SERS-based microdevices for use as in vitro diagnostic biosensors

Advances in surface-enhanced Raman scattering (SERS) detection have helped to overcome the limitations of traditional in vitro diagnostic methods, such as fluorescence and chemiluminescence, owing to its high sensitivity and multiplex detection capability. However, for the implementation of SERS detection technology in disease diagnosis, a SERS-based assay platform capable of analyzing clinical samples is essential. Moreover, infectious diseases like COVID-19 require the development of point-of-care (POC) diagnostic technologies that can rapidly and accurately determine infection status. As an effective assay platform, SERS-based bioassays utilize SERS nanotags labeled with protein or DNA receptors on Au or Ag nanoparticles, serving as highly sensitive optical probes. Additionally, a microdevice is necessary as an interface between the target biomolecules and SERS nanotags. This review aims to introduce various microdevices developed for SERS detection, available for POC diagnostics, including LFA strips, microfluidic chips, and microarray chips. Furthermore, the article presents research findings reported in the last 20 years for the SERS-based bioassay of various diseases, such as cancer, cardiovascular diseases, and infectious diseases. Finally, the prospects of SERS bioassays are discussed concerning the integration of SERS-based microdevices and portable Raman readers into POC systems, along with the utilization of artificial intelligence technology.

[Progress of schistosomiasis control in People's Republic of China in 2022]

This report presented the endemic status of schistosomiasis and analyzed the data collected from the national schistosomiasis prevention and control system and national schistosomiasis surveillance program in the People's Republic of China in 2022. Among the 12 provinces (municipality and autonomous region) endemic for schistosomiasis, Shanghai Municipality, Zhejiang Province, Fujian Province, Guangdong Province and Guangxi Zhuang Autonomous Region continued to maintain the achievements of schistosomiasis elimination, and Sichuan and Jiangsu provinces maintained the criteria of transmission interruption, while Yunnan, Hubei, Anhui, Jiangxi and Hunan provinces maintained the criteria of transmission control by the end of 2022. A total of 452 counties (cites, districts) were found to be endemic for schistosomiasis in China in 2022, with 27 434 endemic villages covering 73 424 400 people at risk of infections. Among the 452 endemic counties (cities, districts), 75.89% (343/452), 23.45% (106/452) and 0.66% (3/452) achieved the criteria of elimination, transmission interruption and transmission control of schistosomiasis, respectively. In 2022, 4 317 356 individuals received serological tests for schistosomiasis, and 62 228 were sero-positive. A total of 208 646 individuals received stool examinations for schistosomiasis, with one positive and another two cases positive for urine microscopy, and these three 3 cases were imported schistosomiasis patients from Africa. There were 28 565 cases with advanced schistosomiasis documented in China by the end of 2022. Oncomelania hupensis snail survey was performed in 18 891 endemic villages in China in 2022 and O. hupensis snails were found in 6 917 villages (36.62% of all surveyed villages), with 8 villages identified with emerging snail habitats. Snail survey was performed at an area of 655 703.01 hm² and 183 888.60 hm² snail habitats were found, including 110.58 hm² emerging snail habitats and 844.35 hm² re-emerging snail habitats. There were 477 200 bovines raised in the schistosomiasis endemic areas of China in 2022, and 113 946 bovines received serological examinations for schistosomiasis, with 204 sero-positives detected. Among the 131 715 bovines received stool examinations, no positives were identified. In 2022, there were 19 726 schistosomiasis patients receiving praziquantel chemotherapy, and expanded chemotherapy was performed in 714 465 person-time for humans and 234 737 herd-time for bovines in China. In 2022, snail control with chemical treatment was performed at an area of 119 134.07 hm², and the actual area of chemical treatment was 65 825.27 hm², while environmental improvements were performed at an area of 1 163.96 hm². Data from the national schistosomiasis surveillance program of China showed that the mean prevalence of Schistosoma japonicum infections was both zero in humans and bovines in 2022, and no S. japonicum infection was detected in O. hupensis snails. These data demonstrated that the endemic status of schistosomiasis continued to decline in China in 2022, with 3 confirmed schistosomiasis patients that had a foreign nationality and all imported from Africa, and the areas of snail habitats remained high. Further improvements in the construction of the schistosomaisis surveillance and forecast system, and reinforcement of O. hupensis survey and control are required to prevent the re-emerging schistosomiasis.

[Progress of schistosomiasis control in People's Republic of China in 2021]

This report presented the endemic status of schistosomiasis and analyzed the data collected from the national schistosomiasis prevention and control system and national schistosomiasis surveillance sites in the People's Republic of China at a national level in 2021. Among the 12 provinces (municipality and autonomous region) endemic for schistosomiasis in China, Shanghai Municipality, Zhejiang Province, Fujian Province, Guangdong Province and Guangxi Zhuang Autonomous Region continued to consolidate the achievements of schistosomiasis elimination, and Sichuan and Jiangsu provinces maintained the criteria of transmission interruption, while Yunnan, Hubei, Anhui, Jiangxi and Hunan provinces maintained the criteria of transmission control by the end of 2021. A total of 451 counties (cites, districts) were found to be endemic for schistosomiasis in China in 2021, with 27 571 endemic villages covering 73 250 600 people at risk of infections. Among the 451 endemic counties (cities, districts), 75.17% (339/451), 22.17% (100/451) and 2.66% (12/451) achieved the criteria of elimination, transmission interruption and transmission control of schistosomiasis, respectively. By the end of 2021, 29 037 cases with advanced schistosomiasis were documented in China. In 2021, 4 405 056 individuals received serological tests and 72 937 were sero-positive. A total of 220 629 individuals received stool examinations and 3 were positive. In 2021, snail survey was performed in 19 291 endemic villages in China and Oncomelania snails were found in 7 026 villages, accounting for 36.42% of all surveyed villages, with 12 villages identified with emerging snail habitats. Snail survey was performed at an area of 686 574.46 hm² and 191 159.91 hm² snail habitats were found, including 1 063.08 hm² emerging snail habitats and 5 113.87 hm² reemerging snail habitats. In 2021, 525 878 bovines were raised in the schistosomiasis endemic areas of China, and 115 437 received serological examinations, with 231 positives detected. Among the 128 719 bovines received stool examinations, no positives were identified. In 2021, there were 19 927 schistosomiasis patients receiving praziquantel chemotherapy, and 729 113 person-time individuals and 256 913 herd-time bovines were given expanded chemotherapy. In 2021, snail control with chemicals was performed in 117 372.74 hm² snail habitats, and the actual area of chemical treatment was 65 640.50 hm², while environmental improvements were performed in snail habitats covering an area of 1 244.25 hm². Data from the national schistosomiasis surveillance sites of China showed that the mean prevalence of Schistosoma japonicum infections were both zero in humans and bovines in 2021, and no S. japonicum infection was detected in snails. The results demonstrate that the overall endemic status of schistosomiasis remained at a low level in China in 2021; however, the progress towards schistosomiasis elimination was slowed and the areas of snail habitats rebounded mildly. Strengthening researches on snail diffusion and control, and improving schistosomiasis surveillance and forecast are recommended to prevent reemerging schistosomiasis.

SERS-PCR assays of SARS-CoV-2 target genes using Au nanoparticles-internalized Au nanodimple substrates

The reverse transcription-polymerase chain reaction (RT-PCR) method has been adopted worldwide to diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although this method has good sensitivity and specificity, there is a need to develop a more rapid diagnostic technology, given the virus’s rapid spread. However, the RT-PCR method takes a long time to diagnose SARS-CoV-2 because of the required thermocycling steps. Therefore, we developed a surface-enhanced Raman scattering (SERS)-PCR detection method using an AuNP-internalized Au nanodimple substrate (AuNDS) to shorten the diagnosis time by reducing the number of thermocycling steps needed to amplify the DNA. For the representative target markers, namely, the envelope protein (E) and RNA-dependent RNA polymerase (RdRp) genes of SARS-CoV-2, 25 RT-PCR thermocycles are required to reach a detectable threshold value, while 15 cycles are needed for magnetic bead-based SERS-PCR when the initial DNA concentration was 1.00× 10⁵ copies/μL. However, only 8 cycles are needed for the AuNDS-based SERS-PCR. The corresponding detectable target DNA concentrations were 3.36 × 10¹², 3.28 × 10⁹, and 2.56 × 10⁷ copies/μL, respectively. Therefore, AuNDS-based SERS-PCR is seen as being a new molecular diagnostic platform that can shorten the time required for the thermocycling steps relative to the conventional RT-PCR.

