Entanglement-assisted concatenated quantum codes

Entanglement-assisted concatenated quantum codes (EACQCs), constructed by concatenating two quantum codes, are proposed. These EACQCs show significant advantages over standard concatenated quantum codes (CQCs). First, we prove that, unlike standard CQCs, EACQCs can beat the nondegenerate Hamming bound for entanglement-assisted quantum error-correction codes (EAQECCs). Second, we construct families of EACQCs with parameters better than the best-known standard quantum error-correction codes (QECCs) and EAQECCs. Moreover, these EACQCs require very few Einstein–Podolsky–Rosen (EPR) pairs to begin with. Finally, it is shown that EACQCs make entanglement-assisted quantum communication possible, even if the ebits are noisy. Furthermore, EACQCs can outperform CQCs in entanglement fidelity over depolarizing channels if the ebits are less noisy than the qubits. We show that the error-probability threshold of EACQCs is larger than that of CQCs when the error rate of ebits is sufficiently lower than that of qubits. Specifically, we derive a high threshold of 47% when the error probability of the preshared entanglement is 1% to that of qubits.

Quantum error-correction codes (QECCs) are necessary to realize quantum communications and to make fault-tolerant quantum computers (1, 2). The stabilizer formalism provides a useful way to construct QECCs from classical codes, but certain orthogonality constraints are required (3). The entanglement-assisted (EA) QECC (EAQECC) (4–6) generalizes the stabilizer code. By presharing some entangled states between the sender (Alice) and the receiver (Bob), EAQECCs can be constructed from any classical linear codes without the orthogonality constraints. Therefore, the construction could be greatly simplified. As an important physical resource, entanglement can boost the classical information capacity of quantum channels (7–12). Recently, it has been shown that EAQECCs can violate the nondegenerate quantum Hamming bound (13) or the quantum Singleton bound (14).Compared to standard QECCs, EAQECCs must establish some amount of entanglement before transmission. This preshared entanglement is the price to be paid for enhanced communication capability. In a sense, we need to consider the net transmission of EAQECCs—i.e., the number of qubits transmitted minus that of ebits preshared. Further, it is difficult to preserve too many noiseless ebits in EAQECCs at present. Thus, we have to use as few ebits as possible to conduct the communication—e.g., one or two ebits are preferable (15–18). In addition, EAQECCs with positive net transmission and little entanglement can lead to catalytic quantum codes (4, 6), which are applicable to fault-tolerant quantum computation (FTQC). In ref. 4, a table of best-known EAQECCs of length up to 10 was established through computer search or algebraic methods. Several EAQECCs in ref. 4 have larger minimum distances than the best-known standard QECCs of the same length and net transmission. However, for larger code lengths, the efficient construction of EAQECCs with better parameters than standard QECCs is still unknown.In classical coding theory, concatenated codes (CCs), originally proposed by Forney in the 1960s (19), provide a useful way of constructing long codes from short ones. CCs can achieve very large coding gains with reasonable encoding and decoding complexity (20). Moreover, CCs can have large minimum distances since the distances of the component codes are multiplied. As a result, CCs have been widely used in many digital communication systems—e.g., the NASA standard for the Voyager program (21) and the compact disc (20). Similarly, in QECCs, the concatenated quantum codes (CQCs), introduced by Knill and Laflamme in 1996 (22), are also effective for constructing good quantum codes. In particular, it has been shown that CQCs are of great importance in realizing FTQC (23–25).Moreover, there exists a specific phenomenon in QECCs, called “error degeneracy,” which distinguishes quantum codes from classical ones in essence. It is widely believed that degenerate codes can correct more quantum errors than nondegenerate ones. Indeed, there are some open problems concerning whether degenerate codes can violate the nondegenerate quantum Hamming bound (26) or can improve the quantum-channel capacity (27, 28). Many CQCs have been shown to be degenerate, even if the component codes are nondegenerate—e.g., Shor’s [[9,1,3]] code and the [[25,1,9]] CQC (23, 29). If we introduce extra entanglement to CQCs, it is possible to improve the error-degeneracy performance of CQCs.In this article, we generalize the idea of concatenation to EAQECCs and propose EACQCs. We show that EACQCs can beat the nondegenerate quantum Hamming bound, while standard CQCs cannot. Several families of degenerate EACQCs that can surpass the nondegenerate Hamming bound for EAQECCs are constructed. The same conclusion could be reached for asymmetric error models, in which the phase-flip errors (Z errors) happen more frequently than the bit-flip errors (X errors) (30, 31). Furthermore, we derive a number of EACQCs with better parameters than the best-known QECCs and EAQECCs. In particular, we see that many EACQCs have positive net transmission, and each of them consumes only one or two ebits. Thus, they give rise to catalytic EACQCs with little entanglement and better parameters than the best-known QECCs. Further, we show that the EACQC scheme makes EA quantum communication possible, even if the ebits are noisy. We compute the entanglement fidelity (EF) of the [[15,1,9;10]] EACQC by using Bowen’s [[3,1,3;2]] EAQECC (32) or the [[3,1,3;2]] EA repetition code (4, 6) as the inner code. The outer code is the standard [[5,1,3]] stabilizer code. We show that the [[15,1,9;10]] EACQC performs much better than the [[25,1,9]] CQC over depolarizing channels if the ebits suffer a lower error rate than the qubits. Moreover, we compute the error-probability threshold of EACQCs, and we show that EACQCs have much higher thresholds than CQCs when the error rate of ebits is sufficiently lower than that of qubits.     

