Haploflow: Strain-resolved de novo assembly of viral genomes.

In viral infections often multiple related viral strains are present, due to coinfection or within-host evolution. We describe Haploflow, a de Bruijn graph-based assembler for de novo genome assembly of viral strains from mixed sequence samples using a novel flow algorithm. We assessed Haploflow across multiple benchmark data sets of increasing complexity, showing that Haploflow is faster and more accurate than viral haplotype assemblers and generic metagenome assemblers not aiming to reconstruct strains. Haplotype reconstructed high-quality strain-resolved assemblies from clinical HCMV samples and SARS-CoV-2 genomes from wastewater metagenomes identical to genomes from clinical isolates.

[Clinical analysis of reoperation for secondary hyperparathyroidism].

Objective: To investigate the safety and efficacy for reoperation after parathyroidectomy for persistent and recurrent secondary hyperparathyroidism (HPT). Methods: Totally 10 patients with persistent or recurrent HPT who underwent parathyroidectomy reoperation at Department of General Surgery, China-Japan Friendship Hospital from April 2001 to October 2012 were selected. Among them, 6 were male and 4 were female with age of (46.9±7.7) years (range: 36 to 57 years). There were 8 cases of persistent HPT and 4 cases of recurrent HPT. The general health condition, symptom changes, gland excision and transplantation records, pathological reports and intact parathyroid hormone (iPTH), serum calcium, phosphorus and alkaline phosphatase values of pre-operation, post-operation and during follow-up were collected and the causes of operation failure were analyzed. The efficacy was determined according to postoperative symptom improvement, iPTH values, perioperative mortality and postoperative complications. Results: Of the 10 patients, 8 cases underwent reoperation once (including 7 cases of neck exploration, 1 case of forearm exploration), and 2 cases underwent reoperation twice (all neck explorations). No postoperative death was reported. The laryngeal nerve damage occurred in 2 cases during reoperation, and it was gradually recovered 3 months after surgery with the vocal cord movement recovery after 2 years. Hypocalcemia occurred in all 10 cases after operation, and was effectively controlled with calcium supplement treatment. No complications such as the trachea and esophagus damage, and the neck hematoma were observed. The significant efficacy was demonstrated in 6 patients received 1 reoperation and 2 patients with 2 reoperations. Conclusion: Reoperation is a safe and effective treatment for the persistent or recurrent secondary HPT caused by end-stage renal disease after surgery.

High efficacy and safety of low-dose CD19-directed CAR-T cell therapy in 51 refractory or relapsed B acute lymphoblastic leukemia patients.

Refractory or relapsed B lymphoblastic leukemia (B-ALL) patients have a dismal outcome with current therapy. We treated 42 primary refractory/hematological relapsed (R/R) and 9 refractory minimal residual disease by flow cytometry (FCM-MRD+) B-ALL patients with optimized second generation CD19-directed CAR-T cells. The CAR-T-cell infusion dosages were initially ranged from 0.05 to 14 × 105/kg and were eventually settled at 1 × 105/kg for the most recent 20 cases. 36/40 (90%) evaluated R/R patients achieved complete remission (CR) or CR with incomplete count recovery (CRi), and 9/9 (100%) FCM-MRD+ patients achieved MRD-. All of the most recent 20 patients achieved CR/CRi. Most cases only experienced mild to moderate CRS. 8/51 cases had seizures that were relieved by early intervention. Twenty three of twenty seven CR/CRi patients bridged to allogeneic hematopoietic stem cell transplantation (allo-HCT) remained in MRD- with a median follow-up time of 206 (45-427) days, whereas 9 of 18 CR/CRi patients without allo-HCT relapsed. Our results indicate that a low CAR-T-cell dosage of 1 × 105/kg, is effective and safe for treating refractory or relapsed B-ALL, and subsequent allo-HCT could further reduce the relapse rate.

MicroRNA-155 facilitates skeletal muscle regeneration by balancing pro- and anti-inflammatory macrophages.