High-flow priapism: Highly selective embolization of a traumatic arterio-cavernosal fistula

We report the case of a 14-year-old man who arrived at the emergency department affected by a high-flow priapism due to a traumatic left arterial-sinusoidal fistula. After clinical examination, a colour Doppler ultrasound of the penis was performed which showed a left arterial-sinusoidal fistula measuring 7×16×30mm, with high-speed and turbulent flow. The fistula was successfully treated by three highly selective endovascular embolizations and at the 20days follow-up, clinical examination resulted normal.

Endoscopic sinus surgery improves Eustachian tube function in patients with chronic rhinosinusitis: a multicenter prospective study

BACKGROUND

Patients with chronic rhinosinusitis (CRS) often have Eustachian tube dysfunction (ETD) symptoms. This study aimed to prospectively investigate the effect of endoscopic sinus surgery (ESS) on improvement of Eustachian tube function in CRS patients with ETD from a Chinese population and determine factors associated with improvement.

METHODS

A prospective study was performed in CRS patients with ETD who underwent ESS from 3 tertiary medical centers in south China. The Eustachian tube Dysfunction Questionnaire 7 (ETDQ-7), Sinonasal Outcome Test 22 (SNOT-22), tympanograms, endoscopic findings and Valsalva maneuver were recorded and analyzed preoperatively and postoperatively at 8-12 weeks.

RESULTS

A total of 70 CRS patients with ETD were included in this study. The ETDQ-7 score and the ability of positive Valsalva maneuver in CRS patients were significantly improved postoperatively at 8-12 weeks. The number of patients with type A tympanogram was increased postoperatively. Reduced Eustachian tube mucosal inflammation was also observed postoperatively. In addition, ESS appeared to reverse slight tympanic membrane atelectasis after 8-12 weeks. Moreover, improvement in tympanogram was presented in more than half of CRS patients with concomitant otitis media with effusion postoperatively at 8-12 weeks. Univariate and multivariate analysis revealed failure of normalization of ETDQ-7 postoperatively was associated with concomitant allergic rhinitis and higher preoperative SNOT-22 score.

CONCLUSIONS

This study confirms Eustachian tube function is often improved after ESS in CRS patients with ETD. Concomitant allergic rhinitis and higher preoperative SNOT-22 score are associated with failure of normalization of ETD symptoms.

[Analysis of the clinical characteristics of 24 cases of hematological malignancies with SET-NUP214 fusion gene]

目的

探讨SET-NUP214融合基因在血液恶性肿瘤中的表达，分析其相关的临床及生物学特征。

方法

回顾性分析2012年1月至2018年12月北京大学人民医院诊断的24例SET-NUP214融合基因阳性血液恶性肿瘤患者的临床资料，并采用Kaplan-Meier法进行生存分析。

结果

24例患者中，急性淋巴细胞白血病（ALL）15例（T-ALL 13例，B-ALL 2例）、急性髓系白血病（AML）7例，T/髓混合急性白血病2例。13例T-ALL患者免疫表型以CD3⁺CD2⁻为主要特征，73.3％的ALL患者伴有髓系标志表达，85.7％的AML患者表达CD7。24例患者诱导化疗完全缓解（CR）率91.7％。全部患者均接受异基因造血干细胞移植，中位随访24个月，AML和ALL的3年无复发生存（RFS）率分别为85.7％和33.3％，差异无统计学意义（P＝0.128）。比较13例SET-NUP214阳性与62例SET-NUP214阴性T-ALL患者的疗效，诱导化疗CR率分别为92.3％和93.5％（P＝0.445），诱导化疗4周CR率分别为69.2％和72.6％（P＝0.187），差异均无统计学意义。接受造血干细胞移植后，SET-NUP214阳性T-ALL患者的3年RFS率（38.5％）明显低于SET-NUP214阴性T-ALL患者（66.4％）（P＝0.028）。

结论

SET-NUP214融合基因主要见于T细胞源性血液肿瘤，伴SET-NUP214融合基因T-ALL预后较差。

[Endemic status of schistosomiasis in People's Republic of China in 2020]

This report presented the endemic status of schistosomiasis in the People's Republic of China at a national level in 2020, and analyzed the data collected from the national schistosomiasis prevention and control system and national schistosomiasis surveillance sites. Among the 12 provinces (municipality and autonomous region) endemic for schistosomiasis in China, Shanghai Municipality, Zhejiang Province, Fujian Province, Guangdong Province and Guangxi Zhuang Autonomous Region continued to consolidate the achievements of schistosomiasis elimination, and Sichuan and Jiangsu provinces maintained the criteria of transmission interruption, while Yunnan, Hubei, Anhui, Jiangxi and Hunan provinces maintained the criteria of transmission control by the end of 2020. A total of 450 counties (cites, districts) were found to be endemic for schistosomiasis in China, with 28 376 endemic villages covering 71 370 400 people at risk of infections. Among the 450 endemic counties (cities, districts), 74.89% (337/450), 21.87% (98/450) and 3.33% (15/450) achieved the criteria of elimination, transmission interruption and transmission control of schistosomiasis, respectively. By the end of 2020, 29 517 cases with advanced schistosomiasis were documented in China. In 2020, 11 117 655 individuals received inquiry examinations and 1 798 580 were positive; 5 263 082 individuals received serological tests and 83 179 were sero-positive. A total of 273 712 individuals received stool examinations and 3 were positive, including one case of acute schistosomiasis. In 2020, snail survey was performed in 19 733 endemic villages in China and Oncomelania snails were found in 7 309 villages, accounting for 37.04% of all surveyed villages, with 15 villages identified with emerging snail habitats. Snail survey covered an area of 736 984.13 hm² and 206 125.22 hm² snail habitats were found, including 1 174.67 hm² emerging snail habitats and 1.96 hm² habitats with infected snails. In 2020, 544 424 bovines were raised in the schistosomiasis-endemic areas of China, and 147 887 received serological examinations, with 326 positives detected, while 130 673 bovines received stool examinations, with no positives identified. In 2020, there were 19 214 patients with schistosomiasis receiving praziquantel chemotherapy, and 964 103 person-time individuals and 266 280 herd-time bovines were given expanded chemotherapy. In 2020, molluscicide treatment was performed in 136 141.92 hm² snail habitats, and the actual area of chemical treatment was 71 980.22 hm², while environmental improvements were performed in snail habitats covering an area of 1 464.03 hm². Data from the national schistosomiasis surveillance sites of China showed that the mean prevalence of Schistosoma japonicum infections were both zero in humans and bovines in 2020, and no S. japonicum infection was detected in snails. The results demonstrate that the overall endemic status of schistosomiasis remains at a low level in China and the goal of the National Thirteenth Five-Year Plan for Schistosomiasis Control was achieved as scheduled; however, the endemic situation of schistosomiasis rebounded in local areas. Precision schistosomiasis control and intensified monitoring of the endemic situation and transmission risk of schistosomiasis are required to be performed to facilitate the progress towards elimination of schistosomiasis steadily.

[National surveillance of schistosomiasis morbidity in China, 2015-2019]

OBJECTIVE

To understand the morbidity due to Schistosoma japonicum in national schistosomiasis surveillance sites of China from 2015 to 2019, so as to provide insights into schistosomiasis control and elimination and provide the scientific evidence for formulating the new scheme for schistosomiasis surveillance in China.

