Neoadjuvant chemo- or chemo-radiation-therapy of pancreatic ductal adenocarcinoma differentially shift ECM composition, complement activation, energy metabolism and ribosomal proteins of the residual tumor mass

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, often diagnosed at stages that dis-qualify for surgical resection. Neoadjuvant therapies offer potential tumor regression and improved resectability. Although features of the tumor biology (e.g., molecular markers) may guide adjuvant therapy, biological alterations after neoadjuvant therapy remain largely unexplored. We performed mass spectrometry to characterize the proteomes of 67 PDAC resection specimens of patients who received either neoadjuvant chemo (NCT) or chemo-radiation (NCRT) therapy. We employed data-independent acquisition (DIA), yielding a proteome coverage in excess of 3500 proteins. Moreover, we successfully integrated two publicly available proteome datasets of treatment-naïve PDAC to unravel proteome alterations in response to neoadjuvant therapy, highlighting the feasibility of this approach. We found highly distinguishable proteome profiles. Treatment-naïve PDAC was characterized by enrichment of immunoglobulins, complement and extracellular matrix (ECM) proteins. Post-NCT and post-NCRT PDAC presented high abundance of ribosomal and metabolic proteins as compared to treatment-naïve PDAC. Further analyses on patient survival and protein expression identified treatment-specific prognostic candidates. We present the first proteomic characterization of the residual PDAC mass after NCT and NCRT, and potential protein candidate markers associated with overall survival. We conclude that residual PDAC exhibits fundamentally different proteome profiles as compared to treatment-naïve PDAC, influenced by the type of neoadjuvant treatment. These findings may impact adjuvant or targeted therapy options.

AI-Based Detection of Oral Squamous Cell Carcinoma with Raman Histology

Stimulated Raman Histology (SRH) employs the stimulated Raman scattering (SRS) of photons at biomolecules in tissue samples to generate histological images. Subsequent pathological analysis allows for an intraoperative evaluation without the need for sectioning and staining. The objective of this study was to investigate a deep learning-based classification of oral squamous cell carcinoma (OSCC) and the sub-classification of non-malignant tissue types, as well as to compare the performances of the classifier between SRS and SRH images. Raman shifts were measured at wavenumbers k1 = 2845 cm-1 and k2 = 2930 cm-1. SRS images were transformed into SRH images resembling traditional H&E-stained frozen sections. The annotation of 6 tissue types was performed on images obtained from 80 tissue samples from eight OSCC patients. A VGG19-based convolutional neural network was then trained on 64 SRS images (and corresponding SRH images) and tested on 16. A balanced accuracy of 0.90 (0.87 for SRH images) and F1-scores of 0.91 (0.91 for SRH) for stroma, 0.98 (0.96 for SRH) for adipose tissue, 0.90 (0.87 for SRH) for squamous epithelium, 0.92 (0.76 for SRH) for muscle, 0.87 (0.90 for SRH) for glandular tissue, and 0.88 (0.87 for SRH) for tumor were achieved. The results of this study demonstrate the suitability of deep learning for the intraoperative identification of tissue types directly on SRS and SRH images.

Non-invasive monitoring of neoadjuvant radiation therapy response in soft tissue sarcomas by multiparametric MRI and quantification of circulating tumor DNA-A study protocol

BACKGROUND

Wide resection remains the cornerstone of localized soft-tissue sarcomas (STS) treatment. Neoadjuvant radiation therapy (NRT) may decrease the risk of local recurrences; however, its effectiveness for different histological STS subtypes has not been systematically investigated. The proposed prospective study evaluates the NRT response in STS using liquid biopsies and the correlation of multiparametric magnetic resonance imaging (mpMRI) with histopathology and immunohistochemistry.

METHODS

Patients with localized high-grade STS, who qualify for NRT, are included in this study.

LIQUID BIOPSIES

Quantification of circulating tumor DNA (ctDNA) in patient blood samples is performed by targeted next-generation sequencing. Soft-tissue sarcoma subtype-specific panel sequencing in combination with patient-specific exome sequencing allows the detection of individual structural variants and point mutations. Circulating free DNA is isolated from peritherapeutically collected patient plasma samples and ctDNA quantified therein. Identification of breakpoints is carried out using FACTERA. Bioinformatic analysis is performed using samtools, picard, fgbio, and the MIRACUM Pipeline.