Skeletal muscle has remarkable regeneration capacity and regenerates in response to injury. Muscle regeneration largely relies on muscle stem cells called satellite cells. Satellite cells normally remain quiescent, but in response to injury or exercise they become activated and proliferate, migrate, differentiate, and fuse to form multinucleate myofibers. Interestingly, the inflammatory process following injury and the activation of the myogenic program are highly coordinated, with myeloid cells having a central role in modulating satellite cell activation and regeneration. Here, we show that genetic deletion of microRNA-155 (miR-155) in mice substantially delays muscle regeneration. Surprisingly, miR-155 does not appear to directly regulate the proliferation or differentiation of satellite cells. Instead, miR-155 is highly expressed in myeloid cells, is essential for appropriate activation of myeloid cells, and regulates the balance between pro-inflammatory M1 macrophages and anti-inflammatory M2 macrophages during skeletal muscle regeneration. Mechanistically, we found that miR-155 suppresses SOCS1, a negative regulator of the JAK-STAT signaling pathway, during the initial inflammatory response upon muscle injury. Our findings thus reveal a novel role of miR-155 in regulating initial immune responses during muscle regeneration and provide a novel miRNA target for improving muscle regeneration in degenerative muscle diseases.

Effect of prepyloric gastric transection and anastomosis on sphincter of Oddi cyclic motility in conscious dogs.

PURPOSE: We previously reported significant changes in sphincter of Oddi cyclic motility after proximal duodenal transection and anastomosis. However, the role of intrinsic myoneural continuity between the antrum and duodenum in this respect is not understood. The aim of this study was to elucidate the effects of prepyloric gastric transection on sphincter of Oddi motility in animals in the conscious state. METHODS: Pressures in the bile duct, duodenum, stomach, and sphincter of Oddi and their response to an injection of cholecystokinin-octapeptide were measured in four conscious dogs, with a duodenal cannula, before and after gastric transection and anastomosis 1.5 cm proximal to the pylorus. RESULTS: Gastric transection did not affect the initiation and propagation of the gastroduodenal migration motor complex. Biliary pressure (5.7 +/- 0.15 to 5.5 +/- 0.2 mmHg; P = 0.91), sphincter of Oddi basal pressure (10.6 +/- 0.3 to 10.7 +/- 0.2 mmHg; P = 0.97), and amplitude (26.0 +/- 1.2 to 32.9 +/- 1.7 mmHg; P = 0.304) did not change after gastric transection. Biliary pressure decreased from phase II to phase III of the duodenal migrating motor complex. Cholecystokinin-octapeptide inhibited sphincter of Oddi phasic waves before and after gastric transection. CONCLUSIONS: Intrinsic myoneural transection at the prepyloric region does not influence sphincter of Oddi cyclic motility. Preservation of pyloroduodenal myoneural continuity in pylorus-preserving gastrectomy would be beneficial to maintain normal sphincter of Oddi motility.

Effects of proximal duodenal transection and anastomosis on interdigestive sphincter of Oddi cyclic motility in conscious dogs.

Gallstones formed after gastrectomy are bilirubinate stones probably associated with biliary stasis and infection. Effects of proximal duodenal transection performed during gastrectomy on interdigestive sphincter of Oddi cyclic motility possibly relevant to this phenomenon were investigated in four conscious dogs. Although the cyclic change in sphincter motility was still in concert with the duodenal migrating motor complex after duodenal transection, the mean period was shortened (p < 0.02), and the frequency (p < 0.005) and amplitude (p < 0.001) of sphincter phasic waves during phase III were decreased. The cyclic variation of basal pressure disappeared, and the mean basal pressure throughout the cycle was significantly reduced (p < 0.003). Transient inhibition of sphincter and duodenal contractions normally seen during phase III disappeared. Duodenal transection reversed the response of the sphincter to cholecystokinin-octapeptide from inhibition to stimulation and from reduction of the basal pressure to elevation. These data suggest that duodenal transection produces significant changes in interdigestive sphincter of Oddi motility, possibly contributing to augmented duodenobiliary reflux and then lithogenesis. Myoneural continuity between the stomach and sphincter of Oddi at the proximal duodenum may play an important role in maintaining normal biliary dynamics.

Vector manometric study of the sphincter of Oddi in the dog: functional and morphological correlation.