METHODS

According to the requirements of National Scheme for Schistosomiasis Surveillance in China (2014 Edition), national schistosomiasis surveillance sites were assigned in all schistosomiasis-endemic counties (cities, districts) and the potential endemic counties (cities, districts) in the Three Gorges Reservoir areas, and S. japonicum infections were monitored in local residents, mobile populations and livestock according to different epidemic types. The sero-prevalence of S. japonicum infections, adjusted prevalence of human S. japonicum infections, characteristics of egg-positive individuals and prevalence of S. japonicum infections livestock were analyzed.

RESULTS

S. japonicum infections were monitored in 453 schistosomiasis-endemic counties (cities, districts) from 13 provinces (municipalities, autonomous regions) and 4 potential endemic counties (cities, districts) from the Three Gorges Reservoir areas in China from 2015 to 2019. During the 5-year period from 2015 to 2019, the sero-prevalence of S. japonicum infections reduced from 3.35% to 1.63% among local residents and from 1.15% to 0.75% among mobile populations, while the adjusted prevalence of infections reduced from 0.05% to 0 among local residents and from 0.20% to 0.001 03% among mobile populations. There were significant differences in the sero-prevalence of S. japonicum infections among local residents and mobile populations in terms of province, occupation and age (all P values < 0.05). A total of 132 egg-positives were identified during the 5-year period, including 97 local residents (inter-quartile range for ages, 47 to 61 years), and 35 mobile populations (inter-quartile range for ages, 26 to 48 years), and there was a significant difference in the age distribution between local residents and mobile populations (P < 0.05). There were totally 6 bovines (5 in 2015 and 1 in 2016) identified with S. japonicum infections in national schistosomiasis surveillance sites of China, with no S. japonicum infections detected in bovines from 2017 to 2019.

CONCLUSIONS

The prevalence of schistosomiasis is very low in China. Further surveillance including more mobile surveillance sites seems justified to identify the risk of schistosomiasis as soon as possible and interrupt the transmission route, so as to facilitate the elimination of schistosomiasis in China.

[National surveillance of Oncomelania hupensis in China, 2015-2019]

OBJECTIVE

To analyze the monitoring data of Oncomelania hupensis in the national schistosomiasis surveillance sites of China from 2015 to 2019, so as to understand the changes of Oncomelania snail status in the schistosomiasis-endemic areas of China and to provide the scientific evidence for Oncomelania snail control.

METHODS

According to the requirements of National Scheme for Schistosomiasis Surveillance in China (2014 Edition), national schistosomiasis surveillance sites were assigned in all schistosomiasis-endemic counties (cities, districts) and the potential endemic counties (cities, districts) in the Three Gorges Reservoir areas, and Oncomelania snail status was monitored according to different epidemic types. In endemic areas, Oncomelania snail survey was performed by means of systematic sampling and environmental sampling, and the occurrence of frames with Oncomelania snails and the prevalence of Schistosoma japonicum infections in Oncomelania snails were calculated, while in potential endemic areas, the risk of imported Oncomelania snails and Oncomelania snails in floating debris were monitored.

RESULTS

Oncomelania snail survey was performed covering an area of 116 834.16 hm² in the national schistosomiasis surveillance of China from 2015 to 2019, with 35 007.62 hm² Oncomelania snail habitats identified. A total of 6 908 292 frames were surveyed during the 5-year period, and there were 364 555 frames detected with Oncomelania snails, with a 5.28% mean occurrence of frames with Oncomelania snails. Among 997 508 living Oncomelania snails captured, no S. japonicum infections were detected, and loop-mediated isothermal amplification (LAMP) assay detected 18 positive mixed Oncomelania snail samples. During the period from 2015 to 2019, 147.20 hm² emerging Oncomelania snail habitats were identified, with an overall tendency towards a rise seen in the proportion of emerging Oncomelania snail habitats in plain regions with waterway networks (0.12% to 92.00%), a tendency towards a rise followed by decline seen in marshland and lake regions (0 to 96.72%), and a large fluctuation in hilly regions (0 to 88.49%). A total of 831.10 hm² re-emerging Oncomelania snail habitats were found in the national schistosomiasis surveillance sites of China from 2015 to 2019, with an overall tendency towards a rise seen in the proportion of re-emerging Oncomelania snail habitats in marshland and lake regions (16.05% to 79.66%), an overall tendency towards a decline seen in hilly regions (19.25% to 81.00%), and a minor fluctuation in plain regions with waterway networks (1.10% to 10.14%). During the 5-year period from 2015 to 2019, a total of 48 656 kg floating debris were captured in 4 surveillance sites in the Three Gorges Reservoir areas, and 2 204 snails were found, with no Oncomelania snails identified.

CONCLUSIONS

The areas of Oncomelania snail habitats tended to be stable in the national schistosomiasis surveillance sites of China during the period from 2015 to 2019, however, there was a gradual rise in the area of Oncomelania snail habitats year by year, and LAMP assay identified positive Oncomelania snail samples, suggesting Oncomelania snail control is far from optimistic in China.

A32 EMPAGLIFOZIN IMPROVES GASTROINTESTINAL INFLAMMATION IN A MOUSE MODEL OF COLITIS

Background

Empagliflozin (EMPA) is a highly selective sodium glucose cotransporter-2 (SGLT2) inhibitor and is increasingly being utilized as an antihyperglycemic agent in the management of type 2 diabetes. Interestingly, it has been demonstrated in human trials that EMPA treatment exerts potent cardioprotective effects by reducing cardiac inflammation independently of glycemic control. Further, EMPA has also been shown to suppress LPS-induced renal and systemic inflammation in an animal model. Based on these findings, we hypothesized that EMPA treatment may also be effective in reducing gut inflammation.

Aims

The aim of this study was to examine the effects of treatment with EMPA on gastrointestinal inflammation in an animal model of inflammatory bowel disease and to determine mechanistic insights regarding its direct effects on gut cytokine secretion.

Methods

Adult male and female IL-10-/- mice with established colitis were treated with a daily gavage of EMPA (10mg/kg; n=10) or vehicle (n=10) for 14 days. Disease activity was assessed by measurement of mouse weight, colonic weight and length, histological score, cytokine levels in colonic homogenate and lipocalin-2 levels in stool. To examine for possible direct effects of EMPA, colonic explants from wild-type (n=8) and IL-10-/- (n=8) mice were incubated with increasing doses of EMPA (0.1–5 µM) ± LPS (10µg/ml) for 2 hours and tissue levels of IL-1β and TNFα protein measured by ELISA.

Results

After 14 days EMPA treated IL-10-/- mice had a significant improvement in colonic inflammation as evidenced by decreased colonic weight to length ratio (p=0.019), decreased fecal lipocalin-2 (p=0.03), as well as decreased enterocyte injury (p=0.01), decreased lamina propria neutrophils (p=0.01) and decreased total histological score (p=0.006). EMPA treated mice also maintained their weight over the 14 days while untreated mice continued to lose weight (p=0.04). There were no significant differences in colonic homogenate levels of TNFα, IL-1β, or IL-6 or in blood glucose levels between EMPA-treated mice and controls. In addition, EMPA did not suppress levels of basal or LPS-induced TNFα and IL-1β in colonic explants from either wild-type or IL-10-/- mice suggesting that the beneficial effects in IL-10-/- mice were not due to direct effects of EMPA on colonic TNFα or IL-1β cytokine levels.

Conclusions

EMPA treatment dramatically improved histologic and fecal inflammatory markers and maintained body weight in adult IL-10-/- mice with established colitis. These findings suggest further investigations into the effects of EMPA in treating gut inflammation are warranted.

