Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through 'reverse phenotyping'.

The in vivo phenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells require in vitro antigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we use single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induce transcriptional shifts by antigenic stimulation in vitro and take advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for 'reverse phenotyping'. This allows identification of SARS-CoV-2-reactive TCRs and reveals phenotypic effects introduced by antigen-specific stimulation. We characterize transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and show correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states.

Conservation implications for jaguars and other neotropical mammals using highway underpasses.

The Nuevo Xcan-Playa del Carmen highway in Quintana Roo, bisects the vegetation corridor connecting two Jaguar Conservation Units (JCUs): Yum Balaam (north) and Sian Ka´an (south). The project´s main goal was to describe differential use of available crossing structures (wildlife underpasses and culverts) by mammals present along this highway. We set 28 camera traps along the 54km stretch of the highway covering wildlife underpasses (10), and culverts such as box culverts (9) and pipes (9) from September 2016 until March 2017. A total of 24 jaguar crossings have been recorded exclusively using wildlife underpasses, including four males and two females. At least 18 other mammal species including five of the target priority species (protected by Mexican law) were documented, all of which were native except for two invasive species. In terms of species using the crossing structures, we identified 13 species using wildlife underpasses, nine using concrete box culverts and 10 using concrete pipes. Wildlife underpasses show higher diversity values (Shannon´s exponential index = 5.8 and Inverse Simpson´s index = 4.66) compared to culverts because they allow bigger species to cross. We recommend more highways along the jaguar´s distribution should develop mitigation measures to allow for wildlife connectivity. Wildlife underpasses, along with retrofitted culverts, could help secure not only the permanence of this species by facilitating the functional connectivity between populations but have positive impacts on other neotropical mammalian fauna as well.

Effect of nesting environment on incubation temperature and hatching success of Morelet's crocodile (Crocodylus moreletii) in an urban lake of Southeastern Mexico.

Incubation temperature is an important aspect in terms of biological performance among crocodiles, and several controlled experiments have demonstrated a significant relationship between incubation temperature, success in hatching and survival of hatchlings. However, a few studies have tested these relationships in the wild. The objective of this study was to determine the relationship of nest characteristics and environment (hatch year, nest basal area and height, clutch size, distance to shore line, and vegetation cover), to incubation temperature and hatching success among Morelet's crocodile (Crocodylus moreletii). The study was carried out during the nesting seasons of Morelet's crocodile, from 2007 to 2009 in the Laguna de Las Ilusiones, an urban lake located in Villahermosa, Tabasco, Mexico. We physically characterized 18 nests and inserted a temperature data logger in each nest chamber. At the end of the nesting season and prior to hatching, we recovered the crocodile eggs and data loggers and calculated hatching success, under laboratory conditions. We related the environmental variables of the nest with the mean and fluctuation (standard deviation) of nest temperature, using linear models. We also related the environmental variables affecting the nest, to mean nest temperature and fluctuation in incubation temperature and to hatching success, using linear models. Although we found differences in incubation temperature between nests, mean incubation temperature did not differ between years, but there were differences in nest thermal fluctuation between years. The mean incubation temperature for 11 nests (61.1%) was lower than the suggested Female-Male pivotal temperature (producing 50% of each sex) for this species, and all hatchlings obtained were males. There were no differences in clutch size between years, but hatching success varied. Our study indicates that hatching success depends on certain environmental variables and nest conditions to which the eggs are subjected, including season, nest size and clutch size. We also discuss the importance of the fluctuation of incubation temperature on hatching success and sex determination.

3D cone-beam CT guidance, a novel technique in renal biopsy--results in 41 patients with suspected renal masses.

OBJECTIVE: To determine whether 3D cone-beam computed tomography (CBCT) guidance allows safe and accurate biopsy of suspected small renal masses (SRM), especially in hard-to-reach anatomical locations. MATERIALS AND METHODS: CBCT guidance was used to perform 41 stereotactic biopsy procedures of lesions that were inaccessible for ultrasound guidance or CT guidance. In CBCT guidance, a 3D-volume data set is acquired by rotating a C-arm flat-panel detector angiosystem around the patient. In the data set, a needle trajectory is determined and, after co-registration, a fusion image is created from fluoroscopy and a slice from the data set, enabling the needle to be positioned in real time. RESULTS: Of the 41 lesions, 22 were malignant, 17 were benign, and 2 were nondiagnostic. The two nondiagnostic lesions proved to be renal cell carcinoma. There was no growth during follow-up imaging of the benign lesions (mean 29 months). This resulted in a sensitivity, specificity, PPV, NPV, and accuracy of 91.7, 100, 100, 89.5, and 95.1%, respectively. Mean dose-area product value was 44.0 Gy·cm(2) (range 16.5-126.5). There was one minor bleeding complication. CONCLUSION: With CBCT guidance, safe and accurate biopsy of a suspected SRM is feasible, especially in hard-to-reach locations of the kidney. KEY POINTS : • Cone-beam computed tomography has potential advantages over conventional CT for interventional procedures. • CBCT guidance incorporates 3D CBCT data, fluoroscopy, and guidance software. • In hard-to-reach renal masses, CBCT guidance offers an alternative biopsy method. • CBCT guidance offers good outcome and safety and has potential clinical significance.

