bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum verification of NP problems with single photons and linear optics
Authors: Zhang Aonan , Zhan Hao , Liao Junjie , Zheng Kaimin , Jiang Tao , Mi Minghao , Yao Penghui , Zhang Lijian 
Published: August 2021

AbstractQuantum computing is seeking to realize hardware-optimized algorithms for application-related computational tasks. NP (nondeterministic-polynomial-time) is a complexity class containing many important but intractable problems like the satisfiability of potentially conflict constraints (SAT). According to the well-founded exponential time hypothesis, verifying an SAT instance of size n requires generally the complete solution in an O(n)-bit proof. In contrast, quantum verification algorithms, which encode the solution into quantum bits rather than classical bit strings, can perform the verification task with quadratically reduced information about the solution in $$\tilde O(\sqrt n )$$

O

̃

(

n

)

qubits. Here we realize the quantum verification machine of SAT with single photons and linear optics. By using tunable optical setups, we efficiently verify satisfiable and unsatisfiable SAT instances and achieve a clear completeness-soundness gap even in the presence of experimental imperfections. The protocol requires only unentangled photons, linear operations on multiple modes and at most two-photon joint measurements. These features make the protocol suitable for photonic realization and scalable to large problem sizes with the advances in high-dimensional quantum information manipulation and large scale linear-optical systems. Our results open an essentially new route toward quantum advantages and extend the computational capability of optical quantum computing.
Long-term risk of subsequent ipsilateral lesions after surgery with or without radiotherapy for ductal carcinoma in situ of the breast
Authors: van Seijen Maartje , Lips Esther H. , Fu Liping , Giardiello Daniele , van Duijnhoven Frederieke , de Munck Linda , Elshof Lotte E. , Thompson Alastair , Sawyer Elinor , Ryser Marc D. , Hwang E. Shelley , Schmidt Marjanka K. , Elkhuizen Paula H. M. ,   Grand Challenge PRECISION Consortium, Wesseling Jelle , Schaapveld Michael 
Published: August 2021

Abstract
Background
Radiotherapy (RT) following breast-conserving surgery (BCS) for ductal carcinoma in situ (DCIS) reduces ipsilateral breast event rates in clinical trials. This study assessed the impact of DCIS treatment on a 20-year risk of ipsilateral DCIS (iDCIS) and ipsilateral invasive breast cancer (iIBC) in a population-based cohort.

Methods
The cohort comprised all women diagnosed with DCIS in the Netherlands during 1989–2004 with follow-up until 2017. Cumulative incidence of iDCIS and iIBC following BCS and BCS + RT were assessed. Associations of DCIS treatment with iDCIS and iIBC risk were estimated in multivariable Cox models.

Results
The 20-year cumulative incidence of any ipsilateral breast event was 30.6% (95% confidence interval (CI): 28.9–32.6) after BCS compared to 18.2% (95% CI 16.3–20.3) following BCS  +  RT. Women treated with BCS compared to BCS + RT had higher risk of developing iDCIS and iIBC within 5 years after DCIS diagnosis (for iDCIS: hazard ratio (HR)age < 50 3.2 (95% CI 1.6–6.6); HRage ≥ 50 3.6 (95% CI 2.6–4.8) and for iIBC: HRage<50 2.1 (95% CI 1.4–3.2); HRage ≥ 50 4.3 (95% CI 3.0–6.0)). After 10 years, the risk of iDCIS and iIBC no longer differed for BCS versus BCS + RT (for iDCIS: HRage < 50 0.7 (95% CI 0.3–1.5); HRage ≥ 50 0.7 (95% CI 0.4–1.3) and for iIBC: HRage < 50 0.6 (95% CI 0.4–0.9); HRage ≥ 50 1.2 (95% CI 0.9–1.6)).