Funding Agencies

CAG, CIHR

Recent advances in sensitive surface-enhanced Raman scattering-based lateral flow assay platforms for point-of-care diagnostics of infectious diseases

This review reports the recent advances in surface-enhanced Raman scattering (SERS)-based lateral flow assay (LFA) platforms for the diagnosis of infectious diseases. As observed through the recent infection outbreaks of COVID-19 worldwide, a timely diagnosis of the disease is critical for preventing the spread of a disease and to ensure epidemic preparedness. In this regard, an innovative point-of-care diagnostic method is essential. Recently, SERS-based assay platforms have received increasing attention in medical communities owing to their high sensitivity and multiplex detection capability. In contrast, LFAs provide a user-friendly and easily accessible sensing platform. Thus, the combination of LFAs with a SERS detection system provides a new diagnostic modality for accurate and rapid diagnoses of infectious diseases. In this context, we briefly discuss the recent application of LFA platforms for the POC diagnosis of SARS-CoV-2. Thereafter, we focus on the recent advances in SERS-based LFA platforms for the early diagnosis of infectious diseases and their applicability for the rapid diagnosis of SARS-CoV-2. Finally, the key issues that need to be addressed to accelerate the clinical translation of SERS-based LFA platforms from the research laboratory to the bedside are discussed.

[Endemic status of schistosomiasis in People's Republic of China in 2019]

This report presented the endemic status of schistosomiasis in the People's Republic of China at a national level in 2019, and analyzed the data collected from the national schistosomiasis prevention and control system and 455 national schistosomiasis surveillance sites. Among the 12 provinces (municipality and autonomous region) endemic for schistosomiasis in China, Shanghai, Zhejiang, Fujian, Guangdong and Guangxi continued to consolidate the achievements of schistosomiasis elimination, Sichuan Province achieved transmission interruption, Jiangsu newly achieved the standard of transmission interruption and 5 provinces of Yunnan, Hubei, Anhui, Jiangxi and Hunan maintained transmission control by the end of 2019. There were 450 endemic counties (cities, districts) endemic for schistosomiasis, including 28 500 endemic villages covering 70 667 800 people at risk of infections. Among the 450 endemic counties (citis, districts), 66.89% (301/450), 28.44% (128/450) and 4.67% (21/450) kept the criteria of elimination, transmission interruption and transmission control of schistosomiasis, respectively. By the end of 2019, a total of 30 170 advanced schistosomiasis cases were documented in China. In 2019, a total of 12 090 712 individuals received inquiry examinations and 1 740 764 were positive; 5 158 369 individuals received serological tests and 89 753 were seropositive. A total of 327 475 individuals received stool examinations and 5 were positive, including one case of acute schistosomiasis. In 2019, snail survey was performed in 19 726 endemic villages in China and Oncomelania snails were found in 7 322 villages, accounting for 37.12% of all surveyed villages, with 6 villages with emerging snail habitats. Snail survey covered an area of 585 286.24 hm² and 174 270.42 hm² snail habitats were found, including emerging snail habitats of 64.20 hm²; however, no infected snails were identified. In 2019, a total of 605 965 bovines were raised in the schistosomiasis endemic areas of China, and 183 313 received serological examinations, with 1 176 positives detected, while 134 978 bovines received stool examinations, with 7 positives identified. In 2019, there were 28 557 patients with schistosomiasis receiving praziquantel chemotherapy, and expanded chemotherapy was given to 1 008 083 person-times; there were 7 bovines with schistosomiasis receiving praziquantel chemotherapy, and 296 053 herd-times expanded chemotherapy was given to bovines. In 2019, snail habitats at an area of 128 754.26 hm² were given chemical treatment, and the actual area of chemical treatment was 69 605.55 hm², while environmental improvements were performed in snail habitats covering an area of 2 847.00 hm². Data from the 455 national schistosomiasis surveillance sites of China showed that the mean Schistosoma japonicum infection rates were both zero in humans and bovines in 2019, and no infected snails were found. The results demonstrate that the overall endemic situation of schistosomiasis remains at a lower infection level in China; however, there is still a risk of schistosomiasis transmission. To achieve the target set in the National Thirteenth Five-Year Plan for Schistosomiasis Control and consolidate the achievements of schistosomiasis control, precision control on schistosomiasis still needs to be reinforced in China.

SERS imaging-based aptasensor for ultrasensitive and reproducible detection of influenza virus A

Surface-enhanced Raman scattering (SERS)-based aptasensors display high sensitivity for influenza A/H1N1 virus detection but improved signal reproducibility is required. Therefore, in this study, we fabricated a three-dimensional (3D) nano-popcorn plasmonic substrate using the surface energy difference between a perfluorodecanethiol (PFDT) spacer and the Au layer. This energy difference led to Au nanoparticle self-assembly; neighboring nanoparticles then created multiple hotspots on the substrate. The localized surface plasmon effects at the hot spots dramatically enhanced the incident field. Quantitative evaluation of A/H1N1 virus was achieved using the decrease of Raman peak intensity resulting from the release of Cy3-labeled aptamer DNAs from nano-popcorn substrate surfaces via the interaction between the aptamer DNA and A/H1N1 virus. The use of a Raman imaging technique involving the fast mapping of all pixel points enabled the reproducible quantification of A/H1N1 virus on nano-popcorn substrates. Average ensemble effects obtained by averaging all randomly distributed hot spots mapped on the substrate made it possible to reliably quantify target viruses. The SERS-based imaging aptasensor platform proposed in this work overcomes the issues inherent in conventional approaches (the time-consuming and labor-intensiveness of RT-PCR and low sensitivity and quantitative analysis limits of lateral flow assay kits). Our SERS-based assay for detecting A/H1N1 virus had an estimated limit of detection of 97 PFU mL-1 (approximately three orders of magnitude more sensitive than that determined by the enzyme-linked immunosorbent assay) and the approximate assay time was estimated to be 20 min. Thus, this approach provides an ultrasensitive, reliable platform for detecting viral pathogens.

MetaGeneHunt for protein domain annotation in short-read metagenomes

The annotation of short-reads metagenomes is an essential process to understand the functional potential of sequenced microbial communities. Annotation techniques based solely on the identification of local matches tend to confound local sequence similarity and overall protein homology and thus don't mirror the complex multidomain architecture and the shuffling of functional domains in many protein families. Here, we present MetaGeneHunt to identify specific protein domains and to normalize the hit-counts based on the domain length. We used MetaGeneHunt to investigate the potential for carbohydrate processing in the mouse gastrointestinal tract. We sampled, sequenced, and analyzed the microbial communities associated with the bolus in the stomach, intestine, cecum, and colon of five captive mice. Focusing on Glycoside Hydrolases (GHs) we found that, across samples, 58.3% of the 4,726,023 short-read sequences matching with a GH domain-containing protein were located outside the domain of interest. Next, before comparing the samples, the counts of localized hits matching the domains of interest were normalized to account for the corresponding domain length. Microbial communities in the intestine and cecum displayed characteristic GH profiles matching distinct microbial assemblages. Conversely, the stomach and colon were associated with structurally and functionally more diverse and variable microbial communities. Across samples, despite fluctuations, changes in the functional potential for carbohydrate processing correlated with changes in community composition. Overall MetaGeneHunt is a new way to quickly and precisely identify discrete protein domains in sequenced metagenomes processed with MG-RAST. In addition, using the sister program "GeneHunt" to create custom Reference Annotation Table, MetaGeneHunt provides an unprecedented way to (re)investigate the precise distribution of any protein domain in short-reads metagenomes.

