Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation

Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates

Expression of nm23-H1 gene product in esophageal squamous cell carcinoma and its association with vessel invasion and survival

BACKGROUND: We assessed the nm23-H1 gene product expression and its relationship with lymphatic and blood vessel invasion in patients with esophageal squamous cell carcinoma. METHODS: Formalin-fixed and paraffin-embedded tissue sections from 45 patients who were treated surgically were used in this study. Pathologists graded lymphatic and blood vessel invasion in each of the tissue samples. Expression of nm23-Hl gene product was determined using a specific monoclonal antibody. RESULTS: Expression of nm23-H1 gene product was present in 17 (37.8%) cases. We found an inverse correlation between nm23-H1 gene product expression and lymphatic vessel invasion, whereas no correlation between nm23-H1 gene product expression and blood vessel invasion. Overall survival rate was not different between nm23-H1 gene product positive and negative patients (p = 0.21). However, reduced expression of nm23-H1 gene product was associated with shorter overall survival in patients with involved lymph nodes (p < 0.05), but not in patients without involved lymph nodes (p = 0.87). CONCLUSIONS: In patients with esophageal squamous cell carcinoma, there appears to be an inverse relationship between nm23-H1 gene product expression and lymphatic vessel invasion. Furthermore, nm23-H1 gene product expression might be a prognostic marker in patients with involved lymph nodes. Our data does not demonstrate any correlation between nm23-H1 gene product expression and blood vessel invasion

Radiologist experience and CT examination quality determine metastasis detection in patients with esophageal or gastric cardia cancer

We aimed to separate the influence of radiologist experience from that of CT quality in the evaluation of CT examinations of patients with esophageal or gastric cardia cancer. Two radiologists from referral centers ('expert radiologists') and six radiologists from regional non-referral centers ('non-expert radiologists') performed 240 evaluations of 72 CT examinations of patients diagnosed with esophageal or gastric cardia cancer between 1994 and 2003. We used conditional logistic regression analysis to calculate odds ratios (OR) for the likelihood of a correct diagnosis. Expert radiologists made a correct diagnosis of the presence or absence of distant metastases according to the gold standard almost three times more frequently (OR 2.

Staging investigations for oesophageal cancer: a meta-analysis

The aim of the study was to compare the diagnostic performance of endoscopic ultrasonography (EUS), computed tomography (CT), and 18F-fluoro-2-deoxy-D-glucose positron emission tomography (FDG-PET) in staging of oesophageal cancer. PubMed was searched to identify English-language articles published before January 2006 and reporting on diagnostic performance of EUS, CT, and/or FDG-PET in oesophageal cancer patients. Articles were included if absolute numbers of true-positive, false-negative, false-positive, and true-negative test results were available or derivable for regional, celiac, and abdominal lymph node metastases and/or distant metastases. Sensitivities and specificities were pooled using a random effects model. Summary receiver operating characteristic analysis was performed to study potential effects of study and patient characteristics. Random effects pooled sensitivities of EUS, CT, and FDG-PET for regional lymph node metastases were 0.80 (95% confidence interval 0.75–0.84), 0.50 (0.41–0.60), and 0.57 (0.43–0.70), respectively, and specificities were 0.70 (0.65–0.75), 0.83 (0.77–0.89), and 0.85 (0.76–0.95), respectively. Diagnostic performance did not differ significantly across these tests. For detection of celiac lymph node metastases by EUS, sensitivity and specificity were 0.85 (0.72–0.99) and 0.96 (0.92–1.00), respectively. For abdominal lymph node metastases by CT, these values were 0.42 (0.29–0.54) and 0.93 (0.86–1.00), respectively. For distant metastases, sensitivity and specificity were 0.71 (0.62–0.79) and 0.93 (0.89–0.97) for FDG-PET and 0.52 (0.33–0.71) and 0.91 (0.86–0.96) for CT, respectively. Diagnostic performance of FDG-PET for distant metastases was significantly higher than that of CT, which was not significantly affected by study and patient characteristics. The results suggest that EUS, CT, and FDG-PET each play a distinctive role in the detection of metastases in oesophageal cancer patients. For the detection of regional lymph node metastases, EUS is most sensitive, whereas CT and FDG-PET are more specific tests. For the evaluation of distant metastases, FDG-PET has probably a higher sensitivity than CT. Its combined use could however be of clinical value, with FDG-PET detecting possible metastases and CT confirming or excluding their presence and precisely determining the location(s)

Elevation of circulating big endothelin-1: an independent prognostic factor for tumor recurrence and survival in patients with esophageal squamous cell carcinoma

<p>Abstract</p> <p>Background</p> <p>Endothelin(ET) axis plays a key role in many tumor progression and metastasis via various mechanisms such as angiogenesis, mediating extracellular matrix degradation and inhibition of apoptosis. However, there is limited information regarding the clinical significance of plasma big ET-1 levels in esophageal cancer patients. Circulating plasma big ET-1 levels were measured in patients with esophageal squamous cell carcinoma(ESCC) to evaluate the value of ET-1 as a biomarker for predicting tumor recurrence and patients survival.</p> <p>Methods</p> <p>Preoperative plasma big ET-1 concentrations were measured by an enzyme linked immunosorbent assay(ELISA) in 108 ESCC patients before surgery, and then again at 1,2,3,10 and 30 days after curative radical resection for ESCC. The association between preoperative plasma big ET-1 levels and clinicopathological features, tumor recurrence and patient survival, and their changes following surgery were evaluated.</p> <p>Results</p> <p>The preoperative plasma big ET-1 levels in ESCC patients were significantly higher than those in controls. And there was a significant association between plasma big ET-1 levels and disease stage, as well as invasion depth of the tumor and lymph node status. Furthermore, plasma big ET-1 levels decreased significantly after radical resection of the primary tumor and patients with postoperative recurrence had significantly higher plasma big ET-1 levels than that of patients without recurrence. Finally, the survival rate of patients with higher plasma big ET-1 concentrations (>4.3 pg/ml) was significantly lower than that of patients with lower level (≤ 4.3 pg/ml). Multivariate regression analysis showed that plasma big ET-1 level is an independent prognostic factor for survival in patients with ESCC.</p> <p>Conclusion</p> <p>Plasma big ET-1 level in ESCC patients may reflect malignancy and predict tumor recurrence and patient survival. Therefore, the preoperative plasma big ET-1 levels may be a clinically useful biomarker for choice of multimodality therapy in ESCC patients.</p