Conclusion
RT is associated with lower iDCIS and iIBC risk up to 10 years after BCS, but this effect wanes thereafter.
Human MLH1/3 variants causing aneuploidy, pregnancy loss, and premature reproductive aging
Authors: Singh Priti , Fragoza Robert , Blengini Cecilia S. , Tran Tina N. , Pannafino Gianno , Al-Sweel Najla , Schimenti Kerry J. , Schindler Karen , Alani Eric A. , Yu Haiyuan , Schimenti John C. 
Published: August 2021

AbstractEmbryonic aneuploidy from mis-segregation of chromosomes during meiosis causes pregnancy loss. Proper disjunction of homologous chromosomes requires the mismatch repair (MMR) genes MLH1 and MLH3, essential in mice for fertility. Variants in these genes can increase colorectal cancer risk, yet the reproductive impacts are unclear. To determine if MLH1/3 single nucleotide polymorphisms (SNPs) in human populations could cause reproductive abnormalities, we use computational predictions, yeast two-hybrid assays, and MMR and recombination assays in yeast, selecting nine MLH1 and MLH3 variants to model in mice via genome editing. We identify seven alleles causing reproductive defects in mice including female subfertility and male infertility. Remarkably, in females these alleles cause age-dependent decreases in litter size and increased embryo resorption, likely a consequence of fewer chiasmata that increase univalents at meiotic metaphase I. Our data suggest that hypomorphic alleles of meiotic recombination genes can predispose females to increased incidence of pregnancy loss from gamete aneuploidy.
X-ray transient absorption reveals the 1Au (nπ*) state of pyrazine in electronic relaxation
Authors: Scutelnic Valeriu , Tsuru Shota , Pápai Mátyás , Yang Zheyue , Epshtein Michael , Xue Tian , Haugen Eric , Kobayashi Yuki , Krylov Anna I. , Møller Klaus B. , Coriani Sonia , Leone Stephen R. 
Published: August 2021