[Endemic status of schistosomiasis in People's Republic of China in 2018]

This report presented the endemic status of schistosomiasis in the People's Republic of China at a national level in 2018, and analyzed the data collected from the national schistosomiasis prevention and control system and 453 national schistosomiasis surveillance sites. Among the 12 provinces (municipality and autonomous region) endemic for schistosomiasis in China, 5 provinces (municipality and autonomous region), including Shanghai, Zhejiang, Fujian, Guangdong and Guangxi, continued to consolidate the achievements of schistosomiasis elimination, Sichuan Province achieved transmission interruption and 6 provinces of Yunnan, Jiangsu, Hubei, Anhui, Jiangxi and Hunan achieved transmission control by the end of 2018. There were 450 endemic counties (cities, districts) covering 260 million people, specifically including 28 456 endemic villages covering 70.059 7 million people at risk of infection. Among the 450 endemic counties (cities, districts), 58.44% (263/450), 27.56% (124/450) and 14.00% (63/450) reached the criteria of elimination, transmission interruption and transmission control, respectively. By the end of 2018, a total of 29 214 advanced schistosomiasis cases were documented in China. In 2018, a total of 11.127 6 million individuals received inquiry examinations and 2.062 9 million were positive; 7.191 4 million individuals received serological tests and 138.5 thousand of them were positive, 532.2 thousand individuals received stool examinations and 8 were positive in China. In 2018, snail survey was performed in 19 821 endemic villages and Oncomehania snails were found in 7 321 villages, accounting for 36.94% of all surveyed villages, with 3 newly detected villages with snails in China. Snail survey covered an area of 590 241.01 hm² and 168 319.41 hm² snail habitats were found, including emerging snail habitats of 61.28 hm²; however, no infected snails were identified. In 2018, a total of 646 823 bovines were raised in the schistosomiasis endemic areas of China, and 225 258 received serological examinations, with 2 638 positives detected, while 164 803 bovines received stool examinations, with 2 positives identified. In 2018, there were 90 388 patients with schistosomiasis receiving praziquantel chemotherapy, and expanded chemotherapy was given to 1 490 594 person-times; there were two bovines with schistosomiasis receiving praziquantel chemotherapy, and expanded chemotherapy was given to 352 577 bovine-times; chemical treatment was conducted in an area of 141 660.87 hm², including an actual mollusciciding area of 75 308.26 hm², and environmental improvements were performed in an area of 4 738.37 hm² in China. Data from the 453 national schistosomiasis surveillance sites of China showed that the mean Schistosoma japonicum infection rates were 0.001 5% and zero in humans and bovines in 2018, respectively, and no infected snails were found. The results demonstrate that the endemic situation of schistosomiasis appears a tendency towards a continuous decline in China; however, there is still a risk of schistosomiasis transmission, and challenges remain in achieving the target set in the Thirteenth Five-Year National Plan for Schistosomiasis Control in 2020 in some regions.

Performance Evaluation of Surface-Enhanced Raman Scattering-Polymerase Chain Reaction Sensors for Future Use in Sensitive Genetic Assays

We report a surface-enhanced Raman scattering (SERS)-based polymerase chain reaction (PCR) assay platform for the sensitive and rapid detection of a DNA marker (pagA) of Bacillus anthracis. Real-time quantitative PCR (RT-qPCR) has been recently considered a gold standard for the quantitative evaluation of a target gene, but it still suffers from the problem of a long thermocycling time. To address this issue, we developed a conceptually new SERS-PCR platform and evaluated its performance by sequentially measuring the Raman signals of B. anthracis DNA after the completion of different thermocycling numbers. According to our experimental data, SERS-PCR has lower limits of detection (LODs) than RT-qPCR under the small cycle number of 20. Particularly, it was impossible to detect a target DNA amplicon using RT-qPCR before the number of cycles reached 15, but SERS-PCR enabled DNA detection after only five cycles with an LOD value of 960 pM. In addition, the dynamic range for SERS-PCR (0.1-1000 pM) is wider than that for RT-qPCR (150-1000 pM) under the same condition. We believe that this SERS-PCR technique has a strong potential to be a powerful tool for the rapid and sensitive diagnosis of infectious diseases in the near future.

[Clinical analysis of myeloid neoplasms with t (3;21) (q26;q22)]

目的

探讨伴有t（3;21）（q26;q22）髓系肿瘤的临床特征。

方法

回顾性分析2011年1月至2018年3月北京大学人民医院收治的19例伴有t（3;21）（q26;q22）血液恶性肿瘤患者的临床资料，并汇总文献报道的有详细生存资料的48例患者，采用Kaplan-Meier法进行生存分析。

结果

19例患者中男15例，女4例，中位年龄36（22~68）岁，包括原发急性髓系白血病（AML）4例，骨髓增生异常综合征（MDS）4例，MDS转化的AML3例，慢性髓性白血病（CML）急变8例。19例患者染色体核型均可见t（3;21）（q26;q22），其中13例伴有附加异常。19例中9例进行AML1-MDS1融合基因检测均阳性。9例患者有随访资料，6例接受化疗的患者中4例无效，2例获得完全缓解。随访期内除1例MDS患者因随访期短（6个月）仍存活，其余8例均死亡，中位生存时间为6（4.5~22）个月。汇总文献生存分析结果显示伴有t（3;21）（q26;q22）的髓系肿瘤患者整体预后差，中位生存时间为7个月，尤以AML/治疗相关的AML预后最差，移植和非移植组中位生存时间分别为20.9和4.7个月，差异有统计学意义（P<0.001）。

结论

t（3;21）（q26;q22）是罕见的重现性染色体异常，主要见于髓系血液肿瘤，临床预后差，建议尽早进行造血干细胞移植。

Variations in carbon source-sink relationships in subalpine fir across elevational gradients

Cold-adapted trees display acclimation in both carbon source and carbon sink capacity to low-temperature stress at their upper elevational range limits. Hence a balanced carbon source-sink capacity might be required for their persistence and survival at the elevational tree limits. The present study examined the spatial dynamics of carbon source-sink relationship in subalpine fir (Abies fargesii) trees along elevational gradients in the northern slope of the temperate region and in the southern slope of the subtropics in terms of climate in the Qinling Mountain range, north-central China. The results showed that non-structural carbohydrate (NSC) concentrations in both the source and sink tissues increased with the increase in elevation. The ratio of carbon source-sink displayed a consistent decreasing trend with the increase in elevation and during growing season, showing that it was lowest at a ratio of 2.93 in the northern slope and at a ratio of 2.61 in the southern slope at the upper distribution elevations in the late growing season. Such variations of carbon source-sink ratio might be attributable to the balance between carbon source and sink activities, which changed seasonally across the elevational distribution range. We concluded that a ratio of carbon source-sink of at least 2.6 might be essential for subalpine fir trees to persist at their upper range limits. Therefore, a sufficient source-sink ratio and a balanced source-sink relationship might be required for subalpine fir trees to survive and develop at their upper elevational distribution limits.

Anti-viral therapy is associated with improved survival but is underutilised in patients with hepatitis B virus-related hepatocellular carcinoma: real-world east and west experience

BACKGROUND

Hepatitis B virus (HBV) is the leading cause of hepatocellular carcinoma (HCC) worldwide. It remains incompletely understood in the real world how anti-viral therapy affects survival after HCC diagnosis.

METHODS

This was an international multicentre cohort study of 2518 HBV-related HCC cases diagnosed between 2000 and 2015. Cox proportional hazards models were utilised to estimate hazard ratios (HR) with 95% (CI) for anti-viral therapy and cirrhosis on patients' risk of death.

RESULTS

Approximately, 48% of patients received anti-viral therapy at any time, but only 17% were on therapy at HCC diagnosis (38% at US centres, 11% at Asian centres). Anti-viral therapy would have been indicated for >60% of the patients not on anti-viral therapy based on American criteria. Patients with cirrhosis had lower 5-year survival (34% vs 46%; P < 0.001) while patients receiving anti-viral therapy had increased 5-year survival compared to untreated patients (42% vs 25% with cirrhosis and 58% vs 36% without cirrhosis; P < 0.001 for both). Similar findings were seen for other patient subgroups by cancer stages and cancer treatment types. Anti-viral therapy was associated with a decrease in risk of death, whether started before or after HCC diagnosis (adjusted HR 0.62 and 0.79, respectively; P < 0.001).

CONCLUSIONS

Anti-viral therapy improved overall survival in patients with HBV-related HCC across cancer stages and treatment types but was underutilised at both US and Asia centres. Expanded use of anti-viral therapy in HBV-related HCC and better linkage-to-care for HBV patients are needed.