MPMRI

Combination of conventional MRI sequences with diffusion-weighted imaging, intravoxel-incoherent motion, and dynamic contrast enhancement. Multiparametric MRI is performed before, during, and after NRT. We aim to correlate mpMRI data with the resected specimen's macroscopical, histological, and immunohistochemical findings.

RESULTS

Preliminary data support the notion that quantification of ctDNA in combination with tumor mass characterization through co-registration of mpMRI and histopathology can predict NRT response of STS.

CLINICAL RELEVANCE

The methods presented in this prospective study are necessary to assess therapy response in heterogeneous tumors and lay the foundation of future patient- and tumor-specific therapy concepts. These methods can be applied to various tumor entities. Thus, the participation and support of a wider group of oncologic surgeons are needed to validate these findings on a larger patient cohort.

Multiparametric magnetic resonance imaging for radiation therapy response monitoring in soft tissue sarcomas: a histology and MRI co-registration algorithm

Rationale: To establish a spatially exact co-registration procedure between in vivo multiparametric magnetic resonance imaging (mpMRI) and (immuno)histopathology of soft tissue sarcomas (STS) to identify imaging parameters that reflect radiation therapy response of STS. Methods: The mpMRI-Protocol included diffusion-weighted (DWI), intravoxel-incoherent motion (IVIM), and dynamic contrast-enhancing (DCE) imaging. The resection specimen was embedded in 6.5% agarose after initial fixation in formalin. To ensure identical alignment of histopathological sectioning and in vivo imaging, an ex vivo MRI scan of the specimen was rigidly co-registered with the in vivo mpMRI. The deviating angulation of the specimen to the in vivo location of the tumor was determined. The agarose block was trimmed accordingly. A second ex vivo MRI in a dedicated localizer with a 4 mm grid was performed, which was matched to a custom-built sectioning machine. Microtomy sections were stained with hematoxylin and eosin. Immunohistochemical staining was performed with anti-ALDH1A1 antibodies as a radioresistance and anti-MIB1 antibodies as a proliferation marker. Fusion of the digitized microtomy sections with the in vivo mpMRI was accomplished through nonrigid co-registration to the in vivo mpMRI. Co-registration accuracy was qualitatively assessed by visual assessment and quantitatively evaluated by computing target registration errors (TRE). Results: The study sample comprised nine tumor sections from three STS patients. Visual assessment after nonrigid co-registration showed a strong morphological correlation of the histopathological specimens with ex vivo MRI and in vivo mpMRI after neoadjuvant radiation therapy. Quantitative assessment of the co-registration procedure using TRE analysis of different pairs of pathology and MRI sections revealed highly accurate structural alignment, with a total median TRE of 2.25 mm (histology - ex vivo MRI), 2.22 mm (histology - in vivo mpMRI), and 2.02 mm (ex vivo MRI - in vivo mpMRI). There was no significant difference between TREs of the different pairs of sections or caudal, middle, and cranial tumor parts, respectively. Conclusion: Our initial results show a promising approach to obtaining accurate co-registration between histopathology and in vivo MRI for STS. In a larger cohort of patients, the method established here will enable the prospective identification and validation of in vivo imaging biomarkers for radiation therapy response prediction and monitoring in STS patients via precise molecular and cellular correlation.

Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations

Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from laptops to petascale supercomputers, including combinations of these. Our work features two multiscale applications, in-stent restenosis and cerebrovascular bloodflow, which combine multiple existing single-scale applications to create a multiscale simulation. These applications can be efficiently coupled, deployed and executed on computers up to the largest (peta) scale, incurring a coupling overhead of 1-10% of the total execution time.

Expression of Bax and Bcl2 proteins in small cell lung cancer (SCLC)