Risky Traitor Tracing and New Differential Privacy Negative Results

In this work we seek to construct collusion-resistant traitor tracing systems with small ciphertexts from standard assumptions that also move toward practical efficiency. In our approach we will hold steadfast to the principle of collusion resistance, but relax the requirement on catching a traitor from a successful decoding algorithm. We define a $f$-risky traitor tracing system as one where the probability of identifying a traitor is $f(\lambda,n)$ times the probability a successful box is produced. We then go on to show how to build such systems from prime order bilinear groups with assumptions close to those used in prior works. Our core system achieves, for any $k > 0$, $f(\lambda,n) \approx \frac{k}{n + k - 1}$ where ciphertexts consists of $(k + 4)$ group elements and decryption requires $(k + 3)$ pairing operations. At first glance the utility of such a system might seem questionable since the $f$ we achieve for short ciphertexts is relatively small. Indeed an attacker in such a system can more likely than not get away with producing a decoding box. However, we believe this approach to be viable for four reasons: 1. A risky traitor tracing system will provide deterrence against risk averse attackers. In some settings the consequences of being caught might bear a high cost and an attacker will have to weigh his utility of producing a decryption $D$ box against the expected cost of being caught. 2. Consider a broadcast system where we want to support low overhead broadcast encrypted communications, but will periodically allow for a more expensive key refresh operation. We refer to an adversary produced algorithm that maintains the ability to decrypt across key refreshes as a persistent decoder. We show how if we employ a risky traitor tracing systems in this setting, even for a small $f$, we can amplify the chances of catching such a ``persistent decoder\u27\u27 to be negligibly close to 1. 3. In certain resource constrained settings risky traitor tracing provides a best tracing effort where there are no other collusion-resistant alternatives. For instance, suppose we had to support 100K users over a radio link that had just 10KB of additional resources for extra ciphertext overhead. None of the existing $\sqrt N$ bilinear map systems can fit in these constraints. On the other hand a risky traitor tracing system provides a spectrum of tracing probability versus overhead tradeoffs and can be configured to at least give some deterrence in this setting. 4. Finally, we can capture impossibility results for differential privacy from $\frac{1}{n}$-risky traitor tracing. Since our ciphertexts are short ($O(\lambda)$), we get the negative result which matches what one would get plugging in the obfuscation based tracing system Boneh-Zhandry (CRYPTO 2014) solution into the prior impossibility result of Dwork et al. (STOC 2009)

A Concise Bounded Anonymous Broadcast Yielding Combinatorial Trace-and-Revoke Schemes

Broadcast Encryption is a fundamental primitive supporting sending a secure message to any chosen target set of $N$ users. While many efficient constructions are known, understanding the efficiency possible for an ``Anonymous Broadcast Encryption\u27\u27 (ANOBE), i.e., one which can hide the target set itself, is quite open. The best solutions by Barth, Boneh, and Waters (\u2706) and Libert, Paterson, and Quaglia (\u2712) are built on public key encryption (PKE) and their ciphertext sizes are, in fact, $N$ times that of the underlying PKE (rate=$N$). Kiayias and Samary (\u2712), in turn, showed a lower bound showing that such rate is the best possible if $N$ is an independent unbounded parameter. However, when considering certain user set size bounded by a system parameter (e.g., the security parameter), the problem remains interesting. We consider the problem of comparing ANOBE with PKE under the same assumption. We call such schemes Anonymous Broadcast Encryption for Bounded Universe -- AnoBEB. We first present an AnoBEB construction for up to $k$ users from LWE assumption, where $k$ is bounded by the scheme security parameter. The scheme does not grow with the parameter and beat the PKE method. Actually, our scheme is as efficient as the underlying LWE public-key encryption; namely, the rate is, in fact, $1$ and thus optimal. The scheme is achieved easily by an observation about an earlier scheme with a different purpose. More interestingly, we move on to employ the new AnoBEB in other multimedia broadcasting methods and, as a second contribution, we introduce a new approach to construct an efficient ``Trace and Revoke scheme\u27\u27 which combines the functionalites of revocation and of tracing people (called traitors) who in a broadcasting schemes share their keys with the adversary which, in turn, generates a pirate receiver. Note that, as was put forth by Kiayias and Yung (EUROCRYPT \u2702), combinatorial traitor tracing schemes can be constructed by combining a system for small universe, integrated via an outer traceability codes (collusion-secure code or identifying parent property (IPP) code). There were many efficient traitor tracing schemes from traceability codes, but no known scheme supports revocation as well. Our new approach integrates our AnoBEB system with a Robust IPP code, introduced by Barg and Kabatiansky (IEEE IT \u2713). This shows an interesting use for robust IPP in cryptography. The robust IPP codes were only implicitly shown by an existence proof. In order to make our technique concrete, we propose two explicit instantiations of robust IPP codes. Our final construction gives the most efficient trace and revoke scheme in the bounded collusion model