AbstractElectronic relaxation in organic chromophores often proceeds via states not directly accessible by photoexcitation. We report on the photoinduced dynamics of pyrazine that involves such states, excited by a 267 nm laser and probed with X-ray transient absorption spectroscopy in a table-top setup. In addition to the previously characterized1B2u(ππ*) (S2) and1B3u(nπ*) (S1) states, the participation of the optically dark1Au(nπ*) state is assigned by a combination of experimental X-ray core-to-valence spectroscopy, electronic structure calculations, nonadiabatic dynamics simulations, and X-ray spectral computations. Despite1Au(nπ*) and1B3u(nπ*) states having similar energies at relaxed geometry, their X-ray absorption spectra differ largely in transition energy and oscillator strength. The1Au(nπ*) state is populated in 200 ± 50 femtoseconds after electronic excitation and plays a key role in the relaxation of pyrazine to the ground state.
Etiological and epidemiological features of acute respiratory infections in China
Authors: Li Zhong-Jie , Zhang Hai-Yang , Ren Li-Li , Lu Qing-Bin , Ren Xiang , Zhang Cui-Hong , Wang Yi-Fei , Lin Sheng-Hong , Zhang Xiao-Ai , Li Jun , Zhao Shi-Wen , Yi Zhi-Gang , Chen Xiao , Yang Zuo-Sen , Meng Lei , Wang Xin-Hua , Liu Ying-Le , Wang Xin , Cui Ai-Li , Lai Sheng-Jie , Jiang Tao , Yuan Yang , Shi Lu-Sha , Liu Meng-Yang , Zhu Yu-Liang , Zhang An-Ran , Zhang Zhi-Jie , Yang Yang , Ward Michael P. , Feng Lu-Zhao , Jing Huai-Qi , Huang Liu-Yu , Xu Wen-Bo , Chen Yu , Wu Jian-Guo , Yuan Zheng-Hong , Li Meng-Feng , Wang Yu , Wang Li-Ping , Fang Li-Qun , Liu Wei , Hay Simon I. , Gao George F. , Yang Wei-Zhong ,   The Chinese Centers for Disease Control and Prevention (CDC) Etiology of Respiratory Infection Surveillance Study Team, Yang Wei-Zhong , Gao George F. , Li Zhong-Jie , Wang Li-Ping , Ren Xiang , Wang Yi-Fei , Lin Sheng-Hong , Zhang Cui-Hong , Geng Meng-Jie , Wang Xin , Jing Huai-Qi , Xu Wen-Bo , Cui Ai-Li , Shen Yu-Juan , Jiang Yan-Yan , Sun Qiao , Hao Li-Peng , Ye Chu-Chu , Liu Wei , Zhang Xiao-Ai , Huang Liu-Yu , Wang Yong , Zhang Wen-Yi , Zhang Qi , Liu Wei-Yong , Sun Zi-Yong , Zhan Fa-Xian , Xiong Ying , Yu De-Shan , Wang Chun-Xiang , Zhao Sheng-Cang , Wang Wen-Rui , Lei Xia , Li Juan-Sheng , Wang Yu-Hong , Zhang Yan , Yang Jun-Peng , Wang Yan-Bo , Quan Fu-Cai , Xiong Zhi-Jun , Liang Li-Ping , Chang Quan-E , Wang Yun , Wang Ping , Mao Ling-Ling , Li Jia-Meng , Lv Li-Kun , Xu Jun , Shu Chang , Chen Xiao , Chen Yu , Zhang Yan-Jun , Cui Lun-Biao , Zheng Kui-Cheng , Zhang Xing-Guo , Zhang Xi , Tu Li-Hong , Wang Wei , Zhou Xiao-Fang , Pei Xiao-Fang , Zheng Tian-Li , Zhong Xiao-Ni , Li Qin , Ling Hua , Wang Ding-Ming , Li Shi-Jun , He Shu-Sen , Zhu Xun , Ke Chang-Wen , Xiao Hong , Di Biao , Zhang Ying , Zhou Hong-Wei , Yu Nan , Li Hong-Jian , Yang Fang , Wang Fu-Xiang , Wang Jun 
Published: August 2021

AbstractNationwide prospective surveillance of all-age patients with acute respiratory infections was conducted in China between 2009‒2019. Here we report the etiological and epidemiological features of the 231,107 eligible patients enrolled in this analysis. Children <5 years old and school-age children have the highest viral positivity rate (46.9%) and bacterial positivity rate (30.9%). Influenza virus, respiratory syncytial virus and human rhinovirus are the three leading viral pathogens with proportions of 28.5%, 16.8% and 16.7%, and Streptococcus pneumoniae, Mycoplasma pneumoniae and Klebsiella pneumoniae are the three leading bacterial pathogens (29.9%, 18.6% and 15.8%). Negative interactions between viruses and positive interactions between viral and bacterial pathogens are common. A Join-Point analysis reveals the age-specific positivity rate and how this varied for individual pathogens. These data indicate that differential priorities for diagnosis, prevention and control should be highlighted in terms of acute respiratory tract infection patients’ demography, geographic locations and season of illness in China.
Grafting of iPS cell-derived tenocytes promotes motor function recovery after Achilles tendon rupture
Authors: Nakajima Taiki , Nakahata Akihiro , Yamada Naoki , Yoshizawa Keiko , Kato Tomoaki M. , Iwasaki Mio , Zhao Chengzhu , Kuroki Hiroshi , Ikeya Makoto 
Published: August 2021

