bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum information criteria for model selection in quantum state estimation
Authors: Yano Hiroshi , Yamamoto Naoki 
Published: September 2023

Abstract
Quantum state estimation (or state tomography) is an indispensable task in quantum information processing. Because full state tomography that determines all elements of the density matrix is computationally demanding, one usually takes the strategy of assuming a certain model of quantum states and identifying the model parameters. However, it is difficult to make a valid assumption given little prior knowledge on a quantum state of interest, and thus we need a reasonable model selection method for quantum state estimation. Actually, in the classical statistical estimation theory, several types of information criteria have been established and widely used in practice for appropriately choosing a classical statistical model. In this study, we propose quantum information criteria for evaluating the quality of the estimated quantum state in terms of the quantum relative entropy, which is a natural quantum analogue of the classical information criterion defined in terms of Kullback–Leibler divergence. In particular, we derive two quantum information criteria depending on the type of an estimator for the quantum relative entropy; one uses the log-likelihood and the other uses the classical shadow. The general role of information criteria is to predict the performance of an estimated model for unseen data, although it is a function of only sampled data; this generalization capability of the proposed quantum information criteria is evaluated in numerical simulations.
First-passage functionals for Ornstein–Uhlenbeck process with stochastic resetting
Authors: Dubey Ashutosh , Pal Arnab 
Published: September 2023

Abstract
We study the statistical properties of first-passage Brownian functionals (FPBFs) of an Ornstein–Uhlenbeck process in the presence of stochastic resetting. We consider a one dimensional set-up where the diffusing particle sets off from x
0 and resets to

x

R

at a certain rate r. The particle diffuses in a harmonic potential (with strength k) which is centered around the origin. The center also serves as an absorbing boundary for the particle and we denote the first passage time (FPT) of the particle to the center as

t

f

. In this set-up, we investigate the following functionals: (i) local time

T

l
o
c

=

∫
0

t

f

d

τ

δ
(
x
−

x

R

)

i.e. the time a particle spends around

x

R

until the first passage, (ii) occupation or residence time

T

r
e
s

=

∫
0

t

f

d

τ

θ
(
x
−

x

R

)

i.e. the time a particle typically spends above

x

R

until the first passage and (iii) the FPT

t

f

to the origin. We employ the Feynman–Kac formalism for renewal process to derive the analytical expression for the first moment of all the three FPBFs mentioned above. In particular, we find that resetting can either prolong or shorten the mean residence and FPT depending on the system parameters. The transition between these two behaviors or phases can be characterized precisely in terms of optimal resetting rates, which interestingly undergo a continuous transition as we vary the trap stiffness k. We characterize this transition and identify the critical-parameter and -coefficient for both the cases. We also showcase other interesting interplay between the resetting rate and potential strength on the statistics of these observables. Our analytical results are in excellent agreement with the numerical simulations.
Electrical resistance-based monitoring of CFRP thickness during vacuum assisted resin infusion
Authors: Jeong Woo Nam , Um Moon-Kwang , Kim Wie-Dae , Roh Hyung Doh 
Published: September 2023

Abstract
During vacuum-assisted resin infusion (VARI), the thickness of the fabric manufactured into carbon fiber (CF)-reinforced plastic was monitored using electrical resistance, which was correlated with the mechanical and electrical status of the CF with respect to resin infiltration. Furthermore, the electrical network within CF varied in terms of its volume and number of electrical contacts. These phenomena were monitored by installing a Cu tape on the mold. Thus, an in-situ qualitative monitoring system for composite manufacturing was developed utilizing the electrical resistance variations in the fabric. The proposed thickness-monitoring system for VARI can potentially minimize the cost, time, and labor in composite industries.
Probing NV and SiV charge state dynamics using high-voltage nanosecond pulse and photoluminescence spectral analysis
Authors: Pambukhchyan Artur , Weng Sizhe , Aravind Indu , Cronin Stephen B , Takahashi Susumu 
Published: September 2023