[Comparative study of cytogenetic response evaluated by conventional banding analysis and fluorescence in situ hybridization in chronic myeloid leukemia patients during tyrosine kinase inhibitor treatment]

Objective: To compare the cytogenetic response detected by conventional banding analysis (CBA) and fluorescence in situ hybridization (FISH) and to explore the correlation between the cytogenetic and molecular response in chronic myeloid leukemia (CML) patients during tyrosine kinase inhibitor (TKI) treatment. Methods: CBA, FISH and real-time quantitative reverse transcriptase polymerase chain reaction (RQ-PCR) methods were performed to detect the cytogenetic and molecular response simultaneously in 504 bone marrow samples from 367 CML patients who received TKI treatment. Results: Among 504 samples, 344 were detected to reach complete cytogenetic response (CCyR) by CBA, while 297 samples reached CCyR by FISH which were considered to carry BCR-ABL positive cells<1%. When the results of CBA, FISH and RQ-PCR were compared in 493 samples at the same time, it showed that in 337 samples with CBA-CCyR, 273 (81.0%) reached FISH-CCyR and 289 (85.8%) were BCR-ABL(IS) (International Scale, IS) ≤1% by RQ-PCR, compared to 9.0 (261/290) were BCR-ABL(IS) ≤1% among 290 samples with FISH-CCyR. There was no significant difference in the median value of BCR-ABL(IS) between samples in CBA-CCyR and FISH-CCyR (0.21% vs 0.13%, z=-1.875, P=0.061) . Furthermore, when the samples were divided into three groups according to BCR-ABL positive cells (0,>0~<1%, 1%~5%) by FISH, the statistical difference was observed, the proportion of samples with BCR-ABL(IS) ≤1% in the three groups were 94.1%, 57.6% and 27.7% respectively (χ(2)=43.499, P<0.001; χ(2)=9.734, P=0.003) , while the median value of BCR-ABL(IS) were 0.10%, 0.64% and 1.80% respectively (z=-5.864, P<0.001; z=-4.787, P<0.001) . Conclusion: FISH results were in good concordance with CBA in identify samples in CCyR, FISH was more sensitive and had better correlation with RQ-PCR results than CBA, but how to define FISH-CCyR need further study.

Task-Based Regularization Design for Detection of Intracranial Hemorrhage in Cone-Beam CT

Prompt and reliable detection of acute intracranial hemorrhage (ICH) is critical to treatment of a number of neurological disorders. Cone-beam CT (CBCT) systems are potentially suitable for detecting ICH (contrast 40-80 HU, size down to 1 mm) at the point of care but face major challenges in image quality requirements. Statistical reconstruction demonstrates improved noise-resolution tradeoffs in CBCT head imaging, but its capability in improving image quality with respect to the task of ICH detection remains to be fully investigated. Moreover, statistical reconstruction typically exhibits nonuniform spatial resolution and noise characteristics, leading to spatially varying detectability of ICH for a conventional penalty. In this work, we propose a spatially varying penalty design that maximizes detectability of ICH at each location throughout the image. We leverage theoretical analysis of spatial resolution and noise for a penalized weighted least-squares (PWLS) estimator, and employ a task-based imaging performance descriptor in terms of detectability index using a nonprewhitening observer model. Performance prediction was validated using a 3D anthropomorphic head phantom. The proposed penalty achieved superior detectability throughout the head and improved detectability in regions adjacent to the skull base by ~10% compared to a conventional uniform penalty. PWLS reconstruction with the proposed penalty demonstrated excellent visualization of simulated ICH in different regions of the head and provides further support for development of dedicated CBCT head scanning at the point-of-care in the neuro ICU and OR.

Reconstruction of difference in sequential CT studies using penalized likelihood estimation

Characterization of anatomical change and other differences is important in sequential computed tomography (CT) imaging, where a high-fidelity patient-specific prior image is typically present, but is not used, in the reconstruction of subsequent anatomical states. Here, we introduce a penalized likelihood (PL) method called reconstruction of difference (RoD) to directly reconstruct a difference image volume using both the current projection data and the (unregistered) prior image integrated into the forward model for the measurement data. The algorithm utilizes an alternating minimization to find both the registration and reconstruction estimates. This formulation allows direct control over the image properties of the difference image, permitting regularization strategies that inhibit noise and structural differences due to inconsistencies between the prior image and the current data. Additionally, if the change is known to be local, RoD allows local acquisition and reconstruction, as opposed to traditional model-based approaches that require a full support field of view (or other modifications). We compared the performance of RoD to a standard PL algorithm, in simulation studies and using test-bench cone-beam CT data. The performances of local and global RoD approaches were similar, with local RoD providing a significant computational speedup. In comparison across a range of data with differing fidelity, the local RoD approach consistently showed lower error (with respect to a truth image) than PL in both noisy data and sparsely sampled projection scenarios. In a study of the prior image registration performance of RoD, a clinically reasonable capture ranges were demonstrated. Lastly, the registration algorithm had a broad capture range and the error for reconstruction of CT data was 35% and 20% less than filtered back-projection for RoD and PL, respectively. The RoD has potential for delivering high-quality difference images in a range of sequential clinical scenarios including image-guided surgeries and treatments where accurate and quantitative assessments of anatomical change is desired.

Statistical reconstruction for cone-beam CT with a post-artifact-correction noise model: application to high-quality head imaging

Non-contrast CT reliably detects fresh blood in the brain and is the current front-line imaging modality for intracranial hemorrhage such as that occurring in acute traumatic brain injury (contrast ~40-80 HU, size  >  1 mm). We are developing flat-panel detector (FPD) cone-beam CT (CBCT) to facilitate such diagnosis in a low-cost, mobile platform suitable for point-of-care deployment. Such a system may offer benefits in the ICU, urgent care/concussion clinic, ambulance, and sports and military theatres. However, current FPD-CBCT systems face significant challenges that confound low-contrast, soft-tissue imaging. Artifact correction can overcome major sources of bias in FPD-CBCT but imparts noise amplification in filtered backprojection (FBP). Model-based reconstruction improves soft-tissue image quality compared to FBP by leveraging a high-fidelity forward model and image regularization. In this work, we develop a novel penalized weighted least-squares (PWLS) image reconstruction method with a noise model that includes accurate modeling of the noise characteristics associated with the two dominant artifact corrections (scatter and beam-hardening) in CBCT and utilizes modified weights to compensate for noise amplification imparted by each correction. Experiments included real data acquired on a FPD-CBCT test-bench and an anthropomorphic head phantom emulating intra-parenchymal hemorrhage. The proposed PWLS method demonstrated superior noise-resolution tradeoffs in comparison to FBP and PWLS with conventional weights (viz. at matched 0.50 mm spatial resolution, CNR = 11.9 compared to CNR = 5.6 and CNR = 9.9, respectively) and substantially reduced image noise especially in challenging regions such as skull base. The results support the hypothesis that with high-fidelity artifact correction and statistical reconstruction using an accurate post-artifact-correction noise model, FPD-CBCT can achieve image quality allowing reliable detection of intracranial hemorrhage.