The relationship between sphincter of Oddi pressure and the morphological structure of the sphincter was studied in eight dogs prepared with a duodenal cannula. Sphincter of Oddi manometry was performed in awake animals in three directions, ventral, left dorsal, and right dorsal, using a catheter with three radial side holes for recording at one level. The pressure in the ventral direction (26.6+/-1.06 mmHg) (mean+/-SEM) was significantly lower than that in the left and right dorsal directions (30.6+/-1.42 and 31.2+/-1.23 mmHg, respectively). This functional manometric difference in the three directions correlated closely with the morphological structure of the sphincter of Oddi; the sum of the thickness of the sphincter of Oddi muscle and duodenal proper muscle was greater on the dorsal than on the ventral side. To our knowledge, this is the first report of axial asymmetry in sphincter of Oddi pressure.

Polymorphisms of dopamine D2-like (D2, D3, and D4) receptors in schizophrenia.

The result of most association studies and linkage analyses have suggested a negative association between schizophrenia and D2-like (D2, D3, and D4) receptor polymorphisms. Although the polymorphisms of the D2-like receptor in themselves may not account for the etiology of schizophrenia, they can contribute to the severity of the symptoms. Thus, we studied the associations between the polymorphisms and their combinations, and the vulnerability of schizophrenics. Fragments of the D2-like receptor genes were amplified by means of the polymerase chain reaction, and the polymorphisms were identified by the restriction fragment length polymorphism and single-stranded conformation polymorphism methods. There were no statistically significant differences in the polymorphisms and their combinations between schizophrenics and controls. Schizophrenics with D4E1(A1/A2), which contains 2 and 1 tandem repeats of a 12-base-pair sequence in exon 1, had a lower total positive symptom score before medication than schizophrenics with D4E1(A1/A1). There was no association between the polymorphisms and negative symptoms.

Effects of intraduodenal air insufflation on sphincter of Oddi motility in conscious dogs.

To investigate effects of intraduodenal air insufflation on sphincter of Oddi motility, manometric recordings were obtained during fasting from the sphincter and duodenum in four conscious dogs with duodenal cannula. At 40% of the mean cycle length of the migrating motor complex predetermined from baseline recording, 160 ml of air was injected into the duodenum. In both the sphincter and duodenum, air insufflation produced premature phase III-like activity in seven of 20 experiments (35%) or nonspecific excitatory reaction in eight (40%). In the remaining five experiments (25%), the sphincter exhibited a transient inhibitory response, while the duodenum showed the nonspecific excitatory reaction. Basal pressure of the sphincter increased immediately after air insufflation in 90% of the 20 experiments. The mean basal pressure increased from 12.3 +/- 1.6 mm Hg to 22.4 +/- 2.1 mm Hg (P < 0.0001) and minimum basal pressure from 2.9 +/- 0.9 mm Hg to 4.7 +/- 0.8 mm Hg (P < 0.001). These results indicate that intraduodenal air insufflation does affect motility of the sphincter of Oddi and duodenum in conscious dogs.

The genes encoding the 5HT1D alpha and 5HT1D beta receptors are unchanged in patients with panic disorder.

To determine the serotonergic function in panic disorder, sequencing of the genes encoding the 5HT1D alpha and 5HT1D beta receptors was carried out. The genes for the 5HT1D alpha and 5HT1D beta receptors were amplified by polymerase chain reaction and sequenced by the dideoxy method. Some patients have both nucleotides C and T at position 1080 in 5HT1D alpha receptor gene; however, both of them code the same amino acid, asparagine. The 5HT1D beta receptor gene had a substitution from GCA276 to GCG276, not only panic disorder but also in controls; however, this substitution does not change the corresponding amino acid, alanine92.

Male breast cancer--a report of 4 cases and a review of the literature.

Male breast cancer represents only about 1% of all breast cancers. Of 451 patients with breast cancer, we have experienced four cases of male breast cancer. Characteristics of these male patients with breast cancer were an older age at diagnosis (mean: 68.5 years old), prolonged duration of symptom (ranged from 1 month to 6 years with a mean of 25.5 months), centrally located tumor, advanced staging and infiltrating ductal carcinoma in histologic type. Some reported risk factors for the development of male breast cancer, such as radiation exposure, hormonal factors and gallstone disease were present.

The gene encoding the 5-HT1A receptor is intact in mood disorders.