Abstract
Nitrogen-vacancy (NV) and silicon-vacancy (SiV) color defects in diamond are promising systems for applications in quantum technology. The NV and SiV centers have multiple charge states, and their charge states have different electronic, optical and spin properties. For the NV centers, most investigations for quantum sensing applications are targeted on the negatively charged NV (NV−), and it is important for the NV centers to be in the NV− state. However, it is known that the NV centers are converted to the neutrally charged state (NV0) under laser excitation. An energetically favorable charge state for the NV and SiV centers depends on their local environments. It is essential to understand and control the charge state dynamics for their quantum applications. In this work, we discuss the charge state dynamics of NV and SiV centers under high-voltage nanosecond pulse discharges. The NV and SiV centers coexist in the diamond crystal. The high-voltage pulses enable manipulating the charge states efficiently. These voltage-induced changes in charge states are probed by their photoluminescence spectral analysis. The analysis result from the present experiment shows that the high-voltage nanosecond pulses cause shifts of the chemical potential and can convert the charge states of NV and SiV centers with the transition rates of ∼MHz. This result also indicates that the major population of the SiV centers in the sample is the doubly negatively charged state (SiV2−), which is often overlooked because of its non-fluorescent and non-magnetic nature. This demonstration paves a path for a method of rapid manipulation of the NV and SiV charge states in the future.
Letter to the editor: testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis
Authors: Leventhal Emily L , Daamen Andrea R , Lipsky Peter E 
Published: September 2023

Abstract
Because of the clinical heterogeneity among patients with systemic lupus erythematosus (SLE), developing molecular profiles that predict clinical features can be useful in creating a personalized approach to treatment. Toro-Domínguez et al. created a web tool to aid in therapeutic decision making for clinicians that predicts clinical features associated with SLE from blood transcriptomic data. Specifically, they present a machine learning model that predicts the presence of proliferative nephritis from blood transcriptomics. Here, we report use of the tool in independent datasets and found that it did not perform sufficiently well to consider replacement of the standard kidney biopsy as a diagnostic procedure.
3D based generative PROTAC linker design with reinforcement learning
Authors: Li Baiqing , Ran Ting , Chen Hongming 
Published: September 2023

Abstract
Proteolysis targeting chimera (PROTAC), has emerged as an effective modality to selectively degrade disease-related proteins by harnessing the ubiquitin-proteasome system. Due to PROTACs’ hetero-bifunctional characteristics, in which a linker joins a warhead binding to a protein of interest (POI), conferring specificity and a E3-ligand binding to an E3 ubiquitin ligase, this could trigger the ubiquitination and transportation of POI to the proteasome, followed by degradation. The rational PROTAC linker design is challenging due to its relatively large molecular weight and the complexity of maintaining the binding mode of warhead and E3-ligand in the binding pockets of counterpart. Conventional linker generation method can only generate linkers in either 1D SMILES or 2D graph, without taking into account the information of ternary structures. Here we propose a novel 3D linker generative model PROTAC-INVENT which can not only generate SMILES of PROTAC but also its 3D putative binding conformation coupled with the target protein and the E3 ligase. The model is trained jointly with the RL approach to bias the generation of PROTAC structures toward pre-defined 2D and 3D based properties. Examples were provided to demonstrate the utility of the model for generating reasonable 3D conformation of PROTACs. On the other hand, our results show that the associated workflow for 3D PROTAC conformation generation can also be used as an efficient docking protocol for PROTACs.
Melatonin-pretreated human umbilical cord mesenchymal stem cells improved endometrium regeneration and fertility recovery through macrophage immunomodulation in rats with intrauterine adhesions
Authors: Qin Weili , Wang Jiawei , Hu Qianwen , Qin Rongyan , Ma Nana , Zheng Fengque , Tian Wencai , Jiang Jinghang , Li Ting , Jin Yufu , Liao Ming , Qin Aiping 
Published: September 2023