Cone-Beam CT of Traumatic Brain Injury Using Statistical Reconstruction with a Post-Artifact-Correction Noise Model

Traumatic brain injury (TBI) is a major cause of death and disability. The current front-line imaging modality for TBI detection is CT, which reliably detects intracranial hemorrhage (fresh blood contrast 30-50 HU, size down to 1 mm) in non-contrast-enhanced exams. Compared to CT, flat-panel detector (FPD) cone-beam CT (CBCT) systems offer lower cost, greater portability, and smaller footprint suitable for point-of-care deployment. We are developing FPD-CBCT to facilitate TBI detection at the point-of-care such as in emergent, ambulance, sports, and military applications. However, current FPD-CBCT systems generally face challenges in low-contrast, soft-tissue imaging. Model-based reconstruction can improve image quality in soft-tissue imaging compared to conventional filtered backprojection (FBP) by leveraging high-fidelity forward model and sophisticated regularization. In FPD-CBCT TBI imaging, measurement noise characteristics undergo substantial change following artifact correction, resulting in non-negligible noise amplification. In this work, we extend the penalized weighted least-squares (PWLS) image reconstruction to include the two dominant artifact corrections (scatter and beam hardening) in FPD-CBCT TBI imaging by correctly modeling the variance change following each correction. Experiments were performed on a CBCT test-bench using an anthropomorphic phantom emulating intra-parenchymal hemorrhage in acute TBI, and the proposed method demonstrated an improvement in blood-brain contrast-to-noise ratio (CNR = 14.2) compared to FBP (CNR = 9.6) and PWLS using conventional weights (CNR = 11.6) at fixed spatial resolution (1 mm edge-spread width at the target contrast). The results support the hypothesis that FPD-CBCT can fulfill the image quality requirements for reliable TBI detection, using high-fidelity artifact correction and statistical reconstruction with accurate post-artifact-correction noise models.

Early gene expression in salivary gland after isoproterenol treatment

Isoproterenol, a β-adrenergic agonist, has been shown to induce salivary gland hyperplasia. However, the mechanism involved in this pharmacological phenomenon is not well understood. To gain a better understanding of the underlying changes, including genes, networks and pathways altered by isoproterenol, microarray-based gene expression analysis was conducted on rat parotid glands at 10, 30, and 60 min after isoproterenol injection. After isoproterenol treatment, the number of differentially expressed genes was increased in a time-dependent manner. Pathway analysis showed that cell hyperplasia, p38(MAPK), and IGF-1 were the most altered function, network and pathway, respectively. The balanced regulation of up- and down-expression of genes related to cell proliferation/survival may provide a better understanding of the mechanism of isoproterenol-induced parotid gland enlargement without tumor transformation.

dPIRPLE: a joint estimation framework for deformable registration and penalized-likelihood CT image reconstruction using prior images

Sequential imaging studies are conducted in many clinical scenarios. Prior images from previous studies contain a great deal of patient-specific anatomical information and can be used in conjunction with subsequent imaging acquisitions to maintain image quality while enabling radiation dose reduction (e.g., through sparse angular sampling, reduction in fluence, etc). However, patient motion between images in such sequences results in misregistration between the prior image and current anatomy. Existing prior-image-based approaches often include only a simple rigid registration step that can be insufficient for capturing complex anatomical motion, introducing detrimental effects in subsequent image reconstruction. In this work, we propose a joint framework that estimates the 3D deformation between an unregistered prior image and the current anatomy (based on a subsequent data acquisition) and reconstructs the current anatomical image using a model-based reconstruction approach that includes regularization based on the deformed prior image. This framework is referred to as deformable prior image registration, penalized-likelihood estimation (dPIRPLE). Central to this framework is the inclusion of a 3D B-spline-based free-form-deformation model into the joint registration-reconstruction objective function. The proposed framework is solved using a maximization strategy whereby alternating updates to the registration parameters and image estimates are applied allowing for improvements in both the registration and reconstruction throughout the optimization process. Cadaver experiments were conducted on a cone-beam CT testbench emulating a lung nodule surveillance scenario. Superior reconstruction accuracy and image quality were demonstrated using the dPIRPLE algorithm as compared to more traditional reconstruction methods including filtered backprojection, penalized-likelihood estimation (PLE), prior image penalized-likelihood estimation (PIPLE) without registration, and prior image penalized-likelihood estimation with rigid registration of a prior image (PIRPLE) over a wide range of sampling sparsity and exposure levels.

Identification of a KIR antisense lncRNA expressed by progenitor cells

Human NK cells express cell surface class I MHC receptors (KIR) in a probabilistic manner. Previous studies have shown that a distal promoter acts in conjunction with a proximal bidirectional promoter to control the selective activation of KIR genes. We report here the presence of an intron 2 promoter in several KIR genes that produces a spliced antisense transcript. This lncRNA transcript contains antisense sequence complementary to KIR-coding exons 1 and 2 as well as the proximal promoter region of the KIR genes. The antisense promoter contains MZF-1 binding sites, a transcription factor found in hematopoietic progenitors and myeloid precursors. The KIR antisense lncRNA was only detected in progenitor cells or pluripotent cell lines, suggesting a function that is specific for stem cells. Overexpression of MZF-1 in developing NK cells led to decreased KIR expression, consistent with a role for the KIR antisense lncRNA in silencing KIR gene expression early in development.

The healing of dental extraction sockets in patients with Type 2 diabetes on oral hypoglycaemics: a prospective cohort

BACKGROUND

The aim of this study was to determine whether there is a difference in delayed healing following dental extractions for Type 2 diabetics on oral hypoglycaemics and non-diabetic patients.

METHODS

Prospective patients referred for dental extractions were recruited into two groups: known diabetics and non-diabetics with no conditions associated with poor healing. All had a random blood glucose level (BGL). Extractions were performed using local anaesthesia. Delayed healing cases were identified and statistical evaluation performed to identify risk factors.

RESULTS

There were 224 Type 2 diabetics on oral hypoglycaemics (BGL 7.51, range 4.1-17.4) and 232 non-diabetics. The diabetic group were older, more males and less smokers than the control group. Twenty-eight patients, 12 (5%) diabetic and 16 (7%) control group, had socket healing delayed for more than one week but all healed in four weeks. There were no statistical differences between delayed healing and age, gender, diabetic state, BGL or smoking. The younger control group had more healing problems.

CONCLUSIONS

The traditional view that diabetics have increased delayed healing was not supported. Type 2 diabetics on oral hypoglycaemics should be treated the same as non-diabetic patients for extractions.

Overcoming Nonlinear Partial Volume Effects in Known-Component Reconstruction of Cochlear Implants

Nonlinear partial volume (NLPV) effects can be significant for objects with large attenuation differences and fine detail structures near the spatial resolution limits of a tomographic system. This is particularly true for small metal devices like cochlear implants. While traditional model-based approaches might alleviate these artifacts through very fine sampling of the image volume and subsampling of rays to each detector element, such solutions can be extremely burdensome in terms of memory and computational requirements. The work presented in this paper leverages the model-based approach called "known-component reconstruction" (KCR) where prior knowledge of a surgical device is integrated into the estimation. In KCR, the parameterization of the object separates the volume into an unknown background anatomy and a known component with unknown registration. Thus, one can model projections of an implant at very high spatial resolution while limiting the spatial resolution of the anatomy - in effect, modeling NLPV effects where they are most significant. We present modifications of the KCR approach that can be used to largely eliminate NLPV artifacts, and demonstrate the efficacy of the modified technique (with improved image quality and accurate implant position estimates) for the cochlear implant imaging scenario.

Robust methods for automatic image-to-world registration in cone-beam CT interventional guidance

PURPOSE

Real-time surgical navigation relies on accurate image-to-world registration to align the coordinate systems of the image and patient. Conventional manual registration can present a workflow bottleneck and is prone to manual error and intraoperator variability. This work reports alternative means of automatic image-to-world registration, each method involving an automatic registration marker (ARM) used in conjunction with C-arm cone-beam CT (CBCT). The first involves a Known-Model registration method in which the ARM is a predefined tool, and the second is a Free-Form method in which the ARM is freely configurable.

METHODS

Studies were performed using a prototype C-arm for CBCT and a surgical tracking system. A simple ARM was designed with markers comprising a tungsten sphere within infrared reflectors to permit detection of markers in both x-ray projections and by an infrared tracker. The Known-Model method exercised a predefined specification of the ARM in combination with 3D-2D registration to estimate the transformation that yields the optimal match between forward projection of the ARM and the measured projection images. The Free-Form method localizes markers individually in projection data by a robust Hough transform approach extended from previous work, backprojected to 3D image coordinates based on C-arm geometric calibration. Image-domain point sets were transformed to world coordinates by rigid-body point-based registration. The robustness and registration accuracy of each method was tested in comparison to manual registration across a range of body sites (head, thorax, and abdomen) of interest in CBCT-guided surgery, including cases with interventional tools in the radiographic scene.