Association of Albumin and Globulin with Mortality Risk in Incident Peritoneal Dialysis Patients

Background: Nutrition and inflammation have been implicated in predicting mortality in patients on peritoneal dialysis (PD). Serum albumin and globulin can be regarded for the nutritional and inflammatory status. However, there is lack of data to evaluate the synergistic effect of albumin and globulin on mortality prediction. Methods: In 554 patients initiating PD from January 2001 to July 2016, we divided them into four groups by the combination of two categories of low vs. high albumin and low vs. high globulin. The median values for albumin and globulin were chosen to classify them into low or high groups. Their associations with all-cause and cardiovascular (CV) mortality were examined in Cox regression models adjusted for confounding clinical and laboratory data. Results: Patients, 52.91 ± 15.2 years old and 47.8% men, had a median (interquartile range) value of 3.3 (2.9–3.8) g/dL for albumin and 2.8 (2.5–3.2) g/dL for globulin, respectively. Patients with low albumin and high globulin had the highest all-cause mortality and CV mortality, with adjusted hazard ratios of 3.87 (95% CI 1.83–8.20, p < 0.001) and 5.65 (95% CI 2.23–14.34, p < 0.001), respectively, compared with those with a high albumin and low globulin having the lowest mortality rate. Sensitivity analyses further confirmed this relationship. Conclusions: A patient profile of either low albumin or high globulin is linked to a higher risk for mortality, particularly for a profile of both low albumin and high globulin compared with one without either of them. Further studies are needed to explore the mechanisms underlying this phenomenon and how to improve clinical outcomes in those high-risk patients.     

Combination of CRAFITY score with Alpha-fetoprotein response predicts a favorable outcome of atezolizumab plus bevacizumab for unresectable hepatocellular carcinoma

Immune checkpoint inhibitors (ICIs) with atezolizumab plus bevacizumab are promising agents for unresectable hepatocellular carcinoma (HCC). We tried to guide the treatment based on recent developed CRAFITY score combining with on-treatment AFP response. Eighty-nine patients who received atezolizumab plus bevacizumab regardless of as a first-line therapy or not for unresectable HCC were enrolled for analyses. Radiologic evaluation was based on modified Response Evaluation Criteria in Solid Tumors (mRECIST). The objective response rate (ORR) and disease control rate (DCR) were 25.0% and 65.5%, respectively. Multivariate analysis showed that low CRAFITY score (AFP<100 ng/ml or CRP<10 mg/l) and satisfactory AFP response at 6 weeks (≥75% decrease or ≤10% increase from baseline) were independent factors determining good overall survival (OS) (hazard ratio [HR]=0.143, P=0.002 & HR=0.337, P=0.031), progression-free survival (PFS) (HR=0.419, P=0.022 & HR=0.429, P=0.025) and good responder (odds ratio [OR]=1.763, P=0.044 & OR=3.881, P=0.011). Patients were further divided into three classes by combination of CRAFITY score and AFP response at 6 weeks [The CAR (CRAFITY score and AFP-Response) classification)]: low CRAFITY score with satisfactory AFP response at 6 weeks (class I), either high CRAFITY score or unsatisfactory AFP response at 6 weeks (class II) and high CRAFITY score together with unsatisfactory AFP response at 6 weeks (class III). ORR was 35.0%, 18.2%, and 0% in class I, II and III patients, respectively (overall P=0.034). Patients in the class I had the best OS and PFS, followed by class II and class III (median OS: not reached vs. 11.1 vs. 4.3 months, log-rank P<0.001; median PFS: 7.9 vs. 6.6 vs. 2.6 months, log-rank P=0.001). Combination CRAFITY score and AFP response at 6 weeks with AUROC predicts OS and tumor response to be 0.809 and 0.798, respectively, better than either CRAFITY score (0.771 & 0.750) or AFP response at 6 weeks (0.725 & 0.680) alone. In conclusions, the CAR classification which combining CRAFITY score and AFP response at 6 weeks provides a practical guidance for atezolizumab plus bevacizumab therapy in unresectable HCC patients.     

Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages

The ecology and genetic diversity of the model yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part of this yeast''s geographic birthplace, where the most divergent natural lineage was discovered. Here, we extensively sampled the broadleaf forests across this continental island to probe the ancestral species’ diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages that diverged from Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Three lineages are endemic to Taiwan and six are widespread in Asia, making this region a focal biodiversity hotspot. Both ancient and recent admixture events were detected between the natural lineages, and a genetic ancestry component associated with isolates from fruits was detected in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We identified different selection patterns shaping the coding sequences of natural lineages and found fewer gene family expansion and contractions that contrast with domesticated lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.

The yeast genus Saccharomyces, which includes S. cerevisiae, is a powerful model system for revealing patterns of genomic variation underlying reproductive isolation and adaptation in eukaryotic microorganisms. Surveys of population genetic data have been used in S. cerevisiae to date the origin of key domestication events (Gallone et al. 2016; Duan et al. 2018; Peter et al. 2018), to determine life cycle frequencies in nature (Tsai et al. 2008), to determine the genomic basis of adaptation at continental scale (Duan et al. 2018; Peter et al. 2018), and, more recently, to establish its geographical origin and dispersal history (Xia et al. 2017). Phylogenomic analyses of the Saccharomyces sensu stricto complex and extensive sequencing of collections across the world suggest that S. cerevisiae originated in East Asia (Duan et al. 2018; Peter et al. 2018). The 1011 Genome Project—the most broad large-scale yeast population genomic study—discovered that three wild isolates from Taiwan showed an unprecedented high genetic diversity compared with populations from the rest of the world (Peter et al. 2018). Population genomics of 266 domestic and wild isolates in China revealed six wild lineages from primeval forests. The newly identified CHN-IX group represents the most diverged lineage (Duan et al. 2018). Isolates from this group and the three Taiwanese isolates were grouped into a single lineage that showed a disjunct geographic distribution (Bendixsen et al. 2021). Although considerable knowledge is available on the biogeography and population genetics of plants and animals across continents (Whittaker et al. 2017), little is known about how eukaryotic microorganisms such as S. cerevisiae disperse, establish, reproduce, and persist in nature (Liti 2015).Most S. cerevisiae biology has been based on experiments on a handful of laboratory domesticated strains, but comprehensive analyses of the ecology and evolutionary biology of S. cerevisiae in the wild are still unavailable. In nature, S. cerevisiae have been isolated from the bark, fruits, surrounding soil, and leaves of plants belonging to several different families (Naumov et al. 2013), with early reports suggesting that the yeast is most successfully isolated from the oak family Fagaceae (Sniegowski et al. 2002; Sampaio and Gonçalves 2008; Wang et al. 2012). S. cerevisiae contains high genetic diversity in certain populations, including lineage-specific variants that display clear population structures (Barnett 1992; Wang et al. 2012; Cromie et al. 2013; Strope et al. 2015; Gallone et al. 2016; Gonçalves et al. 2016; Zhu et al. 2016; Duan et al. 2018; Legras et al. 2018; Peter et al. 2018) and explain phenotypic variance similar to common variants (Fournier et al. 2019). Samples from natural habitats tend to be homozygous diploids forming unique populations with minimal genetic admixture, whereas lineages associated with human activities were likely heterozygous, containing higher ploidy and greater genetic admixture leading to a mosaic genome makeup (Diezmann and Dietrich 2009; Liti et al. 2009; Wang et al. 2012; Almeida et al. 2015). The diverse natural lineages of S. cerevisiae present in East Asia provide an excellent opportunity to study the natural diversity of this species, which was previously believed to be fully domesticated (Fay and Benavides 2005).Taiwan is a continental shelf island with the fifth highest tree density in the world (Crowther et al. 2015). Among the 13 climate-related forests types in Taiwan, five are Fagaceae-dominated natural forests on low- and mid-elevation mountains (Li et al. 2013), thus a potentially ideal natural habitat for S. cerevisiae. Taiwan also harbors a high phylogenetic diversity of flowering plants (53 out of 64 angiosperm orders present under the APG IV classification system) (Lin and Chung 2017) and endemism compared with other oceanic islands (Hsieh 2002), raising the possibility that the associated microbial populations are genetically different from their continental counterparts. Here, we set out to characterize the intra-genetic diversity, relative abundance, and distribution of S. cerevisiae in Taiwanese forests over 4 yr of broad sampling. Our study provides novel insights of the predomestication phase of S. cerevisiae and broadens our understanding of the ecological and biogeographic implications before anthropogenic impacts.     