Abstract
Intrauterine adhesions (IUA) are a common gynecological problem. Stem cell therapy has been widely used in the treatment of IUA. However, due to the complex and harsh microenvironment of the uterine cavity, the effectiveness of such therapy is greatly inhibited. This study aimed to investigate whether melatonin pretreatment enhances the efficacy of human umbilical cord mesenchymal stem cells (HucMSCs) in IUA treatment in rats. First, we explored the effect of melatonin on the biological activity of HucMSCs in vitro through a macrophage co-culture system, Cell Counting Kit 8 (CCK-8), 5-Ethynyl-2′-deoxyuridine (EdU), flow cytometry, immunofluorescence staining, and qRT-PCR. Subsequently, we established the IUA rat model and tracked the distribution of HucMSCs in this model. In addition, we observed the number of M1 and M2 macrophages through immunofluorescence staining and detected the levels of inflammatory cytokines. Four weeks after cell transplantation, HE, Masson, and immunohistochemical staining were performed. In vitro experiments showed that melatonin pretreatment of HucMSCs promoted proliferation, reduced apoptosis, up-regulated the stemness gene, and regulated macrophage polarization. In vivo, melatonin pretreatment caused more HucMSCs to remain in the uterine cavity. Melatonin-pretreated HucMSCs recruited more macrophages, regulated macrophage polarization, and reduced inflammation. Melatonin-pretreated HucMSCs relieved fibrosis, increased endometrium thickness, and up-regulated CD34, vimentin, proliferating cell nuclear antigen (PCNA), and alpha small muscle antigen (α-SMA) expression. Fertility tests showed that melatonin-pretreated HucMSCs increased the number of embryos. In summary, pretreatment with melatonin was beneficial for HucMSC treatment because it enhanced the cell’s ability to recruit macrophages and regulate macrophage polarization, which led to the regeneration of the endometrium and improved pregnancy outcomes.
What (wo)men want? Evidence from a factorial survey on preferred work hours in couples after childbirth
Authors: Begall Katia 
Published: September 2023

Abstract
The division of labour remains persistently gendered, in particular among couples with children. Previous research shows that women’s lower economic resources are an important factor driving these inequalities, but because gender and (relative) earnings are highly correlated in male–female couples, their relative importance is difficult to disentangle with observational data. Using a factorial survey conducted among approximately 700 employed men and women of childbearing age in Sweden, the United Kingdom, and the Netherlands, the contribution of relative earnings and gender in explaining work-care divisions in couples with children is disentangled. The results show that men and women do not differ in their preferences for their own work hours after childbirth, but both prefer the father to work more hours than the mother. Moreover, the combination of own and partners’ preferred hours shows that men and women in all three countries prefer a modified male-breadwinner model after childbirth in scenarios where the male partner earns more or partners have equal earnings. Preferences for egalitarian divisions of labour appear to be slightly stronger in men compared to women and respondents with more egalitarian views on care tasks show less gender-specialization.
Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes
Authors: Weiner Agnes K M , Sehein Taylor , Cote-L’Heureux Auden , Sleith Robin S , Greco Mattia , Malekshahi Clara , Ryan-Embry Chase , Ostriker Naomi , Katz Laura A 
Published: September 2023

Abstract
The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostly due to limited ‘omics data. Instead, most genetics studies of microeukaryotes have thus far relied on single loci, which can be misleading and do not easily allow for detection of recombination, a hallmark of sexual reproduction. Here, we analyze &gt;40 genes from 72 single-cell transcriptomes from two morphospecies—Hyalosphenia papilio and Hyalosphenia elegans—of testate amoebae (Arcellinida, Amoebozoa) to assess genetic diversity in samples collected over four years from New England bogs. We confirm the existence of cryptic species based on our multilocus dataset, which provides evidence of recombination within and high levels of divergence between the cryptic species. At the same time, total levels of genetic diversity within cryptic species are low, suggesting that these abundant organisms have small effective population sizes, perhaps due to extinction and repopulation events coupled with efficient modes of dispersal. This study is one of the first to investigate population genetics in uncultivable heterotrophic protists using transcriptomics data and contributes towards understanding cryptic species of nonmodel microeukaryotes.
The fitness landscape of a community of Darwin’s finches
Authors: Beausoleil Marc-Olivier , Carrión Paola Lorena , Podos Jeffrey , Camacho Carlos , Rabadán-González Julio , Richard Roxanne , Lalla Kristen , Raeymaekers Joost A M , Knutie Sarah A , De León Luis F , Chaves Jaime A , Clayton Dale H , Koop Jennifer A H , Sharpe Diana M T , Gotanda Kiyoko M , Huber Sarah K , Barrett Rowan D H , Hendry Andrew P 
Published: September 2023