RESULTS

The automatic methods exhibited similar target registration error (TRE) and were comparable or superior to manual registration for placement of the ARM within ∼200 mm of C-arm isocenter. Marker localization in projection data was robust across all anatomical sites, including challenging scenarios involving the presence of interventional tools. The reprojection error of marker localization was independent of the distance of the ARM from isocenter, and the overall TRE was dominated by the configuration of individual fiducials and distance from the target as predicted by theory. The median TRE increased with greater ARM-to-isocenter distance (e.g., for the Free-Form method, TRE increasing from 0.78 mm to 2.04 mm at distances of ∼75 mm and 370 mm, respectively). The median TRE within ∼200 mm distance was consistently lower than that of the manual method (TRE = 0.82 mm). Registration performance was independent of anatomical site (head, thorax, and abdomen). The Free-Form method demonstrated a statistically significant improvement (p = 0.0044) in reproducibility compared to manual registration (0.22 mm versus 0.30 mm, respectively).

CONCLUSIONS

Automatic image-to-world registration methods demonstrate the potential for improved accuracy, reproducibility, and workflow in CBCT-guided procedures. A Free-Form method was shown to exhibit robustness against anatomical site, with comparable or improved TRE compared to manual registration. It was also comparable or superior in performance to a Known-Model method in which the ARM configuration is specified as a predefined tool, thereby allowing configuration of fiducials on the fly or attachment to the patient.

Mucus clearance, MyD88-dependent and MyD88-independent immunity modulate lung susceptibility to spontaneous bacterial infection and inflammation

It has been postulated that mucus stasis is central to the pathogenesis of obstructive lung diseases. In Scnn1b-transgenic (Scnn1b-Tg⁺ mice, airway-targeted overexpression of the epithelial Na⁺ channel β subunit causes airway surface dehydration, which results in mucus stasis and inflammation. Bronchoalveolar lavage from neonatal Scnn1b-Tg⁺ mice, but not wild-type littermates, contained increased mucus, bacteria, and neutrophils, which declined with age. Scnn1b-Tg⁺ mice lung bacterial flora included environmental and oropharyngeal species, suggesting inhalation and/or aspiration as routes of entry. Genetic deletion of the Toll-interleukin-1 receptor adapter molecule MyD88 in Scnn1b-Tg⁺ mice did not modify airway mucus obstruction, but caused defective neutrophil recruitment and increased bacterial infection, which persisted into adulthood. Scnn1b-Tg⁺ mice derived into germ-free conditions exhibited mucus obstruction similar to conventional Scnn1b-Tg⁺ mice and sterile inflammation. Collectively, these data suggest that dehydration-induced mucus stasis promotes infection, compounds defects in other immune mechanisms, and alone is sufficient to trigger airway inflammation.

Abstract P6-04-10: Genetic Discrimination of Aggressive from Indolent DCIS

Background: Treatment options for DCIS vary from surgical excision with or without radiation and/or chemopreventive therapy, or mastectomy. Intuitively, more aggressive treatment options should lead to improved survival rates, however, studies have shown no difference in breast cancer mortality between women treated with wide excision only versus those with excision plus radiation and treatments can be costly, lengthy and associated with side effects. To avoid over-treating women with indolent disease, while intensively treating women with aggressive disease, new molecular tools must be developed to supplement pathological information to classify DCIS lesions and predict clinical outcome.

Methods: Formalin-fixed paraffin-embedded (FFPE) pure DCIS biopsy specimens were collected from the pathology archives of the Anne Arundel Medical Center. Samples included those with poor prognosis characterized by either recurrence of DCIS or progression to invasive cancer (n=7) and those good prognosis, having ≥5-year disease-free survival (n=10). RNA was isolated after laser-microdissection of pure tumor cells and hybridized to Breast Cancer DSA™ microarrays (Almac Diagnostics). S-way ANOVA was used to account for batch effects and then Support Vector Machine (SVM) was used to identify candidate genes effective at discriminating good from poor prognosis DCIS. Pathway analysis was performed using MetaCore (GeneGeo).

Results: 328 genes were found to be differentially expressed between good and poor prognosis specimens (P&lt;0.01). Preliminary analysis with SVM found that a 70-gene candidate signature from these 328 genes wasoptimal under the tested conditions for discriminating favorable from poor prognosis DCIS. This candidate signature included genes such as MEF2C, PTK2 and ZBTB2. Pathway analysis revealed that genes involved in cytoskeleton modeling, apoptosis and survival, DNA damage repair and cell adhesion are expressed at lower levels in poor prognosis DCIS while those involved in cell cycle, immune response and cell proliferation are expressed at higher levels.

Conclusions: While studies have attempted to identify molecular profiles associated with aggressive DCIS by comparing DCIS co-occurring with invasive disease to pure DCIS, to our knowledge, this is the first study that identified a candidate molecular signature of prognosis in pure DCIS. Although many of the 70 genes found to differ between favorable and poor prognosis DCIS have not been previously associated with breast cancer or have unknown function, MEF2C and PTK2 have been implicated in invasion and migration, while ZBTB2 is a master regulator of p53 and stimulates cellular proliferation. These data demonstrate aggressive DCIS do differ from indolent DCIS at the genetic level and that these differences may be useful in developing molecular tools to classify DCIS lesions and guide appropriate treatment.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-04-10.

Identification of a globally distributed clinical streptomycin-resistance plasmid and other resistance determinants in a coastal bay of China

AIMS

To study streptomycin-resistant bacteria isolated from Jiaozhou Bay and their molecular determinants of resistance.

METHODS AND RESULTS

Twenty-seven tetracycline-resistant and 49 chloramphenicol-resistant bacterial isolates from surface seawater of Jiaozhou Bay were selected for investigation. More than 88% of these isolates were resistant to streptomycin. Half of the streptomycin-resistant bacteria harboured the strA-strB gene pair, and six isolates carried Tn5393-like transposons by PCR detection. The p9123-related plasmids containing the sul2-strA-strB gene cluster were characterized in two environmental Escherichia coli isolates. Transposon Tn5393 was first identified on a Klebsiella pneumoniae plasmid, which also carried Tn1721, estP and umu genes responsible for antimicrobial and insecticide resistance.

CONCLUSIONS

Coresistance to streptomycin and tetracycline or chloramphenicol was found with high frequency. p9123-related plasmid and Tn5393 transposon may contribute to the wide distribution and spread of the strA-strB gene pair in Jiaozhou Bay. The detection of streptomycin-resistance plasmid pQ1-1 from Jiaozhou Bay seawater bacteria and human bacterial pathogens from USA indicates its global dissemination and transmission, across different components of the microbiota on earth.

SIGNIFICANCE AND IMPACT OF THE STUDY

Streptomycin resistance can be recognized as an important bioindicator of environmental quality, owing to its association with anthropogenic pollution and the multidrug-resistant microbiota.

Modulation of Masseteric Reflexes by Simulated Mastication

It is well-known that limb muscle reflexes are modulated during human movements. However, little is known about the existence of equivalent masticatory muscle reflex modulation. We hypothesized that masticatory reflexes would be modulated during chewing so that smooth masticatory movements occur. To examine this hypothesis, we studied the modulation of inhibitory reflexes evoked by periodontal mechanoreceptor activation and of excitatory reflexes evoked by muscle spindle activation during simulated mastication. In 28 participants, 1- and 2-N mechanical taps were delivered to the incisor. Reflex responses to these taps were examined in the average masseteric electromyogram. To differentiate between periodontal mechanoreceptor- and muscle-spindle-mediated reflex components, we performed experiments prior to, and in the presence of, periodontal anesthesia. Both periodontal mechanoreceptor and muscle spindle reflexes were reduced during simulated masticatory movements.