of the 30 cases randomly retrieved from the database. We also verified that ArdA has a good anti-restriction function (P < 0.05) through two aspects of HGT (transformation, transduction), and explored the non-occurrence interaction of ArdA and the hsdM subunit protein of EcoKI enzyme from the perspective of protein molecules.

Conclusions

These findings suggest that the coexistence advantage of ArdA with the blaKPC-2 plasmids may provide KPC-producing K. pneumoniae with a very efficient evasion of the restriction of type I systems, which not only favours ArdA-containing mobile genetic elements in the same species HGT between bacteria also facilitates HGT between other bacterial species.