AbstractTendon self-renewal is a rare occurrence because of the poor vascularization of this tissue; therefore, reconstructive surgery using autologous tendon is often performed in severe injury cases. However, the post-surgery re-injury rate is relatively high, and the collection of autologous tendons leads to muscle weakness, resulting in prolonged rehabilitation. Here, we introduce an induced pluripotent stem cell (iPSC)-based technology to develop a therapeutic option for tendon injury. First, we derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in vertebrate embryos. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSC-derived tenocytes. We demonstrated that iPSC-tenocyte grafting contributed to motor function recovery after Achilles tendon injury in rats via engraftment and paracrine effects. The biomechanical strength of regenerated tendons was comparable to that of healthy tendons. We suggest that iPSC-tenocytes will provide a therapeutic option for tendon injury.
Lipidomic profile of human nasal mucosa and associations with circulating fatty acids and olfactory deficiency
Authors: Khoury Spiro , Gudziol Volker , Grégoire Stéphane , Cabaret Stéphanie , Menzel Susanne , Martine Lucy , Mézière Esther , Soubeyre Vanessa , Thomas-Danguin Thierry , Grosmaitre Xavier , Bretillon Lionel , Berdeaux Olivier , Acar Niyazi , Hummel Thomas , Le Bon Anne Marie 
Published: August 2021

AbstractThe nasal mucosa (NM) contains olfactory mucosa which contributes to the detection of odorant molecules and the transmission of olfactory information to the brain. To date, the lipid composition of the human NM has not been adequately characterized. Using gas chromatography, liquid chromatography coupled to mass spectrometry and thin layer chromatography, we analyzed the fatty acids and the phospholipid and ceramide molecular species in adult human nasal and blood biopsies. Saturated and polyunsaturated fatty acids (PUFAs) accounted for 45% and 29% of the nasal total fatty acids, respectively. Fatty acids of the n-6 family were predominant in the PUFA subgroup. Linoleic acid and arachidonic acid (AA) were incorporated in the main nasal phospholipid classes. Correlation analysis revealed that the nasal AA level might be positively associated with olfactory deficiency. In addition, a strong positive association between the AA levels in the NM and in plasma cholesteryl esters suggested that this blood fraction might be used as an indicator of the nasal AA level. The most abundant species of ceramides and their glycosylated derivatives detected in NM contained palmitic acid and long-chain fatty acids. Overall, this study provides new insight into lipid species that potentially contribute to the maintenance of NM homeostasis and demonstrates that circulating biomarkers might be used to predict nasal fatty acid content.
Neighbors-based prediction of physical function after total knee arthroplasty
Authors: Kim Chong , Colborn Kathryn L. , van Buuren Stef , Loar Timothy , Stevens-Lapsley Jennifer E. , Kittelson Andrew J. 
Published: August 2021

AbstractThe purpose of this study was to develop and test personalized predictions for functional recovery after Total Knee Arthroplasty (TKA) surgery, using a novel neighbors-based prediction approach. We used data from 397 patients with TKA to develop the prediction methodology and then tested the predictions in a temporally distinct sample of 202 patients. The Timed Up and Go (TUG) Test was used to assess physical function. Neighbors-based predictions were generated by estimating an index patient’s prognosis from the observed recovery data of previous similar patients (a.k.a., the index patient’s “matches”). Matches were determined by an adaptation of predictive mean matching. Matching characteristics included preoperative TUG time, age, sex and Body Mass Index. The optimal number of matches was determined to be m = 35, based on low bias (− 0.005 standard deviations), accurate coverage (50% of the realized observations within the 50% prediction interval), and acceptable precision (the average width of the 50% prediction interval was 2.33 s). Predictions were well-calibrated in out-of-sample testing. These predictions have the potential to inform care decisions both prior to and following TKA surgery.
Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia
Authors: Freilich Suzanne , Ringbauer Harald , Los Dženi , Novak Mario , Pavičić Dinko Tresić , Schiffels Stephan , Pinhasi Ron 
Published: August 2021