We studied the 5-HT1A receptor gene in 50 mood disorders and 50 normal volunteers. The 5-HT1A receptor gene was amplified by polymerase chain reaction and sequenced by the dideoxy method. The sequence of the 5-HT1A receptor encodes a protein of 422 amino acids, that is, one amino acid longer than the reported sequence (Kobilka et al. 1987). The DNA sequence at positions 454 to 459 is CGC GCC GCT, not CCG CGT, and the amino acids sequence at these positions is changing from proline arginine to arginine alanine alanine. These differences, however, were observed in both mood disorders and controls. One silent polymorphism, CTG to GTA at position 294, was found. These results suggest that the 5-HT1A receptor gene is intact in mood disorders.

The influence of age and location of arterial lesion on the pathogenesis and development of early atherosclerotic lesions in youth.

From 1986 to 1989, 324 aortae from accidental death aged 15-39 were collected from two locations, one of higher prevalence (Beijing in North China), and the other of lower prevalence (Nanning in South China) of atherosclerosis (AS) and coronary heart disease (CHD). Morphometry and biochemical analyses, were used in the study with emphasis on the changes of smooth muscle cells (SMC) in the aortic intima and on the aortic proteoglycans (PGs) of specimens from both locations to elucidate their relationship with the pathogenesis and development of AS and to find ways, if any, for the prevention and control of AS. The results showed that the densities, especially the area density of the cell nuclei of aortic SMC were significantly higher in specimens from the North than those from the South (P < 0.01). Nuclear densities of SMC negatively correlated with alcian blue-positive substances; both total PGs and Heparin sulfate PG (HSPG, inhibitory to SMC proliferation) of the aortic intima and media were lower in specimens from the North than those from the South (P < 0.01). The percentage of sudanophilic lesion (SL) in the total intimal area, showing the extent of fatty infiltration of aortae from the two locations, was similar except that of the male abdominal aortae which was higher in the North (P < 0.01). The above findings showed that decreased content of HSPG which is inhibitory to SMC proliferation might be one of the causes of the augmentation of aortic SMC proliferation in Beijing specimens; and also the increased serum cholesterol concentration of the population in Nanning was reflected in the SL of the aortic intima.(ABSTRACT TRUNCATED AT 250 WORDS)

Human aortic proteoglycans of subjects from districts of high and low prevalence of atherosclerosis in China.

The contents of three species of proteoglycans (PGs), heparan sulfate PG(HSPG), chondroitin sulfate PG(CSPG) and dermatan sulfate chondroitin sulfate PG(DSCSPG), in human thoracic aortas of subjects from districts of high (Beijin, in North China) and low (Nanning, in South China) prevalence of atherosclerosis in China were quantitated. Higher aortic HSPG and DSCSPG (but lower DS) in samples from Nanning than those from Beijing might be implicated in the lower prevalence of atherosclerosis in the former.

Human penicilliosis marneffei and its relation to the bamboo rat (Rhizomys pruinosus).

Fourteen cases of penicilliosis marneffei occurred in persons in the Guangxi region of the People's Republic of China; the first known case of that disease had been found in Vietnamese bamboo rats (Rhizomys sinensis). A survey of the wild rats in this region was initiated to determine if any of these animals were infected by Penicillium marneffei. Although R. sinensis rats live in the study area, they are relatively rare. The only rats captured were another species of bamboo rat (R. pruinosus). Of the 19 rats captured, 18 yielded cultures of P. marneffei from one or more of their internal organs. The implications of this finding in respect to the epidemiology of penicilliosis marneffei are discussed.

Progressive disseminated penicilliosis caused by Penicillium marneffei. Report of eight cases and differentiation of the causative organism from Histoplasma capsulatum.

Eight patients with fatal penicilliosis caused by Penicillium marneffei are reported. All were natives of southern rural Guangxi, and none had a predisposing illness or evidence of altered immunity. The distinctive features of P. marneffei include proliferation of yeast-like cells within histiocytes, followed by the development of focal necrosis and, eventually, large abscesses. Outside the histiocytes, the fungi elongate, become slightly curved, and form septa. In vitro, P. marneffei produces a red pigment which diffuses into the culture medium. The differentiation between P. marneffei and Histoplasma capsulatum is described, and possible reservoirs for P. marneffei are discussed.