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Background: Bax and Bcl2 proteins are members of Bcl-2 family which plays a critical role in the regulation of apoptosis. There are few data on the occurrence and clinical relevance of these proteins in SCLC. Methods: We have analyzed expression of Bax and Bcl2 in 86 SCLC patients. All patients had limited disease and were treated with surgery followed by chemotherapy between 1982 and 2001 (median follow up 2 years). In all cases the diagnosis of SCLC was established only after the examination of surgical specimen. This series included 59 males and 22 females, 11 T1, 46 T2, 13 T3 and 11 T4 tumors, 41 N0, 15 N1, 24 N2 and 1 N3. Expression of both proteins was evaluated by immunohistochemistry and scored, taking into account proportion of cells with positive staining and staining intensity. H-score was calculated as a proportion of positive cells times staining intensity. Continues data on H-score were used to assess relationships with clinical data. Results: Median H-scores for Bax and Bcl2 were 70 (range 0–300) and 90 (range 0–300) respectively. The positive immunostaining rates (cut-off point of 10%) for Bax and Bcl-2 in the entire group were 81% and 79% respectively. Bax and Bcl-2 expression did not correlate with any clinicopathological parameters such as age, tumor size, lymph node involvement and stage of the disease. Survival was not influenced by expression of Bax (p=0.6) or Bcl2 (p=0.86). There was a significant positive correlation between Bax and Bcl2 expression rates (p=0.018, regression coefficient 0.23). Conclusions: Bax an Bcl2 proteins are commonly overexpressed in SCLC, with tendency for co-expression. Clinical relevance of these markers is questionable in this patient cohort.

No significant financial relationships to disclose.

Clarithromycin-induced alterations in vaginal flora

Many antibiotics have been shown to alter both the bacterial and the fungal flora of the vagina, in some cases potentially increasing a woman's propensity toward urinary tract infections and vaginal candidiasis. The effects of some of the newer macrolide antibiotics on women's vaginal flora have not been previously studied, and almost none of the previous studies specifically cultured for effects on vaginal lactobacillus. Young women (ages 18-45 years) who were about to go onto therapy with clarithromycin, who did not have any conditions known to affect the vaginal flora (eg, diabetes mellitus, spermicide use, menopausal status without hormone replacement therapy), and who agreed to participate in the study were cultured with aerobic and anaerobic and fungal vaginal cultures before starting the antibiotic. These same women were then retested about 4 to 6 weeks after the start of their antibiotic course, and the results of their preantibiotic and postantibiotic cultures were compared. Lactobacillus was present in 33% of patients by vaginal culture before treatment, but this decreased to 0% after treatment. Escherichia coli was present in only 8% of patients before treatment, but this increased to 17% of patients after treatment. Enterococcus was present in 25% of patients before treatment but in only 8% of patients after treatment. The incidence of Gardnerella vaginalis was not affected by the treatment. Candida species incidence increased from 17% to 33% with treatment. The overall effects of clarithromycin on the vaginal flora are similar to other older antibiotics that have been tested.

The preparticipation athletic evaluation

A comprehensive medical history that includes questions about a personal and family history of cardiovascular disease is the most important initial component of the preparticipation athletic evaluation. Additional questions should focus on any history of neurologic or musculoskeletal problems. A limited physical examination should emphasize cardiac auscultation with provocative maneuvers to screen for hypertrophic cardiomyopathy. This condition is the most common cause of sudden death in young male athletes. Other components of the physical examination include an evaluation of the spine and extremities. Screening tests such as electrocardiography, treadmill stress testing and urinalysis are not indicated in the absence of symptoms or a significant history of risk factors. Specific conditions that would exclude or limit athletic participation include hypertrophic cardiomyopathy, long QT interval syndrome, concussion, significant knee injury, sickle cell disease and uncontrolled seizures. Overall, about 1 percent of athletes who are screened are completely disqualified from sports participation.

The mapping from sound structure to the lexicon in aphasia: evidence from rhyme and repetition priming

Two studies were conducted to explore the hypothesis that Broca's and Wernicke's aphasics have deficits arising from the processes involved in activating the lexicon from phonological form. The first study explored whether phonologically similar lexical entries differing only in their initial consonants show "rhyme priming." Results revealed that Broca's aphasics failed to show facilitation when the target was identical to the prime (i.e. identity priming) and they showed significant inhibition when targets were preceded by rhyming words. Wernicke's aphasics showed a pattern of results similar to that of normal subjects, i.e., identity priming and rhyme priming as well as significantly slower reaction-times in the rhyming condition compared to the identity condition. The second study investigated form-based repetition priming in aphasic patients at a number of intervals including when no other stimuli intervened between repeated stimuli (0 lag) or when 4, 8, or 12 stimuli intervened. Results showed that, unlike old normal subjects who showed repetition priming for both words and nonwords, both Broca's and Wernicke's aphasics showed repetition priming for word targets only. Moreover, in contrast to old normal subjects who showed a greater magnitude of priming at 0 lag for word targets, neither Broca's aphasics or Wernicke's aphasics showed priming at 0 lag. Implications of these findings are considered with respect to the hypotheses that Broca's and Wernicke's aphasics have deficits in the nature of the activation patterns within the lexicon itself and in auditory (working) memory.