AbstractAncient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age transformed the social and genetic structure of European societies. Present-day Croatia lies at the heart of ancient migration routes through Europe, yet our knowledge about social and genetic processes here remains sparse. To shed light on these questions, we report new whole-genome data for 28 individuals dated to between ~ 4700 BCE–400 CE from two sites in present-day eastern Croatia. In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple closely related males suggesting a patrilocal social organisation. We also find in that community an unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today.
Comparative analysis of nuclear and mitochondrial DNA from tissue and liquid biopsies of colorectal cancer patients
Authors: Haupts Anna , Vogel Anne , Foersch Sebastian , Hartmann Monika , Maderer Annett , Wachter Nicolas , Huber Tobias , Kneist Werner , Roth Wilfried , Lang Hauke , Moehler Markus , Hartmann Nils 
Published: August 2021

AbstractThe current standard for molecular profiling of colorectal cancer (CRC) is using resected or biopsied tissue specimens. However, they are limited regarding sampling frequency, representation of tumor heterogeneity, and sampling can expose patients to adverse side effects. The analysis of cell-free DNA (cfDNA) from blood plasma, which is part of a liquid biopsy, is minimally invasive and in principle enables detection of all tumor-specific mutations. Here, we analyzed cfDNA originating from nucleus and mitochondria and investigated their characteristics and mutation status in a cohort of 18 CRC patients and 10 healthy controls using targeted next-generation sequencing (NGS) and digital PCR. Longitudinal analyses of nuclear cfDNA level and size during chemotherapy revealed a decreasing cfDNA content and a shift from short to long fragments, indicating an appropriate therapy response, while shortened cfDNAs and increased cfDNA content corresponded with tumor recurrence. Comparative NGS analysis of nuclear tissue and plasma DNA demonstrated a good patient-level concordance and cfDNA revealed additional variants in three of the cases. Analysis of mitochondrial cfDNA surprisingly revealed a higher plasma copy number in healthy subjects than in CRC patients. These results highlight the potential clinical utility of liquid biopsies in routine diagnostics and surveillance of CRC patients as complementation to tissue biopsies or as an attractive alternative in cases where tissue biopsies are risky or the quantity/quality does not allow testing.
Dynamics of cocoa fermentation and its effect on quality
Authors: Calvo Ana M. , Botina Blanca L. , García Maria C. , Cardona William A. , Montenegro Andrea C. , Criollo Jenifer 
Published: August 2021

AbstractSeveral research efforts on cocoa have been focused on parameters for controlling the transformation process to guarantee homogeneity and quality of cocoa beans, the main raw material in the chocolate industry. The main changes that determine the final quality of cocoa—and also the product’s homogeneity—occur during fermentation, given the great number of factors that affect the process. This research seeks to identify the most relevant factors affecting quality in order to offer higher-quality and more homogeneous cocoa for the chocolate industry. The dynamics of the fermentation process were observed in three contrasting locations, monitoring different variables and evaluating the final quality of the cocoa. Results show that temperature and pH profile are the key factors to be monitored and controlled in order to achieve high-quality cocoa beans.
Characterization and clinical implications of ankle impedance during walking in chronic stroke
Authors: Shorter Amanda L. , Richardson James K. , Finucane Suzanne B. , Joshi Varun , Gordon Keith , Rouse Elliott J. 
Published: August 2021