Alopecia in bats from Tabasco, Mexico.

We report alopecic syndrome (hair loss in areas of the body, including chest, abdomen, and back) in four frugivorous bat species (Artibeus jamaicensis, Artibeus lituratus, Sturnira lilium, and Sturnira ludovici) within urban and periurban areas of Villahermosa, Tabasco, México, during 2007 and 2008. The overall prevalence of alopecic syndrome was 5.25% (135/2,567 bats). The highest prevalence was found in A. lituratus (5.6%; 62/1,105), followed by A. jamaicensis (5%; 3/1,462). We found a higher prevalence in the dry season, when more than 90% of the alopecic individuals (n=122) were captured. Higher prevalence of alopecia was recorded in urban areas (80% of captured alopecic bats, n=108) than in periurban areas (20%, n=27). Histopathologic studies revealed no evidence of infectious agents. The syndrome may be related to nutritional or endocrinal deficiencies. Spatial and seasonal aggregation in urban areas suggests that anthropogenic activities may interfere with nutritional processes. Further studies are needed to confirm the etiology of the syndrome as well as its impact on population dynamics. This is the first report of alopecic syndrome in sylvatic bats.

[Choledochal cyst as a complex malformation of the intra and extrahepatic bile ducts]. / Chist coledocian congenital--anomalie complexa a cailor biliare intra si extrahepatice.

The authors present the case of a 64 years woman with a choledochal cyst along with a complex malformation of both intra and extrahepatic bile ducts. The patient was admitted with a diagnosis of acute and underestimated cholecystitis, which was in fact a real acute severe suppurated angiocolitis located at the cystic cavity level along with severe hepato-renal failure. As long as the choledochal cyst evolves as a stand-alone entity, it can frequently be associated with other malformations of the bile ducts--such as choledochal duct stenosis or abnormal connection of the common hepatic duct with pancreatic ducts. The main dilatation was engulfing the whole common bile duct with a fusiform aspect, and the cranial end is opening into a long hepatic duct from which were emerging several biliary segments branches, for both hepatic lobes. This aspect of a multistage convergence with four branches which is opening into a long hepatic bile duct and then in the choledochal cyst, represents an unusual malformation which does not respect the rules described by former published authors.

[Extraperitoneal transomphalic drainage of the posthydatid hepatic restant cavity by coelioscopic approach]. / Drenajul transomfalic extraperitoneal al cavitatii restante hepatice posthidatice pe cale laparoscopica.

Being often biliary contaminated and suppurative, the hydatid hepatic cyst is in fact a real parasitic abscess. So far its surgical approach represents the only credible possibility of treatment. Authors impart their experience regarding the external drainage of the restant posthydatid cavity, by using a completely extraperitoneal way of bringing out the drain, by means of the round ligament, an original method conceived and put into practice by Prof. D. Burlui in 1968. This technique is simple, without risks or complications, possible for most of the parasite hepatic locations, especially for the central segments, for which this method is superior to other surgical procedures. The greatest advantage of the extraperitoneal transomphalic route of the drain is the absence of the peritoneal losses and so the impossibility of biliary leakage occurrence. The radiological and the ultrasonic controls confirm the reduction and finally total fibrosis and disappearance of the remaining cavity, about two months after the surgery. In this moment the drainage may be suppressed. In December 2001, we added to this method an other original variant: the coelioscopic approach of the extraperitoneal transomphalic drainage of the restant posthydatid cavity, representing the aim of this paper.

[The extraperitoneal transomphalic drainage of the postoperative hydatid cavity through the transposed round ligament detached from the liver]. / Drenajul transomfalic extraperitoneal în chistul hidatic al lobului stâng hepatic prin transpozitia ligamentului rotund detasat de ficat.

The transomphalic and then the transligamentary extraperitoneal drainage imagined by D. Burlui and its multiple use in the liver and the biliary tract surgery, is well known. Concerning the hepatic hydatid cysts, the drainage of the remaining cavity by the round ligament way is possible for most of the locations of the parasite, but it is less performed in the right liver lateral segments locations, too far situated, and also in the left liver locations. On the other hand, this specific method implies to place the drainage tube using the round ligament "in situ ", normally placed and inserted. We encountered an extremely large hydatid cyst of the left hepatic lobe, adherent to the anterior and posterior abdominal wall, spleen, stomach, pancreas and large bowel, which required to extend the incision to the left and make the necessary segmentation of the round ligament at its hepatic insertion. After pericystotomy and the evacuation of the cyst, the remaining cavity drainage was performed through the same round ligament whose free end was tightly fixed to the partial pericystotomy border. This transposition allowed the exteriorisation of the drainage tube in the same way as for the transligamentary and total extraperitoneal original method.