Abstract
Divergent natural selection should lead to adaptive radiation—that is, the rapid evolution of phenotypic and ecological diversity originating from a single clade. The drivers of adaptive radiation have often been conceptualized through the concept of “adaptive landscapes,” yet formal empirical estimates of adaptive landscapes for natural adaptive radiations have proven elusive. Here, we use a 17-year dataset of Darwin’s ground finches (Geospiza spp.) at an intensively studied site on Santa Cruz (Galápagos) to estimate individual apparent lifespan in relation to beak traits. We use these estimates to model a multi-species fitness landscape, which we also convert to a formal adaptive landscape. We then assess the correspondence between estimated fitness peaks and observed phenotypes for each of five phenotypic modes (G. fuliginosa, G. fortis [small and large morphotypes], G. magnirostris, and G. scandens). The fitness and adaptive landscapes show 5 and 4 peaks, respectively, and, as expected, the adaptive landscape was smoother than the fitness landscape. Each of the five phenotypic modes appeared reasonably close to the corresponding fitness peak, yet interesting deviations were also documented and examined. By estimating adaptive landscapes in an ongoing adaptive radiation, our study demonstrates their utility as a quantitative tool for exploring and predicting adaptive radiation.
AcbHLH144 transcription factor negatively regulates phenolic biosynthesis to modulate pineapple internal browning
Authors: Li Qian , Wang Guang , Zhang Ling , Zhu Shijiang 
Published: September 2023

Abstract
Internal browning (IB), a major physiological disorder of pineapples, usually happens in postharvest processes, but the underlying mechanism remains elusive. The bHLH transcription factors are involved in regulating various biological processes, but whether they could regulate tissue browning in fruit during storage remains unknown. Here we showed that the phenolic biosynthesis pathway was activated in pineapples showing IB following 9 days of storage. AcbHLH144 expression was the highest of the 180 transcription factors identified, downregulated in pineapple with IB, and negatively correlated with the major phenolic biosynthetic genes. AcbHLH144 was shown to be localized in the nucleus and its transient overexpression in pineapples and overexpression in Arabidopsis decreased phenolic biosynthesis. The yeast one-hybrid assay and electrophoretic mobility shift assay showed that AcbHLH144 directly bound to the Ac4CL5 promoter and the dual-luciferase reporter assay showed that it inactivated Ac4CL5 transcription. These results strongly suggest AcbHLH144 as a repressor for phenolic biosynthesis. Abscisic acid (ABA) alleviated IB, reduced phenolic accumulation, and downregulated phenolic biosynthetic genes, including Ac4CL5. Transcriptomic analysis showed that AcbHLH144 was the most upregulated of all 39 bHLHs in response to ABA. ABA enhanced AcbHLH144 expression, reduced phenolic contents, and downregulated phenolic biosynthetic genes in pineapples transiently overexpressing AcbHLH144. Moreover, ABA enhanced enzyme activity of GUS driven by the AcbHLH144 promoter. These results showed that AcbHLH144 as a repressor for phenolic biosynthesis could be activated by ABA. Collectively, the work demonstrated that AcbHLH144 negatively regulated phenolic biosynthesis via inactivating Ac4CL5 transcription to modulate pineapple IB. The findings provide novel insight into the role of AcbHLH144 in modulating pineapple IB during postharvest processes.
Management of Perianal Fistulizing Crohn’s Disease
Authors: Singh Arshdeep , Midha Vandana , Kochhar Gursimran Singh , Shen Bo , Sood Ajit 
Published: September 2023