AbstractIndividuals post-stroke experience persisting gait deficits due to altered joint mechanics, known clinically as spasticity, hypertonia, and paresis. In engineering, these concepts are described as stiffness and damping, or collectively as joint mechanical impedance, when considered with limb inertia. Typical clinical assessments of these properties are obtained while the patient is at rest using qualitative measures, and the link between the assessments and functional outcomes and mobility is unclear. In this study we quantify ankle mechanical impedance dynamically during walking in individuals post-stroke and in age-speed matched control subjects, and examine the relationships between mechanical impedance and clinical measures of mobility and impairment. Perturbations were applied to the ankle joint during the stance phase of walking, and least-squares system identification techniques were used to estimate mechanical impedance. Stiffness of the paretic ankle was decreased during mid-stance when compared to the non-paretic side; a change independent of muscle activity. Inter-limb differences in ankle joint damping, but not joint stiffness or passive clinical assessments, strongly predicted walking speed and distance. This work provides the first insights into how stroke alters joint mechanical impedance during walking, as well as how these changes relate to existing outcome measures. Our results inform clinical care, suggesting a focus on correcting stance phase mechanics could potentially improve mobility of chronic stroke survivors.
Association between overall diet quality and postmenopausal breast cancer risk in five Finnish cohort studies
Authors: Männistö Satu , Harald Kennet , Härkänen Tommi , Maukonen Mirkka , Eriksson Johan G. , Heikkinen Sanna , Jousilahti Pekka , Kaartinen Niina E. , Kanerva Noora , Knekt Paul , Koskinen Seppo , Laaksonen Maarit A. , Malila Nea , Rissanen Harri , Pitkäniemi Janne 
Published: August 2021

AbstractThere is limited evidence for any dietary factor, except alcohol, in breast cancer (BC) risk. Therefore, studies on a whole diet, using diet quality indices, can broaden our insight. We examined associations of the Nordic Diet (mNDI), Mediterranean diet (mMEDI) and Alternative Healthy Eating Index (mAHEI) with postmenopausal BC risk. Five Finnish cohorts were combined including 6374 postmenopausal women with dietary information. In all, 8–9 dietary components were aggregated in each index, higher total score indicating higher adherence to a healthy diet. Cox proportional hazards regression was used to estimate the combined hazard ratio (HR) and 95% confidence interval (CI) for BC risk. During an average 10-year follow-up period, 274 incident postmenopausal BC cases were diagnosed. In multivariable models, the HR for highest vs. lowest quintile of index was 0.67 (95 %CI 0.48–1.01) for mNDI, 0.88 (0.59–1.30) for mMEDI and 0.89 (0.60–1.32) for mAHEI. In this combined dataset, a borderline preventive finding of high adherence to mNDI on postmenopausal BC risk was found. Of the indices, mNDI was more based on the local food culture than the others. Although a healthy diet has beneficially been related to several chronic diseases, the link with the etiology of postmenopausal BC does not seem to be that obvious.
Comparison of early F-18 Florbetaben PET/CT to Tc-99m ECD SPECT using voxel, regional, and network analysis
Authors: Kwon Soo Jin , Ha Seunggyun , Yoo Sang-Won , Shin Na-Young , O Joo Hyun , Yoo Ie Ryung , Kim Joong-Seok 
Published: August 2021

AbstractThis study aimed to validate early-phase F-18 Florbetaben positron emission tomography (eFBB PET) as a brain perfusion test and determine the optimal reference region. A total of 27 patients with early Parkinson’s disease with Tc-99m ethyl cysteinate dimer single photon emission tomography (ECD SPECT) and FBB PET were included. Six reference regions, including whole brain (GN), pons, central white matter (CWM), whole cerebellum (WC), WC with brain stem (WC + B), and cerebellar grey matter (CG), were applied to obtain SUVR using cortex volume-of-interest (VOI). Reference regions of WC (r 0.886), WC + B (r 0.897), and CG (r 0.904) had highest correlation values of cortex-VOI SUVR between both perfusion images (all p < 0.001). Early-phase FBB PET had a significant linear correlation of CG-normalized SUVR of the cortex, basal ganglia, thalamus, and midbrain with ECD SPECT in voxel-wise analysis (FDR adjusted-p < 0.05). Early-phase FBB PET extracts more ICNS than ECD SPECT, as 9 ICNS and 4 ICNs, respectively. Both eFBB PET and ECD SPECT well discriminated PD from DLB (Area-under-curve of receiver-operating-characteristics, 0.911 for eFBB PET, 0.922 for ECD SPECT). Our findings suggest that eFBB PET is a reliable perfusion test based on a high correlation with ECD SPECT using cerebellum-based normalization methods.