CD34, CD117, and actin expression in phyllodes tumor of the breast

BACKGROUND: This study investigated the immunophenotypic patterns of CD34, CD117 (a product of the c-kit proto-oncogene), and actin (HHF35) in benign and malignant phyllodes tumors (PTs). We correlated the expression of CD34, CD117, and actin with histopathological grade. MATERIALS AND RESULTS: We analyzed 19 cases (7 benign and 12 malignant cases) of PTs using immunohistochemical analysis. Six of 7 benign PT stromal lesions stained positively for CD34, while only 3 of 12 cases of malignant PT were focally CD34 positive (P = 0.0106). Only 1 of the 7 benign PTs stromal lesions expressed CD117. Nine of the malignant PTs were composed CD117-positive fibroblasts. This result demonstrated that CD117 expression is associated with the malignant potential of PTs (P = 0. 0106). Actin (HHF-35) expression was found in 8 of 12 cases of malignant PTs (P = 0.027), but in only 1 of 7 cases of benign PTs. Actin expression was significantly (P = 0.04) correlated to frequent mitotic activity (>5 mitoses per 10 high-power fields). The immunophenotypic markers were not related to tumor size. Additionally, we sequenced part of the juxtamembrane region of the c-kit proto-oncogene and found point mutations in two malignant PTs. CONCLUSION: Our results demonstrated that expression of CD34 was associated with benign PTs, while CD117 and actin were preferentially expressed in malignant PTs. Our results implied that these immunohistological markers might be used for the histopathological grading of PTs.     

Dapagliflozin Ameliorates Lipopolysaccharide Related Acute Kidney Injury in Mice with Streptozotocin-induced Diabetes Mellitus

Sepsis, which is a serious medical condition induced by infection, has been the most common cause of acute kidney injury (AKI) and is associated with high mortality and morbidity. Sodium-glucose cotransporter 2 (SGLT2) inhibitor is a new oral antidiabetic drug that has greatly improved the cardiovascular and renal outcomes in patients with type 2 diabetes independent of its sugar lowering effect, possibly by attenuation of the inflammatory process. We investigated the effect of the SGLT2 inhibitor dapagliflozin on lipopolysaccharide (LPS)-induced endotoxic shock with AKI in streptozotocin-induced diabetic mice. Endotoxin shock with AKI was induced by intravenous injection of 10 mg/kg LPS in C57BL6 mice with streptozotocin-induced diabetic mellitus with or without dapagliflozin treatment. Observation was done for 48 hours thereafter. In addition, NRK-52E cells incubated with LPS or dapagliflozin were evaluated for the possible mechanism. Treatment with dapagliflozin attenuated LPS-induced endotoxic shock associated AKI and decreased the inflammatory cytokines in diabetic mice. In the in vitro study, dapagliflozin decreased the expression of inflammatory cytokines and reactive oxygen species and increased the expressions of AMP-activated protein kinase (AMPK), nuclear factor erythroid-2-related factor, and heme oxygenase 1. These results demonstrated that dapagliflozin can attenuate LPS-induced endotoxic shock associated with AKI; this was possibly mediated by activation of the AMPK pathway.     

Visfatin Polymorphisms,Lifestyle Risk Factors and Risk of Oral Squamous Cell Carcinoma in a Cohort of Taiwanese Males

Oral cancer is the eighth greatest generally diagnosed cancer amongst males worldwide and the fourth most generally malignancy amongst Taiwanese males. The pro-inflammatory adipocytokine visfatin promotes tumor growth. Elevated plasma visfatin levels have been identified in patients with oral squamous cell carcinoma (OSCC), although the biological mechanisms underlying the involvement of visfatin in the pathogenesis of OSCC are not well understood. Moreover, no information is available regarding associations between visfatin polymorphisms and carcinogenic lifestyle factors with OSCC. This study, therefore, investigated the effects of four visfatin gene polymorphisms (rs11977021, rs61330082, rs2110385, and rs4730153) and carcinogenic lifestyle factors (betel nut chewing, alcohol consumption and cigarette smoking) on the risk of developing OSCC in 1,275 Taiwanese males with OSCC, and 1,195 healthy males (controls). We also examined the associations between these visfatin genotypes and OSCC histopathological prognostic factors (pathological stage, tumor status, lymph node status, and metastasis). We found that compared with subjects with the CC genotype of SNP rs11977021, those with the CT+TT genotype were less likely to progress OSCC. In addition, an association was found between the rs4730153 variant and lymph node metastasis in the OSCC cohort.