[Congenital esophago-tracheal fistula in an adult]

A 33 year old man with recurrent respiratory tract infections was admitted to surgery ward. During esophagoscopy and bronchoscopy--esophago-tracheal fistula was found. Diagnosis was confirmed by radiologic examination of esophagus. Surgical treatment was performed with good result.

The women with dysuria

Bacterial cystitis is the most common bacterial infection occurring in women. Thirty percent of women will experience at least one episode of cystitis during their lifetime. About one third of patients presenting with symptoms of cystitis have upper urinary tract infection. A careful history to identify risk factors for subclinical pyelonephritis is important. Symptoms of chronic cystitis accompanied by sterile urine without pyuria may represent interstitial cystitis. Dysuria may also be the principal complaint of women with vaginitis (infectious, atrophic or chemical) or urethritis. A stepwise diagnostic approach, accompanied by inexpensive office laboratory testing, is usually sufficient to determine the cause of dysuria.

On-line processing of filler-gap construction in aphasia

Two experiments were conducted exploring on-line processing of filler-gap construction in aphasia. An auditory-auditory lexical decision paradigm was used to investigate whether Broca's and Wernicke's aphasic patients show, as do normals, reactivation of the filler at the gap site. Experiment I investigated the processing of a number of filler-gap constructions including wh-questions, relative clauses as subject, relative clauses as object, and embedded wh-questions. Broca's aphasics showed reactivation of the filler at the gap site, whereas Wernicke's aphasics did not. Experiment II examined object relative clauses and their processing by Broca's aphasics. In addition, we investigated whether the presence (or absence) of the relative pronoun played any role in on-line processing. Broca's aphasics performed as did normals. In addition, their performance was unaffected by the presence or absence of the relative pronoun. The results of these experiments suggest that Broca's aphasics do not have an impairment in processing or representing thematic relationships of NP arguments to predicates or relating traces to their antecedents.

The characteristics of voicing in syllable-initial fricatives in American English

This study investigated the acoustic characteristics of voicing in the production of fricative consonants. The fricatives [f v s z] were used in combination with the vowels [i e a o u] to create CV syllables, which were produced by four subjects both in a context condition (following voiced and voiceless velar stops) and in isolation. Analyses were conducted of the time course of glottal excitation during the fricative noise interval in the voiced and voiceless fricative stimuli. Results showed that the patterns of voicing in the fricative noise interval were influenced by the voicing characteristics of preceding stop consonants. Nonetheless, these carryover coarticulatory effects were short-lived, influencing only the first 10's of ms of the following segment. Despite the influence of phonetic context on the patterns of voicing, an acoustic measure relating to the presence or absence of glottal excitation at the acoustic boundaries of the fricative noise reliably classified a majority (93%) of the fricative consonants in terms of the phonetic category of voicing. Thus, while phonetic context affected the patterns of glottal excitation in the fricative noise interval, it did not affect the criterial attribute associated with the phonetic category of voicing.

[Hypertension in a case of pancreatic pseudocyst]

A 33-year-old male is described in whom compression of the renal artery by a pancreatic pseudocyst caused hypertension refractory to conservative treatment. After operation with removal of the contents of the cyst and Roux-type enterostomy the arterial blood pressure fell to normal level.

Perceptual integration of the murmur and formant transitions for place of articulation in nasal consonants

This study reassessed the role of the nasal murmur and formant transitions as perceptual cues for place of articulation in nasal consonants across a number of vowel environments. Five types of computer-edited stimuli were generated from natural utterances consisting of [m n] followed by [i e a o u]: (1) full murmurs; (2) transitions plus vowel segments; (3) the last six pulses of the murmur; (4) the six pulses starting from the beginning of the formant transitions; and (5) the six pulses surrounding the nasal release (three pulses before and three pulses after). Results showed that the murmur provided as much information for the perception of place of articulation as did the transitions. Moreover, the highest performance scores for place of articulation were obtained in the six-pulse condition containing both murmur and transition information. The data support the view that it is the combination of nasal murmur plus formant transitions which forms an integrated property for the perception of place of articulation.