Abstract
Perianal fistulizing Crohn’s disease (CD) represents a severe phenotype of CD that is associated with significant morbidity and reduction in quality of life. Perianal fistulizing CD is caused by a complex interplay of genetic predisposition, immune dysregulation, gut dysbiosis, and various unknown physiological and mechanical factors. A multidisciplinary approach is hence required for optimal management . A detailed anatomical description and classification of perianal fistula, including comprehensive clinical, endoscopic, and radiological diagnostic workup, is an important prerequisite to treatment. For simple perianal fistulas, use of antibiotics and immunomodulators, with or without fistulotomy, are appropriate measures. The medical management of complex perianal fistula, on the other hand, requires adequate control of infection before initiation of therapy with immunomodulators. In active complex perianal fistula, anti-tumor necrosis factors remain the most accepted therapy, with concomitant use of antibiotics or immunomodulators enhancing the efficacy. For patients refractory to anti-tumor necrosis factors, treatment with anti-integrins, anti-interleukins, and small molecules is being evaluated. Mesenchymal stem cells, hyperbaric oxygen therapy, and exclusive enteral nutrition have also been investigated as adjunct therapies. Despite the expansion of the medical armamentarium, a large proportion of the patients require surgical interventions. In this review, we provide an up-to-date overview of the pathophysiology, clinical presentation, diagnosis, and medical management of perianal fistulizing CD. A brief overview of the surgical management of perianal fistulizing CD is also provided.
Solar reflection and effect of roof surfaces material characteristics in heat island mitigation: toward green building and urban sustainability in Ha’il, Saudi Arabia
Authors: Boujelbene Mohamed , Boukholda Ismail , Guesmi Tawfik , Amara Mouldi Ben , Khalilpoor Nima 
Published: September 2023

Abstract
Several materials have the ability to absorb, accumulate and transmit solar radiation to their surrounding environment. The thermal island effect and micro-climate of urban areas are subject to notable influence from the composition of materials within the city’s crust. The present investigation was carried out with the aim of assessing the impact of roofing and pavement materials’ properties on solar reflection and their potential to mitigate urban heat islands (UHIs). A study of an experimental nature was carried out on a total of 20 conventional materials that are commonly used in the construction of roofs, sidewalks, streets and rooftops in Ha’il, Saudi Arabia. The objective of the research was to investigate the impact of different urban surface materials on the rise of ambient air temperature in their vicinity. The present investigation aimed to assess the thermal performance of the specimens, with the purpose of ascertaining the impact of the thermophysical and radiative characteristics of the substances. The findings of the experiments indicate that the Solar Reflectance and temperature of the surrounding environment are primarily influenced by the color and substance of surface materials. Conversely, the texture’s condition has a comparatively minor effect. Both effective factors play an equally significant role in the overall mechanism of increasing the ambient air temperature. The results suggest that a significant proportion of the samples exhibit a maximum surface temperature exceeding 59.4°C, while concurrently displaying a Solar Reflectance Index and albedo &lt;49%. Meanwhile, the implementation of green roofs composed of various types of vegetation, including grass, can effectively alleviate the UHI phenomenon.
Human Shields and the Gulf War
Authors: de la Paz Alexander 
Published: September 2023

Abstract
From late August to early December 1990, Iraq held hundreds of Western and Japanese civilians at strategic sites as “human shields” against the Gulf War coalition. While there is a consensus that these foreign nationals would have influenced the coalition’s offensive had they not been released before the onset of hostilities, their impact remains poorly understood. This note draws on newly available archival records, among other sources, to throw new light on this old question. The record shows that leaders were reconciled with the prospect of hostage casualties and the expected political fallout. Military necessity and limited intelligence about the hostages’ whereabouts precluded avoiding every shielded target. At the same time, public opinion was divided on the hostage problem, especially in the United States. In response, leaders planned to take special precautionary measures and mount a rescue operation in Kuwait City. These measures, overall, appeared to exceed those employed for other targets, and exposed coalition forces to additional risks. US decision-makers may also have been motivated by the belief that proceeding undeterred could discourage others from resorting to the same stratagem in the future. The findings advance research on the Gulf War and the problem of human shields in war.